Initial release of AlphaFold.

PiperOrigin-RevId: 384954738

alphafold/model/r3.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Transformations for 3D coordinates.
+
+This Module contains objects for representing Vectors (Vecs), Rotation Matrices
+(Rots) and proper Rigid transformation (Rigids). These are represented as
+named tuples with arrays for each entry, for example a set of
+[N, M] points would be represented as a Vecs object with arrays of shape [N, M]
+for x, y and z.
+
+This is being done to improve readability by making it very clear what objects
+are geometric objects rather than relying on comments and array shapes.
+Another reason for this is to avoid using matrix
+multiplication primitives like matmul or einsum, on modern accelerator hardware
+these can end up on specialized cores such as tensor cores on GPU or the MXU on
+cloud TPUs, this often involves lower computational precision which can be
+problematic for coordinate geometry. Also these cores are typically optimized
+for larger matrices than 3 dimensional, this code is written to avoid any
+unintended use of these cores on both GPUs and TPUs.
+"""
+
+import collections
+from typing import List
+
+import jax.numpy as jnp
+import tree
+
+from alphafold.model import quat_affine
+
+# Array of 3-component vectors, stored as individual array for
+# each component.
+Vecs = collections.namedtuple('Vecs', ['x', 'y', 'z'])
+
+# Array of 3x3 rotation matrices, stored as individual array for
+# each component.
+Rots = collections.namedtuple('Rots', ['xx', 'xy', 'xz',
+                                       'yx', 'yy', 'yz',
+                                       'zx', 'zy', 'zz'])
+# Array of rigid 3D transformations, stored as array of rotations and
+# array of translations.
+Rigids = collections.namedtuple('Rigids', ['rot', 'trans'])
+
+
+def squared_difference(x, y):
+  return jnp.square(x - y)
+
+
+def invert_rigids(r: Rigids) -> Rigids:
+  """Computes group inverse of rigid transformations 'r'."""
+  inv_rots = invert_rots(r.rot)
+  t = rots_mul_vecs(inv_rots, r.trans)
+  inv_trans = Vecs(-t.x, -t.y, -t.z)
+  return Rigids(inv_rots, inv_trans)
+
+
+def invert_rots(m: Rots) -> Rots:
+  """Computes inverse of rotations 'm'."""
+  return Rots(m.xx, m.yx, m.zx,
+              m.xy, m.yy, m.zy,
+              m.xz, m.yz, m.zz)
+
+
+def rigids_from_3_points(
+    point_on_neg_x_axis: Vecs,  # shape (...)
+    origin: Vecs,  # shape (...)
+    point_on_xy_plane: Vecs,  # shape (...)
+) -> Rigids:  # shape (...)
+  """Create Rigids from 3 points.
+
+  Jumper et al. (2021) Suppl. Alg. 21 "rigidFrom3Points"
+  This creates a set of rigid transformations from 3 points by Gram Schmidt
+  orthogonalization.
+
+  Args:
+    point_on_neg_x_axis: Vecs corresponding to points on the negative x axis
+    origin: Origin of resulting rigid transformations
+    point_on_xy_plane: Vecs corresponding to points in the xy plane
+  Returns:
+    Rigid transformations from global frame to local frames derived from
+    the input points.
+  """
+  m = rots_from_two_vecs(
+      e0_unnormalized=vecs_sub(origin, point_on_neg_x_axis),
+      e1_unnormalized=vecs_sub(point_on_xy_plane, origin))
+
+  return Rigids(rot=m, trans=origin)
+
+
+def rigids_from_list(l: List[jnp.ndarray]) -> Rigids:
+  """Converts flat list of arrays to rigid transformations."""
+  assert len(l) == 12
+  return Rigids(Rots(*(l[:9])), Vecs(*(l[9:])))
+
+
+def rigids_from_quataffine(a: quat_affine.QuatAffine) -> Rigids:
+  """Converts QuatAffine object to the corresponding Rigids object."""
+  return Rigids(Rots(*tree.flatten(a.rotation)),
+                Vecs(*a.translation))
+
+
+def rigids_from_tensor4x4(
+    m: jnp.ndarray  # shape (..., 4, 4)
+) -> Rigids:  # shape (...)
+  """Construct Rigids object from an 4x4 array.
+
+  Here the 4x4 is representing the transformation in homogeneous coordinates.
+
+  Args:
+    m: Array representing transformations in homogeneous coordinates.
+  Returns:
+    Rigids object corresponding to transformations m
+  """
+  assert m.shape[-1] == 4
+  assert m.shape[-2] == 4
+  return Rigids(
+      Rots(m[..., 0, 0], m[..., 0, 1], m[..., 0, 2],
+           m[..., 1, 0], m[..., 1, 1], m[..., 1, 2],
+           m[..., 2, 0], m[..., 2, 1], m[..., 2, 2]),
+      Vecs(m[..., 0, 3], m[..., 1, 3], m[..., 2, 3]))
+
+
+def rigids_from_tensor_flat9(
+    m: jnp.ndarray  # shape (..., 9)
+) -> Rigids:  # shape (...)
+  """Flat9 encoding: first two columns of rotation matrix + translation."""
+  assert m.shape[-1] == 9
+  e0 = Vecs(m[..., 0], m[..., 1], m[..., 2])
+  e1 = Vecs(m[..., 3], m[..., 4], m[..., 5])
+  trans = Vecs(m[..., 6], m[..., 7], m[..., 8])
+  return Rigids(rot=rots_from_two_vecs(e0, e1),
+                trans=trans)
+
+
+def rigids_from_tensor_flat12(
+    m: jnp.ndarray  # shape (..., 12)
+) -> Rigids:  # shape (...)
+  """Flat12 encoding: rotation matrix (9 floats) + translation (3 floats)."""
+  assert m.shape[-1] == 12
+  x = jnp.moveaxis(m, -1, 0)  # Unstack
+  return Rigids(Rots(*x[:9]), Vecs(*x[9:]))
+
+
+def rigids_mul_rigids(a: Rigids, b: Rigids) -> Rigids:
+  """Group composition of Rigids 'a' and 'b'."""
+  return Rigids(
+      rots_mul_rots(a.rot, b.rot),
+      vecs_add(a.trans, rots_mul_vecs(a.rot, b.trans)))
+
+
+def rigids_mul_rots(r: Rigids, m: Rots) -> Rigids:
+  """Compose rigid transformations 'r' with rotations 'm'."""
+  return Rigids(rots_mul_rots(r.rot, m), r.trans)
+
+
+def rigids_mul_vecs(r: Rigids, v: Vecs) -> Vecs:
+  """Apply rigid transforms 'r' to points 'v'."""
+  return vecs_add(rots_mul_vecs(r.rot, v), r.trans)
+
+
+def rigids_to_list(r: Rigids) -> List[jnp.ndarray]:
+  """Turn Rigids into flat list, inverse of 'rigids_from_list'."""
+  return list(r.rot) + list(r.trans)
+
+
+def rigids_to_quataffine(r: Rigids) -> quat_affine.QuatAffine:
+  """Convert Rigids r into QuatAffine, inverse of 'rigids_from_quataffine'."""
+  return quat_affine.QuatAffine(
+      quaternion=None,
+      rotation=[[r.rot.xx, r.rot.xy, r.rot.xz],
+                [r.rot.yx, r.rot.yy, r.rot.yz],
+                [r.rot.zx, r.rot.zy, r.rot.zz]],
+      translation=[r.trans.x, r.trans.y, r.trans.z])
+
+
+def rigids_to_tensor_flat9(
+    r: Rigids  # shape (...)
+) -> jnp.ndarray:  # shape (..., 9)
+  """Flat9 encoding: first two columns of rotation matrix + translation."""
+  return jnp.stack(
+      [r.rot.xx, r.rot.yx, r.rot.zx, r.rot.xy, r.rot.yy, r.rot.zy]
+      + list(r.trans), axis=-1)
+
+
+def rigids_to_tensor_flat12(
+    r: Rigids  # shape (...)
+) -> jnp.ndarray:  # shape (..., 12)
+  """Flat12 encoding: rotation matrix (9 floats) + translation (3 floats)."""
+  return jnp.stack(list(r.rot) + list(r.trans), axis=-1)
+
+
+def rots_from_tensor3x3(
+    m: jnp.ndarray,  # shape (..., 3, 3)
+) -> Rots:  # shape (...)
+  """Convert rotations represented as (3, 3) array to Rots."""
+  assert m.shape[-1] == 3
+  assert m.shape[-2] == 3
+  return Rots(m[..., 0, 0], m[..., 0, 1], m[..., 0, 2],
+              m[..., 1, 0], m[..., 1, 1], m[..., 1, 2],
+              m[..., 2, 0], m[..., 2, 1], m[..., 2, 2])
+
+
+def rots_from_two_vecs(e0_unnormalized: Vecs, e1_unnormalized: Vecs) -> Rots:
+  """Create rotation matrices from unnormalized vectors for the x and y-axes.
+
+  This creates a rotation matrix from two vectors using Gram-Schmidt
+  orthogonalization.
+
+  Args:
+    e0_unnormalized: vectors lying along x-axis of resulting rotation
+    e1_unnormalized: vectors lying in xy-plane of resulting rotation
+  Returns:
+    Rotations resulting from Gram-Schmidt procedure.
+  """
+  # Normalize the unit vector for the x-axis, e0.
+  e0 = vecs_robust_normalize(e0_unnormalized)
+
+  # make e1 perpendicular to e0.
+  c = vecs_dot_vecs(e1_unnormalized, e0)
+  e1 = Vecs(e1_unnormalized.x - c * e0.x,
+            e1_unnormalized.y - c * e0.y,
+            e1_unnormalized.z - c * e0.z)
+  e1 = vecs_robust_normalize(e1)
+
+  # Compute e2 as cross product of e0 and e1.
+  e2 = vecs_cross_vecs(e0, e1)
+
+  return Rots(e0.x, e1.x, e2.x, e0.y, e1.y, e2.y, e0.z, e1.z, e2.z)
+
+
+def rots_mul_rots(a: Rots, b: Rots) -> Rots:
+  """Composition of rotations 'a' and 'b'."""
+  c0 = rots_mul_vecs(a, Vecs(b.xx, b.yx, b.zx))
+  c1 = rots_mul_vecs(a, Vecs(b.xy, b.yy, b.zy))
+  c2 = rots_mul_vecs(a, Vecs(b.xz, b.yz, b.zz))
+  return Rots(c0.x, c1.x, c2.x, c0.y, c1.y, c2.y, c0.z, c1.z, c2.z)
+
+
+def rots_mul_vecs(m: Rots, v: Vecs) -> Vecs:
+  """Apply rotations 'm' to vectors 'v'."""
+  return Vecs(m.xx * v.x + m.xy * v.y + m.xz * v.z,
+              m.yx * v.x + m.yy * v.y + m.yz * v.z,
+              m.zx * v.x + m.zy * v.y + m.zz * v.z)
+
+
+def vecs_add(v1: Vecs, v2: Vecs) -> Vecs:
+  """Add two vectors 'v1' and 'v2'."""
+  return Vecs(v1.x + v2.x, v1.y + v2.y, v1.z + v2.z)
+
+
+def vecs_dot_vecs(v1: Vecs, v2: Vecs) -> jnp.ndarray:
+  """Dot product of vectors 'v1' and 'v2'."""
+  return v1.x * v2.x + v1.y * v2.y + v1.z * v2.z
+
+
+def vecs_cross_vecs(v1: Vecs, v2: Vecs) -> Vecs:
+  """Cross product of vectors 'v1' and 'v2'."""
+  return Vecs(v1.y * v2.z - v1.z * v2.y,
+              v1.z * v2.x - v1.x * v2.z,
+              v1.x * v2.y - v1.y * v2.x)
+
+
+def vecs_from_tensor(x: jnp.ndarray  # shape (..., 3)
+                    ) -> Vecs:  # shape (...)
+  """Converts from tensor of shape (3,) to Vecs."""
+  num_components = x.shape[-1]
+  assert num_components == 3
+  return Vecs(x[..., 0], x[..., 1], x[..., 2])
+
+
+def vecs_robust_normalize(v: Vecs, epsilon: float = 1e-8) -> Vecs:
+  """Normalizes vectors 'v'.
+
+  Args:
+    v: vectors to be normalized.
+    epsilon: small regularizer added to squared norm before taking square root.
+  Returns:
+    normalized vectors
+  """
+  norms = vecs_robust_norm(v, epsilon)
+  return Vecs(v.x / norms, v.y / norms, v.z / norms)
+
+
+def vecs_robust_norm(v: Vecs, epsilon: float = 1e-8) -> jnp.ndarray:
+  """Computes norm of vectors 'v'.
+
+  Args:
+    v: vectors to be normalized.
+    epsilon: small regularizer added to squared norm before taking square root.
+  Returns:
+    norm of 'v'
+  """
+  return jnp.sqrt(jnp.square(v.x) + jnp.square(v.y) + jnp.square(v.z) + epsilon)
+
+
+def vecs_sub(v1: Vecs, v2: Vecs) -> Vecs:
+  """Computes v1 - v2."""
+  return Vecs(v1.x - v2.x, v1.y - v2.y, v1.z - v2.z)
+
+
+def vecs_squared_distance(v1: Vecs, v2: Vecs) -> jnp.ndarray:
+  """Computes squared euclidean difference between 'v1' and 'v2'."""
+  return (squared_difference(v1.x, v2.x) +
+          squared_difference(v1.y, v2.y) +
+          squared_difference(v1.z, v2.z))
+
+
+def vecs_to_tensor(v: Vecs  # shape (...)
+                  ) -> jnp.ndarray:  # shape(..., 3)
+  """Converts 'v' to tensor with shape 3, inverse of 'vecs_from_tensor'."""
+  return jnp.stack([v.x, v.y, v.z], axis=-1)

alphafold/model/tf/data_transforms.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Data for AlphaFold."""
+import numpy as np
+import tensorflow.compat.v1 as tf
+
+from alphafold.common import residue_constants
+from alphafold.model.tf import shape_helpers
+from alphafold.model.tf import shape_placeholders
+from alphafold.model.tf import utils
+
+# Pylint gets confused by the curry1 decorator because it changes the number
+#   of arguments to the function.
+# pylint:disable=no-value-for-parameter
+
+
+NUM_RES = shape_placeholders.NUM_RES
+NUM_MSA_SEQ = shape_placeholders.NUM_MSA_SEQ
+NUM_EXTRA_SEQ = shape_placeholders.NUM_EXTRA_SEQ
+NUM_TEMPLATES = shape_placeholders.NUM_TEMPLATES
+
+
+def cast_64bit_ints(protein):
+
+  for k, v in protein.items():
+    if v.dtype == tf.int64:
+      protein[k] = tf.cast(v, tf.int32)
+  return protein
+
+
+_MSA_FEATURE_NAMES = [
+    'msa', 'deletion_matrix', 'msa_mask', 'msa_row_mask', 'bert_mask',
+    'true_msa'
+]
+
+
+def make_seq_mask(protein):
+  protein['seq_mask'] = tf.ones(
+      shape_helpers.shape_list(protein['aatype']), dtype=tf.float32)
+  return protein
+
+
+def make_template_mask(protein):
+  protein['template_mask'] = tf.ones(
+      shape_helpers.shape_list(protein['template_domain_names']),
+      dtype=tf.float32)
+  return protein
+
+
+def curry1(f):
+  """Supply all arguments but the first."""
+
+  def fc(*args, **kwargs):
+    return lambda x: f(x, *args, **kwargs)
+
+  return fc
+
+
+@curry1
+def add_distillation_flag(protein, distillation):
+  protein['is_distillation'] = tf.constant(float(distillation),
+                                           shape=[],
+                                           dtype=tf.float32)
+  return protein
+
+
+def make_all_atom_aatype(protein):
+  protein['all_atom_aatype'] = protein['aatype']
+  return protein
+
+
+def fix_templates_aatype(protein):
+  """Fixes aatype encoding of templates."""
+  # Map one-hot to indices.
+  protein['template_aatype'] = tf.argmax(
+      protein['template_aatype'], output_type=tf.int32, axis=-1)
+  # Map hhsearch-aatype to our aatype.
+  new_order_list = residue_constants.MAP_HHBLITS_AATYPE_TO_OUR_AATYPE
+  new_order = tf.constant(new_order_list, dtype=tf.int32)
+  protein['template_aatype'] = tf.gather(params=new_order,
+                                         indices=protein['template_aatype'])
+  return protein
+
+
+def correct_msa_restypes(protein):
+  """Correct MSA restype to have the same order as residue_constants."""
+  new_order_list = residue_constants.MAP_HHBLITS_AATYPE_TO_OUR_AATYPE
+  new_order = tf.constant(new_order_list, dtype=protein['msa'].dtype)
+  protein['msa'] = tf.gather(new_order, protein['msa'], axis=0)
+
+  perm_matrix = np.zeros((22, 22), dtype=np.float32)
+  perm_matrix[range(len(new_order_list)), new_order_list] = 1.
+
+  for k in protein:
+    if 'profile' in k:  # Include both hhblits and psiblast profiles
+      num_dim = protein[k].shape.as_list()[-1]
+      assert num_dim in [20, 21, 22], (
+          'num_dim for %s out of expected range: %s' % (k, num_dim))
+      protein[k] = tf.tensordot(protein[k], perm_matrix[:num_dim, :num_dim], 1)
+  return protein
+
+
+def squeeze_features(protein):
+  """Remove singleton and repeated dimensions in protein features."""
+  protein['aatype'] = tf.argmax(
+      protein['aatype'], axis=-1, output_type=tf.int32)
+  for k in [
+      'domain_name', 'msa', 'num_alignments', 'seq_length', 'sequence',
+      'superfamily', 'deletion_matrix', 'resolution',
+      'between_segment_residues', 'residue_index', 'template_all_atom_masks']:
+    if k in protein:
+      final_dim = shape_helpers.shape_list(protein[k])[-1]
+      if isinstance(final_dim, int) and final_dim == 1:
+        protein[k] = tf.squeeze(protein[k], axis=-1)
+
+  for k in ['seq_length', 'num_alignments']:
+    if k in protein:
+      protein[k] = protein[k][0]  # Remove fake sequence dimension
+  return protein
+
+
+def make_random_crop_to_size_seed(protein):
+  """Random seed for cropping residues and templates."""
+  protein['random_crop_to_size_seed'] = utils.make_random_seed()
+  return protein
+
+
+@curry1
+def randomly_replace_msa_with_unknown(protein, replace_proportion):
+  """Replace a proportion of the MSA with 'X'."""
+  msa_mask = (tf.random.uniform(shape_helpers.shape_list(protein['msa'])) <
+              replace_proportion)
+  x_idx = 20
+  gap_idx = 21
+  msa_mask = tf.logical_and(msa_mask, protein['msa'] != gap_idx)
+  protein['msa'] = tf.where(msa_mask,
+                            tf.ones_like(protein['msa']) * x_idx,
+                            protein['msa'])
+  aatype_mask = (
+      tf.random.uniform(shape_helpers.shape_list(protein['aatype'])) <
+      replace_proportion)
+
+  protein['aatype'] = tf.where(aatype_mask,
+                               tf.ones_like(protein['aatype']) * x_idx,
+                               protein['aatype'])
+  return protein
+
+
+@curry1
+def sample_msa(protein, max_seq, keep_extra):
+  """Sample MSA randomly, remaining sequences are stored as `extra_*`.
+
+  Args:
+    protein: batch to sample msa from.
+    max_seq: number of sequences to sample.
+    keep_extra: When True sequences not sampled are put into fields starting
+      with 'extra_*'.
+
+  Returns:
+    Protein with sampled msa.
+  """
+  num_seq = tf.shape(protein['msa'])[0]
+  shuffled = tf.random_shuffle(tf.range(1, num_seq))
+  index_order = tf.concat([[0], shuffled], axis=0)
+  num_sel = tf.minimum(max_seq, num_seq)
+
+  sel_seq, not_sel_seq = tf.split(index_order, [num_sel, num_seq - num_sel])
+
+  for k in _MSA_FEATURE_NAMES:
+    if k in protein:
+      if keep_extra:
+        protein['extra_' + k] = tf.gather(protein[k], not_sel_seq)
+      protein[k] = tf.gather(protein[k], sel_seq)
+
+  return protein
+
+
+@curry1
+def crop_extra_msa(protein, max_extra_msa):
+  """MSA features are cropped so only `max_extra_msa` sequences are kept."""
+  num_seq = tf.shape(protein['extra_msa'])[0]
+  num_sel = tf.minimum(max_extra_msa, num_seq)
+  select_indices = tf.random_shuffle(tf.range(0, num_seq))[:num_sel]
+  for k in _MSA_FEATURE_NAMES:
+    if 'extra_' + k in protein:
+      protein['extra_' + k] = tf.gather(protein['extra_' + k], select_indices)
+
+  return protein
+
+
+def delete_extra_msa(protein):
+  for k in _MSA_FEATURE_NAMES:
+    if 'extra_' + k in protein:
+      del protein['extra_' + k]
+  return protein
+
+
+@curry1
+def block_delete_msa(protein, config):
+  """Sample MSA by deleting contiguous blocks.
+
+  Jumper et al. (2021) Suppl. Alg. 1 "MSABlockDeletion"
+
+  Arguments:
+    protein: batch dict containing the msa
+    config: ConfigDict with parameters
+
+  Returns:
+    updated protein
+  """
+  num_seq = shape_helpers.shape_list(protein['msa'])[0]
+  block_num_seq = tf.cast(
+      tf.floor(tf.cast(num_seq, tf.float32) * config.msa_fraction_per_block),
+      tf.int32)
+
+  if config.randomize_num_blocks:
+    nb = tf.random.uniform([], 0, config.num_blocks + 1, dtype=tf.int32)
+  else:
+    nb = config.num_blocks
+
+  del_block_starts = tf.random.uniform([nb], 0, num_seq, dtype=tf.int32)
+  del_blocks = del_block_starts[:, None] + tf.range(block_num_seq)
+  del_blocks = tf.clip_by_value(del_blocks, 0, num_seq - 1)
+  del_indices = tf.unique(tf.sort(tf.reshape(del_blocks, [-1])))[0]
+
+  # Make sure we keep the original sequence
+  sparse_diff = tf.sets.difference(tf.range(1, num_seq)[None],
+                                   del_indices[None])
+  keep_indices = tf.squeeze(tf.sparse.to_dense(sparse_diff), 0)
+  keep_indices = tf.concat([[0], keep_indices], axis=0)
+
+  for k in _MSA_FEATURE_NAMES:
+    if k in protein:
+      protein[k] = tf.gather(protein[k], keep_indices)
+
+  return protein
+
+
+@curry1
+def nearest_neighbor_clusters(protein, gap_agreement_weight=0.):
+  """Assign each extra MSA sequence to its nearest neighbor in sampled MSA."""
+
+  # Determine how much weight we assign to each agreement.  In theory, we could
+  # use a full blosum matrix here, but right now let's just down-weight gap
+  # agreement because it could be spurious.
+  # Never put weight on agreeing on BERT mask
+  weights = tf.concat([
+      tf.ones(21),
+      gap_agreement_weight * tf.ones(1),
+      np.zeros(1)], 0)
+
+  # Make agreement score as weighted Hamming distance
+  sample_one_hot = (protein['msa_mask'][:, :, None] *
+                    tf.one_hot(protein['msa'], 23))
+  extra_one_hot = (protein['extra_msa_mask'][:, :, None] *
+                   tf.one_hot(protein['extra_msa'], 23))
+
+  num_seq, num_res, _ = shape_helpers.shape_list(sample_one_hot)
+  extra_num_seq, _, _ = shape_helpers.shape_list(extra_one_hot)
+
+  # Compute tf.einsum('mrc,nrc,c->mn', sample_one_hot, extra_one_hot, weights)
+  # in an optimized fashion to avoid possible memory or computation blowup.
+  agreement = tf.matmul(
+      tf.reshape(extra_one_hot, [extra_num_seq, num_res * 23]),
+      tf.reshape(sample_one_hot * weights, [num_seq, num_res * 23]),
+      transpose_b=True)
+
+  # Assign each sequence in the extra sequences to the closest MSA sample
+  protein['extra_cluster_assignment'] = tf.argmax(
+      agreement, axis=1, output_type=tf.int32)
+
+  return protein
+
+
+@curry1
+def summarize_clusters(protein):
+  """Produce profile and deletion_matrix_mean within each cluster."""
+  num_seq = shape_helpers.shape_list(protein['msa'])[0]
+  def csum(x):
+    return tf.math.unsorted_segment_sum(
+        x, protein['extra_cluster_assignment'], num_seq)
+
+  mask = protein['extra_msa_mask']
+  mask_counts = 1e-6 + protein['msa_mask'] + csum(mask)  # Include center
+
+  msa_sum = csum(mask[:, :, None] * tf.one_hot(protein['extra_msa'], 23))
+  msa_sum += tf.one_hot(protein['msa'], 23)  # Original sequence
+  protein['cluster_profile'] = msa_sum / mask_counts[:, :, None]
+
+  del msa_sum
+
+  del_sum = csum(mask * protein['extra_deletion_matrix'])
+  del_sum += protein['deletion_matrix']  # Original sequence
+  protein['cluster_deletion_mean'] = del_sum / mask_counts
+  del del_sum
+
+  return protein
+
+
+def make_msa_mask(protein):
+  """Mask features are all ones, but will later be zero-padded."""
+  protein['msa_mask'] = tf.ones(
+      shape_helpers.shape_list(protein['msa']), dtype=tf.float32)
+  protein['msa_row_mask'] = tf.ones(
+      shape_helpers.shape_list(protein['msa'])[0], dtype=tf.float32)
+  return protein
+
+
+def pseudo_beta_fn(aatype, all_atom_positions, all_atom_masks):
+  """Create pseudo beta features."""
+  is_gly = tf.equal(aatype, residue_constants.restype_order['G'])
+  ca_idx = residue_constants.atom_order['CA']
+  cb_idx = residue_constants.atom_order['CB']
+  pseudo_beta = tf.where(
+      tf.tile(is_gly[..., None], [1] * len(is_gly.shape) + [3]),
+      all_atom_positions[..., ca_idx, :],
+      all_atom_positions[..., cb_idx, :])
+
+  if all_atom_masks is not None:
+    pseudo_beta_mask = tf.where(
+        is_gly, all_atom_masks[..., ca_idx], all_atom_masks[..., cb_idx])
+    pseudo_beta_mask = tf.cast(pseudo_beta_mask, tf.float32)
+    return pseudo_beta, pseudo_beta_mask
+  else:
+    return pseudo_beta
+
+
+@curry1
+def make_pseudo_beta(protein, prefix=''):
+  """Create pseudo-beta (alpha for glycine) position and mask."""
+  assert prefix in ['', 'template_']
+  protein[prefix + 'pseudo_beta'], protein[prefix + 'pseudo_beta_mask'] = (
+      pseudo_beta_fn(
+          protein['template_aatype' if prefix else 'all_atom_aatype'],
+          protein[prefix + 'all_atom_positions'],
+          protein['template_all_atom_masks' if prefix else 'all_atom_mask']))
+  return protein
+
+
+@curry1
+def add_constant_field(protein, key, value):
+  protein[key] = tf.convert_to_tensor(value)
+  return protein
+
+
+def shaped_categorical(probs, epsilon=1e-10):
+  ds = shape_helpers.shape_list(probs)
+  num_classes = ds[-1]
+  counts = tf.random.categorical(
+      tf.reshape(tf.log(probs + epsilon), [-1, num_classes]),
+      1,
+      dtype=tf.int32)
+  return tf.reshape(counts, ds[:-1])
+
+
+def make_hhblits_profile(protein):
+  """Compute the HHblits MSA profile if not already present."""
+  if 'hhblits_profile' in protein:
+    return protein
+
+  # Compute the profile for every residue (over all MSA sequences).
+  protein['hhblits_profile'] = tf.reduce_mean(
+      tf.one_hot(protein['msa'], 22), axis=0)
+  return protein
+
+
+@curry1
+def make_masked_msa(protein, config, replace_fraction):
+  """Create data for BERT on raw MSA."""
+  # Add a random amino acid uniformly
+  random_aa = tf.constant([0.05] * 20 + [0., 0.], dtype=tf.float32)
+
+  categorical_probs = (
+      config.uniform_prob * random_aa +
+      config.profile_prob * protein['hhblits_profile'] +
+      config.same_prob * tf.one_hot(protein['msa'], 22))
+
+  # Put all remaining probability on [MASK] which is a new column
+  pad_shapes = [[0, 0] for _ in range(len(categorical_probs.shape))]
+  pad_shapes[-1][1] = 1
+  mask_prob = 1. - config.profile_prob - config.same_prob - config.uniform_prob
+  assert mask_prob >= 0.
+  categorical_probs = tf.pad(
+      categorical_probs, pad_shapes, constant_values=mask_prob)
+
+  sh = shape_helpers.shape_list(protein['msa'])
+  mask_position = tf.random.uniform(sh) < replace_fraction
+
+  bert_msa = shaped_categorical(categorical_probs)
+  bert_msa = tf.where(mask_position, bert_msa, protein['msa'])
+
+  # Mix real and masked MSA
+  protein['bert_mask'] = tf.cast(mask_position, tf.float32)
+  protein['true_msa'] = protein['msa']
+  protein['msa'] = bert_msa
+
+  return protein
+
+
+@curry1
+def make_fixed_size(protein, shape_schema, msa_cluster_size, extra_msa_size,
+                    num_res, num_templates=0):
+  """Guess at the MSA and sequence dimensions to make fixed size."""
+
+  pad_size_map = {
+      NUM_RES: num_res,
+      NUM_MSA_SEQ: msa_cluster_size,
+      NUM_EXTRA_SEQ: extra_msa_size,
+      NUM_TEMPLATES: num_templates,
+  }
+
+  for k, v in protein.items():
+    # Don't transfer this to the accelerator.
+    if k == 'extra_cluster_assignment':
+      continue
+    shape = v.shape.as_list()
+    schema = shape_schema[k]
+    assert len(shape) == len(schema), (
+        f'Rank mismatch between shape and shape schema for {k}: '
+        f'{shape} vs {schema}')
+    pad_size = [
+        pad_size_map.get(s2, None) or s1 for (s1, s2) in zip(shape, schema)
+    ]
+    padding = [(0, p - tf.shape(v)[i]) for i, p in enumerate(pad_size)]
+    if padding:
+      protein[k] = tf.pad(
+          v, padding, name=f'pad_to_fixed_{k}')
+      protein[k].set_shape(pad_size)
+
+  return protein
+
+
+@curry1
+def make_msa_feat(protein):
+  """Create and concatenate MSA features."""
+  # Whether there is a domain break. Always zero for chains, but keeping
+  # for compatibility with domain datasets.
+  has_break = tf.clip_by_value(
+      tf.cast(protein['between_segment_residues'], tf.float32),
+      0, 1)
+  aatype_1hot = tf.one_hot(protein['aatype'], 21, axis=-1)
+
+  target_feat = [
+      tf.expand_dims(has_break, axis=-1),
+      aatype_1hot,  # Everyone gets the original sequence.
+  ]
+
+  msa_1hot = tf.one_hot(protein['msa'], 23, axis=-1)
+  has_deletion = tf.clip_by_value(protein['deletion_matrix'], 0., 1.)
+  deletion_value = tf.atan(protein['deletion_matrix'] / 3.) * (2. / np.pi)
+
+  msa_feat = [
+      msa_1hot,
+      tf.expand_dims(has_deletion, axis=-1),
+      tf.expand_dims(deletion_value, axis=-1),
+  ]
+
+  if 'cluster_profile' in protein:
+    deletion_mean_value = (
+        tf.atan(protein['cluster_deletion_mean'] / 3.) * (2. / np.pi))
+    msa_feat.extend([
+        protein['cluster_profile'],
+        tf.expand_dims(deletion_mean_value, axis=-1),
+    ])
+
+  if 'extra_deletion_matrix' in protein:
+    protein['extra_has_deletion'] = tf.clip_by_value(
+        protein['extra_deletion_matrix'], 0., 1.)
+    protein['extra_deletion_value'] = tf.atan(
+        protein['extra_deletion_matrix'] / 3.) * (2. / np.pi)
+
+  protein['msa_feat'] = tf.concat(msa_feat, axis=-1)
+  protein['target_feat'] = tf.concat(target_feat, axis=-1)
+  return protein
+
+
+@curry1
+def select_feat(protein, feature_list):
+  return {k: v for k, v in protein.items() if k in feature_list}
+
+
+@curry1
+def crop_templates(protein, max_templates):
+  for k, v in protein.items():
+    if k.startswith('template_'):
+      protein[k] = v[:max_templates]
+  return protein
+
+
+@curry1
+def random_crop_to_size(protein, crop_size, max_templates, shape_schema,
+                        subsample_templates=False):
+  """Crop randomly to `crop_size`, or keep as is if shorter than that."""
+  seq_length = protein['seq_length']
+  if 'template_mask' in protein:
+    num_templates = tf.cast(
+        shape_helpers.shape_list(protein['template_mask'])[0], tf.int32)
+  else:
+    num_templates = tf.constant(0, dtype=tf.int32)
+  num_res_crop_size = tf.math.minimum(seq_length, crop_size)
+
+  # Ensures that the cropping of residues and templates happens in the same way
+  # across ensembling iterations.
+  # Do not use for randomness that should vary in ensembling.
+  seed_maker = utils.SeedMaker(initial_seed=protein['random_crop_to_size_seed'])
+
+  if subsample_templates:
+    templates_crop_start = tf.random.stateless_uniform(
+        shape=(), minval=0, maxval=num_templates + 1, dtype=tf.int32,
+        seed=seed_maker())
+  else:
+    templates_crop_start = 0
+
+  num_templates_crop_size = tf.math.minimum(
+      num_templates - templates_crop_start, max_templates)
+
+  num_res_crop_start = tf.random.stateless_uniform(
+      shape=(), minval=0, maxval=seq_length - num_res_crop_size + 1,
+      dtype=tf.int32, seed=seed_maker())
+
+  templates_select_indices = tf.argsort(tf.random.stateless_uniform(
+      [num_templates], seed=seed_maker()))
+
+  for k, v in protein.items():
+    if k not in shape_schema or (
+        'template' not in k and NUM_RES not in shape_schema[k]):
+      continue
+
+    # randomly permute the templates before cropping them.
+    if k.startswith('template') and subsample_templates:
+      v = tf.gather(v, templates_select_indices)
+
+    crop_sizes = []
+    crop_starts = []
+    for i, (dim_size, dim) in enumerate(zip(shape_schema[k],
+                                            shape_helpers.shape_list(v))):
+      is_num_res = (dim_size == NUM_RES)
+      if i == 0 and k.startswith('template'):
+        crop_size = num_templates_crop_size
+        crop_start = templates_crop_start
+      else:
+        crop_start = num_res_crop_start if is_num_res else 0
+        crop_size = (num_res_crop_size if is_num_res else
+                     (-1 if dim is None else dim))
+      crop_sizes.append(crop_size)
+      crop_starts.append(crop_start)
+    protein[k] = tf.slice(v, crop_starts, crop_sizes)
+
+  protein['seq_length'] = num_res_crop_size
+  return protein
+
+
+def make_atom14_masks(protein):
+  """Construct denser atom positions (14 dimensions instead of 37)."""
+  restype_atom14_to_atom37 = []  # mapping (restype, atom14) --> atom37
+  restype_atom37_to_atom14 = []  # mapping (restype, atom37) --> atom14
+  restype_atom14_mask = []
+
+  for rt in residue_constants.restypes:
+    atom_names = residue_constants.restype_name_to_atom14_names[
+        residue_constants.restype_1to3[rt]]
+
+    restype_atom14_to_atom37.append([
+        (residue_constants.atom_order[name] if name else 0)
+        for name in atom_names
+    ])
+
+    atom_name_to_idx14 = {name: i for i, name in enumerate(atom_names)}
+    restype_atom37_to_atom14.append([
+        (atom_name_to_idx14[name] if name in atom_name_to_idx14 else 0)
+        for name in residue_constants.atom_types
+    ])
+
+    restype_atom14_mask.append([(1. if name else 0.) for name in atom_names])
+
+  # Add dummy mapping for restype 'UNK'
+  restype_atom14_to_atom37.append([0] * 14)
+  restype_atom37_to_atom14.append([0] * 37)
+  restype_atom14_mask.append([0.] * 14)
+
+  restype_atom14_to_atom37 = np.array(restype_atom14_to_atom37, dtype=np.int32)
+  restype_atom37_to_atom14 = np.array(restype_atom37_to_atom14, dtype=np.int32)
+  restype_atom14_mask = np.array(restype_atom14_mask, dtype=np.float32)
+
+  # create the mapping for (residx, atom14) --> atom37, i.e. an array
+  # with shape (num_res, 14) containing the atom37 indices for this protein
+  residx_atom14_to_atom37 = tf.gather(restype_atom14_to_atom37,
+                                      protein['aatype'])
+  residx_atom14_mask = tf.gather(restype_atom14_mask,
+                                 protein['aatype'])
+
+  protein['atom14_atom_exists'] = residx_atom14_mask
+  protein['residx_atom14_to_atom37'] = residx_atom14_to_atom37
+
+  # create the gather indices for mapping back
+  residx_atom37_to_atom14 = tf.gather(restype_atom37_to_atom14,
+                                      protein['aatype'])
+  protein['residx_atom37_to_atom14'] = residx_atom37_to_atom14
+
+  # create the corresponding mask
+  restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
+  for restype, restype_letter in enumerate(residue_constants.restypes):
+    restype_name = residue_constants.restype_1to3[restype_letter]
+    atom_names = residue_constants.residue_atoms[restype_name]
+    for atom_name in atom_names:
+      atom_type = residue_constants.atom_order[atom_name]
+      restype_atom37_mask[restype, atom_type] = 1
+
+  residx_atom37_mask = tf.gather(restype_atom37_mask,
+                                 protein['aatype'])
+  protein['atom37_atom_exists'] = residx_atom37_mask
+
+  return protein
+

alphafold/model/tf/input_pipeline.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Feature pre-processing input pipeline for AlphaFold."""
+import tensorflow.compat.v1 as tf
+import tree
+
+from alphafold.model.tf import data_transforms
+from alphafold.model.tf import shape_placeholders
+
+# Pylint gets confused by the curry1 decorator because it changes the number
+#   of arguments to the function.
+# pylint:disable=no-value-for-parameter
+
+
+NUM_RES = shape_placeholders.NUM_RES
+NUM_MSA_SEQ = shape_placeholders.NUM_MSA_SEQ
+NUM_EXTRA_SEQ = shape_placeholders.NUM_EXTRA_SEQ
+NUM_TEMPLATES = shape_placeholders.NUM_TEMPLATES
+
+
+def nonensembled_map_fns(data_config):
+  """Input pipeline functions which are not ensembled."""
+  common_cfg = data_config.common
+
+  map_fns = [
+      data_transforms.correct_msa_restypes,
+      data_transforms.add_distillation_flag(False),
+      data_transforms.cast_64bit_ints,
+      data_transforms.squeeze_features,
+      # Keep to not disrupt RNG.
+      data_transforms.randomly_replace_msa_with_unknown(0.0),
+      data_transforms.make_seq_mask,
+      data_transforms.make_msa_mask,
+      # Compute the HHblits profile if it's not set. This has to be run before
+      # sampling the MSA.
+      data_transforms.make_hhblits_profile,
+      data_transforms.make_random_crop_to_size_seed,
+  ]
+  if common_cfg.use_templates:
+    map_fns.extend([
+        data_transforms.fix_templates_aatype,
+        data_transforms.make_template_mask,
+        data_transforms.make_pseudo_beta('template_')
+    ])
+  map_fns.extend([
+      data_transforms.make_atom14_masks,
+  ])
+
+  return map_fns
+
+
+def ensembled_map_fns(data_config):
+  """Input pipeline functions that can be ensembled and averaged."""
+  common_cfg = data_config.common
+  eval_cfg = data_config.eval
+
+  map_fns = []
+
+  if common_cfg.reduce_msa_clusters_by_max_templates:
+    pad_msa_clusters = eval_cfg.max_msa_clusters - eval_cfg.max_templates
+  else:
+    pad_msa_clusters = eval_cfg.max_msa_clusters
+
+  max_msa_clusters = pad_msa_clusters
+  max_extra_msa = common_cfg.max_extra_msa
+
+  map_fns.append(
+      data_transforms.sample_msa(
+          max_msa_clusters,
+          keep_extra=True))
+
+  if 'masked_msa' in common_cfg:
+    # Masked MSA should come *before* MSA clustering so that
+    # the clustering and full MSA profile do not leak information about
+    # the masked locations and secret corrupted locations.
+    map_fns.append(
+        data_transforms.make_masked_msa(common_cfg.masked_msa,
+                                        eval_cfg.masked_msa_replace_fraction))
+
+  if common_cfg.msa_cluster_features:
+    map_fns.append(data_transforms.nearest_neighbor_clusters())
+    map_fns.append(data_transforms.summarize_clusters())
+
+  # Crop after creating the cluster profiles.
+  if max_extra_msa:
+    map_fns.append(data_transforms.crop_extra_msa(max_extra_msa))
+  else:
+    map_fns.append(data_transforms.delete_extra_msa)
+
+  map_fns.append(data_transforms.make_msa_feat())
+
+  crop_feats = dict(eval_cfg.feat)
+
+  if eval_cfg.fixed_size:
+    map_fns.append(data_transforms.select_feat(list(crop_feats)))
+    map_fns.append(data_transforms.random_crop_to_size(
+        eval_cfg.crop_size,
+        eval_cfg.max_templates,
+        crop_feats,
+        eval_cfg.subsample_templates))
+    map_fns.append(data_transforms.make_fixed_size(
+        crop_feats,
+        pad_msa_clusters,
+        common_cfg.max_extra_msa,
+        eval_cfg.crop_size,
+        eval_cfg.max_templates))
+  else:
+    map_fns.append(data_transforms.crop_templates(eval_cfg.max_templates))
+
+  return map_fns
+
+
+def process_tensors_from_config(tensors, data_config):
+  """Apply filters and maps to an existing dataset, based on the config."""
+
+  def wrap_ensemble_fn(data, i):
+    """Function to be mapped over the ensemble dimension."""
+    d = data.copy()
+    fns = ensembled_map_fns(data_config)
+    fn = compose(fns)
+    d['ensemble_index'] = i
+    return fn(d)
+
+  eval_cfg = data_config.eval
+  tensors = compose(
+      nonensembled_map_fns(
+          data_config))(
+              tensors)
+
+  tensors_0 = wrap_ensemble_fn(tensors, tf.constant(0))
+  num_ensemble = eval_cfg.num_ensemble
+  if data_config.common.resample_msa_in_recycling:
+    # Separate batch per ensembling & recycling step.
+    num_ensemble *= data_config.common.num_recycle + 1
+
+  if isinstance(num_ensemble, tf.Tensor) or num_ensemble > 1:
+    dtype = tree.map_structure(lambda x: x.dtype,
+                               tensors_0)
+    tensors = tf.map_fn(
+        lambda x: wrap_ensemble_fn(tensors, x),
+        tf.range(num_ensemble),
+        parallel_iterations=1,
+        dtype=dtype)
+  else:
+    tensors = tree.map_structure(lambda x: x[None],
+                                 tensors_0)
+  return tensors
+
+
+@data_transforms.curry1
+def compose(x, fs):
+  for f in fs:
+    x = f(x)
+  return x

alphafold/model/tf/protein_features.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Contains descriptions of various protein features."""
+import enum
+from typing import Dict, Optional, Sequence, Tuple, Union
+
+import tensorflow.compat.v1 as tf
+
+from alphafold.common import residue_constants
+
+# Type aliases.
+FeaturesMetadata = Dict[str, Tuple[tf.dtypes.DType, Sequence[Union[str, int]]]]
+
+
+class FeatureType(enum.Enum):
+  ZERO_DIM = 0  # Shape [x]
+  ONE_DIM = 1  # Shape [num_res, x]
+  TWO_DIM = 2  # Shape [num_res, num_res, x]
+  MSA = 3  # Shape [msa_length, num_res, x]
+
+
+# Placeholder values that will be replaced with their true value at runtime.
+NUM_RES = "num residues placeholder"
+NUM_SEQ = "length msa placeholder"
+NUM_TEMPLATES = "num templates placeholder"
+# Sizes of the protein features, NUM_RES and NUM_SEQ are allowed as placeholders
+# to be replaced with the number of residues and the number of sequences in the
+# multiple sequence alignment, respectively.
+
+
+FEATURES = {
+    #### Static features of a protein sequence ####
+    "aatype": (tf.float32, [NUM_RES, 21]),
+    "between_segment_residues": (tf.int64, [NUM_RES, 1]),
+    "deletion_matrix": (tf.float32, [NUM_SEQ, NUM_RES, 1]),
+    "domain_name": (tf.string, [1]),
+    "msa": (tf.int64, [NUM_SEQ, NUM_RES, 1]),
+    "num_alignments": (tf.int64, [NUM_RES, 1]),
+    "residue_index": (tf.int64, [NUM_RES, 1]),
+    "seq_length": (tf.int64, [NUM_RES, 1]),
+    "sequence": (tf.string, [1]),
+    "all_atom_positions": (tf.float32,
+                           [NUM_RES, residue_constants.atom_type_num, 3]),
+    "all_atom_mask": (tf.int64, [NUM_RES, residue_constants.atom_type_num]),
+    "resolution": (tf.float32, [1]),
+    "template_domain_names": (tf.string, [NUM_TEMPLATES]),
+    "template_sum_probs": (tf.float32, [NUM_TEMPLATES, 1]),
+    "template_aatype": (tf.float32, [NUM_TEMPLATES, NUM_RES, 22]),
+    "template_all_atom_positions": (tf.float32, [
+        NUM_TEMPLATES, NUM_RES, residue_constants.atom_type_num, 3
+    ]),
+    "template_all_atom_masks": (tf.float32, [
+        NUM_TEMPLATES, NUM_RES, residue_constants.atom_type_num, 1
+    ]),
+}
+
+FEATURE_TYPES = {k: v[0] for k, v in FEATURES.items()}
+FEATURE_SIZES = {k: v[1] for k, v in FEATURES.items()}
+
+
+def register_feature(name: str,
+                     type_: tf.dtypes.DType,
+                     shape_: Tuple[Union[str, int]]):
+  """Register extra features used in custom datasets."""
+  FEATURES[name] = (type_, shape_)
+  FEATURE_TYPES[name] = type_
+  FEATURE_SIZES[name] = shape_
+
+
+def shape(feature_name: str,
+          num_residues: int,
+          msa_length: int,
+          num_templates: Optional[int] = None,
+          features: Optional[FeaturesMetadata] = None):
+  """Get the shape for the given feature name.
+
+  This is near identical to _get_tf_shape_no_placeholders() but with 2
+  differences:
+  * This method does not calculate a single placeholder from the total number of
+    elements (eg given <NUM_RES, 3> and size := 12, this won't deduce NUM_RES
+    must be 4)
+  * This method will work with tensors
+
+  Args:
+    feature_name: String identifier for the feature. If the feature name ends
+      with "_unnormalized", theis suffix is stripped off.
+    num_residues: The number of residues in the current domain - some elements
+      of the shape can be dynamic and will be replaced by this value.
+    msa_length: The number of sequences in the multiple sequence alignment, some
+      elements of the shape can be dynamic and will be replaced by this value.
+      If the number of alignments is unknown / not read, please pass None for
+      msa_length.
+    num_templates (optional): The number of templates in this tfexample.
+    features: A feature_name to (tf_dtype, shape) lookup; defaults to FEATURES.
+
+  Returns:
+    List of ints representation the tensor size.
+
+  Raises:
+    ValueError: If a feature is requested but no concrete placeholder value is
+        given.
+  """
+  features = features or FEATURES
+  if feature_name.endswith("_unnormalized"):
+    feature_name = feature_name[:-13]
+
+  unused_dtype, raw_sizes = features[feature_name]
+  replacements = {NUM_RES: num_residues,
+                  NUM_SEQ: msa_length}
+
+  if num_templates is not None:
+    replacements[NUM_TEMPLATES] = num_templates
+
+  sizes = [replacements.get(dimension, dimension) for dimension in raw_sizes]
+  for dimension in sizes:
+    if isinstance(dimension, str):
+      raise ValueError("Could not parse %s (shape: %s) with values: %s" % (
+          feature_name, raw_sizes, replacements))
+  return sizes
+

alphafold/model/tf/protein_features_test.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for protein_features."""
+import uuid
+
+from absl.testing import absltest
+from absl.testing import parameterized
+import tensorflow.compat.v1 as tf
+
+from alphafold.model.tf import protein_features
+
+
+def _random_bytes():
+  return str(uuid.uuid4()).encode('utf-8')
+
+
+class FeaturesTest(parameterized.TestCase, tf.test.TestCase):
+
+  def testFeatureNames(self):
+    self.assertEqual(len(protein_features.FEATURE_SIZES),
+                     len(protein_features.FEATURE_TYPES))
+    sorted_size_names = sorted(protein_features.FEATURE_SIZES.keys())
+    sorted_type_names = sorted(protein_features.FEATURE_TYPES.keys())
+    for i, size_name in enumerate(sorted_size_names):
+      self.assertEqual(size_name, sorted_type_names[i])
+
+  def testReplacement(self):
+    for name in protein_features.FEATURE_SIZES.keys():
+      sizes = protein_features.shape(name,
+                                     num_residues=12,
+                                     msa_length=24,
+                                     num_templates=3)
+      for x in sizes:
+        self.assertEqual(type(x), int)
+        self.assertGreater(x, 0)
+
+
+if __name__ == '__main__':
+  tf.disable_v2_behavior()
+  absltest.main()

alphafold/model/tf/proteins_dataset.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Datasets consisting of proteins."""
+from typing import Dict, Mapping, Optional, Sequence
+
+import numpy as np
+import tensorflow.compat.v1 as tf
+
+from alphafold.model.tf import protein_features
+
+TensorDict = Dict[str, tf.Tensor]
+
+
+def parse_tfexample(
+    raw_data: bytes,
+    features: protein_features.FeaturesMetadata,
+    key: Optional[str] = None) -> Dict[str, tf.train.Feature]:
+  """Read a single TF Example proto and return a subset of its features.
+
+  Args:
+    raw_data: A serialized tf.Example proto.
+    features: A dictionary of features, mapping string feature names to a tuple
+      (dtype, shape). This dictionary should be a subset of
+      protein_features.FEATURES (or the dictionary itself for all features).
+    key: Optional string with the SSTable key of that tf.Example. This will be
+      added into features as a 'key' but only if requested in features.
+
+  Returns:
+    A dictionary of features mapping feature names to features. Only the given
+    features are returned, all other ones are filtered out.
+  """
+  feature_map = {
+      k: tf.io.FixedLenSequenceFeature(shape=(), dtype=v[0], allow_missing=True)
+      for k, v in features.items()
+  }
+  parsed_features = tf.io.parse_single_example(raw_data, feature_map)
+  reshaped_features = parse_reshape_logic(parsed_features, features, key=key)
+
+  return reshaped_features
+
+
+def _first(tensor: tf.Tensor) -> tf.Tensor:
+  """Returns the 1st element - the input can be a tensor or a scalar."""
+  return tf.reshape(tensor, shape=(-1,))[0]
+
+
+def parse_reshape_logic(
+    parsed_features: TensorDict,
+    features: protein_features.FeaturesMetadata,
+    key: Optional[str] = None) -> TensorDict:
+  """Transforms parsed serial features to the correct shape."""
+  # Find out what is the number of sequences and the number of alignments.
+  num_residues = tf.cast(_first(parsed_features["seq_length"]), dtype=tf.int32)
+
+  if "num_alignments" in parsed_features:
+    num_msa = tf.cast(_first(parsed_features["num_alignments"]), dtype=tf.int32)
+  else:
+    num_msa = 0
+
+  if "template_domain_names" in parsed_features:
+    num_templates = tf.cast(
+        tf.shape(parsed_features["template_domain_names"])[0], dtype=tf.int32)
+  else:
+    num_templates = 0
+
+  if key is not None and "key" in features:
+    parsed_features["key"] = [key]  # Expand dims from () to (1,).
+
+  # Reshape the tensors according to the sequence length and num alignments.
+  for k, v in parsed_features.items():
+    new_shape = protein_features.shape(
+        feature_name=k,
+        num_residues=num_residues,
+        msa_length=num_msa,
+        num_templates=num_templates,
+        features=features)
+    new_shape_size = tf.constant(1, dtype=tf.int32)
+    for dim in new_shape:
+      new_shape_size *= tf.cast(dim, tf.int32)
+
+    assert_equal = tf.assert_equal(
+        tf.size(v), new_shape_size,
+        name="assert_%s_shape_correct" % k,
+        message="The size of feature %s (%s) could not be reshaped "
+        "into %s" % (k, tf.size(v), new_shape))
+    if "template" not in k:
+      # Make sure the feature we are reshaping is not empty.
+      assert_non_empty = tf.assert_greater(
+          tf.size(v), 0, name="assert_%s_non_empty" % k,
+          message="The feature %s is not set in the tf.Example. Either do not "
+          "request the feature or use a tf.Example that has the "
+          "feature set." % k)
+      with tf.control_dependencies([assert_non_empty, assert_equal]):
+        parsed_features[k] = tf.reshape(v, new_shape, name="reshape_%s" % k)
+    else:
+      with tf.control_dependencies([assert_equal]):
+        parsed_features[k] = tf.reshape(v, new_shape, name="reshape_%s" % k)
+
+  return parsed_features
+
+
+def _make_features_metadata(
+    feature_names: Sequence[str]) -> protein_features.FeaturesMetadata:
+  """Makes a feature name to type and shape mapping from a list of names."""
+  # Make sure these features are always read.
+  required_features = ["aatype", "sequence", "seq_length"]
+  feature_names = list(set(feature_names) | set(required_features))
+
+  features_metadata = {name: protein_features.FEATURES[name]
+                       for name in feature_names}
+  return features_metadata
+
+
+def create_tensor_dict(
+    raw_data: bytes,
+    features: Sequence[str],
+    key: Optional[str] = None,
+    ) -> TensorDict:
+  """Creates a dictionary of tensor features.
+
+  Args:
+    raw_data: A serialized tf.Example proto.
+    features: A list of strings of feature names to be returned in the dataset.
+    key: Optional string with the SSTable key of that tf.Example. This will be
+      added into features as a 'key' but only if requested in features.
+
+  Returns:
+    A dictionary of features mapping feature names to features. Only the given
+    features are returned, all other ones are filtered out.
+  """
+  features_metadata = _make_features_metadata(features)
+  return parse_tfexample(raw_data, features_metadata, key)
+
+
+def np_to_tensor_dict(
+    np_example: Mapping[str, np.ndarray],
+    features: Sequence[str],
+    ) -> TensorDict:
+  """Creates dict of tensors from a dict of NumPy arrays.
+
+  Args:
+    np_example: A dict of NumPy feature arrays.
+    features: A list of strings of feature names to be returned in the dataset.
+
+  Returns:
+    A dictionary of features mapping feature names to features. Only the given
+    features are returned, all other ones are filtered out.
+  """
+  features_metadata = _make_features_metadata(features)
+  tensor_dict = {k: tf.constant(v) for k, v in np_example.items()
+                 if k in features_metadata}
+
+  # Ensures shapes are as expected. Needed for setting size of empty features
+  # e.g. when no template hits were found.
+  tensor_dict = parse_reshape_logic(tensor_dict, features_metadata)
+  return tensor_dict

alphafold/model/tf/shape_helpers.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Utilities for dealing with shapes of TensorFlow tensors."""
+import tensorflow.compat.v1 as tf
+
+
+def shape_list(x):
+  """Return list of dimensions of a tensor, statically where possible.
+
+  Like `x.shape.as_list()` but with tensors instead of `None`s.
+
+  Args:
+    x: A tensor.
+  Returns:
+    A list with length equal to the rank of the tensor. The n-th element of the
+    list is an integer when that dimension is statically known otherwise it is
+    the n-th element of `tf.shape(x)`.
+  """
+  x = tf.convert_to_tensor(x)
+
+  # If unknown rank, return dynamic shape
+  if x.get_shape().dims is None:
+    return tf.shape(x)
+
+  static = x.get_shape().as_list()
+  shape = tf.shape(x)
+
+  ret = []
+  for i in range(len(static)):
+    dim = static[i]
+    if dim is None:
+      dim = shape[i]
+    ret.append(dim)
+  return ret
+

alphafold/model/tf/shape_helpers_test.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for shape_helpers."""
+
+import numpy as np
+import tensorflow.compat.v1 as tf
+
+from alphafold.model.tf import shape_helpers
+
+
+class ShapeTest(tf.test.TestCase):
+
+  def test_shape_list(self):
+    """Test that shape_list can allow for reshaping to dynamic shapes."""
+    a = tf.zeros([10, 4, 4, 2])
+    p = tf.placeholder(tf.float32, shape=[None, None, 1, 4, 4])
+    shape_dyn = shape_helpers.shape_list(p)[:2] + [4, 4]
+
+    b = tf.reshape(a, shape_dyn)
+    with self.session() as sess:
+      out = sess.run(b, feed_dict={p: np.ones((20, 1, 1, 4, 4))})
+
+    self.assertAllEqual(out.shape, (20, 1, 4, 4))
+
+
+if __name__ == '__main__':
+  tf.disable_v2_behavior()
+  tf.test.main()

alphafold/model/tf/shape_placeholders.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Placeholder values for run-time varying dimension sizes."""
+
+NUM_RES = 'num residues placeholder'
+NUM_MSA_SEQ = 'msa placeholder'
+NUM_EXTRA_SEQ = 'extra msa placeholder'
+NUM_TEMPLATES = 'num templates placeholder'

alphafold/model/tf/utils.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Shared utilities for various components."""
+import tensorflow.compat.v1 as tf
+
+
+def tf_combine_mask(*masks):
+  """Take the intersection of float-valued masks."""
+  ret = 1
+  for m in masks:
+    ret *= m
+  return ret
+
+
+class SeedMaker(object):
+  """Return unique seeds."""
+
+  def __init__(self, initial_seed=0):
+    self.next_seed = initial_seed
+
+  def __call__(self):
+    i = self.next_seed
+    self.next_seed += 1
+    return i
+
+seed_maker = SeedMaker()
+
+
+def make_random_seed():
+  return tf.random.uniform([2],
+                           tf.int32.min,
+                           tf.int32.max,
+                           tf.int32,
+                           seed=seed_maker())
+

alphafold/model/utils.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""A collection of JAX utility functions for use in protein folding."""
+
+import collections
+import numbers
+from typing import Mapping
+
+import haiku as hk
+import jax
+import jax.numpy as jnp
+import numpy as np
+
+
+def final_init(config):
+  if config.zero_init:
+    return 'zeros'
+  else:
+    return 'linear'
+
+
+def batched_gather(params, indices, axis=0, batch_dims=0):
+  """Implements a JAX equivalent of `tf.gather` with `axis` and `batch_dims`."""
+  take_fn = lambda p, i: jnp.take(p, i, axis=axis)
+  for _ in range(batch_dims):
+    take_fn = jax.vmap(take_fn)
+  return take_fn(params, indices)
+
+
+def mask_mean(mask, value, axis=None, drop_mask_channel=False, eps=1e-10):
+  """Masked mean."""
+  if drop_mask_channel:
+    mask = mask[..., 0]
+
+  mask_shape = mask.shape
+  value_shape = value.shape
+
+  assert len(mask_shape) == len(value_shape)
+
+  if isinstance(axis, numbers.Integral):
+    axis = [axis]
+  elif axis is None:
+    axis = list(range(len(mask_shape)))
+  assert isinstance(axis, collections.Iterable), (
+      'axis needs to be either an iterable, integer or "None"')
+
+  broadcast_factor = 1.
+  for axis_ in axis:
+    value_size = value_shape[axis_]
+    mask_size = mask_shape[axis_]
+    if mask_size == 1:
+      broadcast_factor *= value_size
+    else:
+      assert mask_size == value_size
+
+  return (jnp.sum(mask * value, axis=axis) /
+          (jnp.sum(mask, axis=axis) * broadcast_factor + eps))
+
+
+def flat_params_to_haiku(params: Mapping[str, np.ndarray]) -> hk.Params:
+  """Convert a dictionary of NumPy arrays to Haiku parameters."""
+  hk_params = {}
+  for path, array in params.items():
+    scope, name = path.split('//')
+    if scope not in hk_params:
+      hk_params[scope] = {}
+    hk_params[scope][name] = jnp.array(array)
+
+  return hk_params

alphafold/relax/__init__.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+"""Amber relaxation."""

alphafold/relax/amber_minimize.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Restrained Amber Minimization of a structure."""
+
+import io
+import time
+from typing import Collection, Optional, Sequence
+
+from absl import logging
+import ml_collections
+import numpy as np
+from simtk import openmm
+from simtk import unit
+from simtk.openmm import app as openmm_app
+from simtk.openmm.app.internal.pdbstructure import PdbStructure
+
+from alphafold.common import protein
+from alphafold.common import residue_constants
+from alphafold.model import folding
+from alphafold.relax import cleanup
+from alphafold.relax import utils
+
+
+ENERGY = unit.kilocalories_per_mole
+LENGTH = unit.angstroms
+
+
+def will_restrain(atom: openmm_app.Atom, rset: str) -> bool:
+  """Returns True if the atom will be restrained by the given restraint set."""
+
+  if rset == "non_hydrogen":
+    return atom.element.name != "hydrogen"
+  elif rset == "c_alpha":
+    return atom.name == "CA"
+
+
+def _add_restraints(
+    system: openmm.System,
+    reference_pdb: openmm_app.PDBFile,
+    stiffness: unit.Unit,
+    rset: str,
+    exclude_residues: Sequence[int]):
+  """Adds a harmonic potential that restrains the end-to-end distance."""
+  assert rset in ["non_hydrogen", "c_alpha"]
+
+  force = openmm.CustomExternalForce(
+      "0.5 * k * ((x-x0)^2 + (y-y0)^2 + (z-z0)^2)")
+  force.addGlobalParameter("k", stiffness)
+  for p in ["x0", "y0", "z0"]:
+    force.addPerParticleParameter(p)
+
+  for i, atom in enumerate(reference_pdb.topology.atoms()):
+    if atom.residue.index in exclude_residues:
+      continue
+    if will_restrain(atom, rset):
+      force.addParticle(i, reference_pdb.positions[i])
+  logging.info("Restraining %d / %d particles.",
+               force.getNumParticles(), system.getNumParticles())
+  system.addForce(force)
+
+
+def _openmm_minimize(
+    pdb_str: str,
+    max_iterations: int,
+    tolerance: unit.Unit,
+    stiffness: unit.Unit,
+    restraint_set: str,
+    exclude_residues: Sequence[int]):
+  """Minimize energy via openmm."""
+
+  pdb_file = io.StringIO(pdb_str)
+  pdb = openmm_app.PDBFile(pdb_file)
+
+  force_field = openmm_app.ForceField("amber99sb.xml")
+  constraints = openmm_app.HBonds
+  system = force_field.createSystem(
+      pdb.topology, constraints=constraints)
+  if stiffness > 0 * ENERGY / (LENGTH**2):
+    _add_restraints(system, pdb, stiffness, restraint_set, exclude_residues)
+
+  integrator = openmm.LangevinIntegrator(0, 0.01, 0.0)
+  platform = openmm.Platform.getPlatformByName("CPU")
+  simulation = openmm_app.Simulation(
+      pdb.topology, system, integrator, platform)
+  simulation.context.setPositions(pdb.positions)
+
+  ret = {}
+  state = simulation.context.getState(getEnergy=True, getPositions=True)
+  ret["einit"] = state.getPotentialEnergy().value_in_unit(ENERGY)
+  ret["posinit"] = state.getPositions(asNumpy=True).value_in_unit(LENGTH)
+  simulation.minimizeEnergy(maxIterations=max_iterations,
+                            tolerance=tolerance)
+  state = simulation.context.getState(getEnergy=True, getPositions=True)
+  ret["efinal"] = state.getPotentialEnergy().value_in_unit(ENERGY)
+  ret["pos"] = state.getPositions(asNumpy=True).value_in_unit(LENGTH)
+  ret["min_pdb"] = _get_pdb_string(simulation.topology, state.getPositions())
+  return ret
+
+
+def _get_pdb_string(topology: openmm_app.Topology, positions: unit.Quantity):
+  """Returns a pdb string provided OpenMM topology and positions."""
+  with io.StringIO() as f:
+    openmm_app.PDBFile.writeFile(topology, positions, f)
+    return f.getvalue()
+
+
+def _check_cleaned_atoms(pdb_cleaned_string: str, pdb_ref_string: str):
+  """Checks that no atom positions have been altered by cleaning."""
+  cleaned = openmm_app.PDBFile(io.StringIO(pdb_cleaned_string))
+  reference = openmm_app.PDBFile(io.StringIO(pdb_ref_string))
+
+  cl_xyz = np.array(cleaned.getPositions().value_in_unit(LENGTH))
+  ref_xyz = np.array(reference.getPositions().value_in_unit(LENGTH))
+
+  for ref_res, cl_res in zip(reference.topology.residues(),
+                             cleaned.topology.residues()):
+    assert ref_res.name == cl_res.name
+    for rat in ref_res.atoms():
+      for cat in cl_res.atoms():
+        if cat.name == rat.name:
+          if not np.array_equal(cl_xyz[cat.index], ref_xyz[rat.index]):
+            raise ValueError(f"Coordinates of cleaned atom {cat} do not match "
+                             f"coordinates of reference atom {rat}.")
+
+
+def _check_residues_are_well_defined(prot: protein.Protein):
+  """Checks that all residues contain non-empty atom sets."""
+  if (prot.atom_mask.sum(axis=-1) == 0).any():
+    raise ValueError("Amber minimization can only be performed on proteins with"
+                     " well-defined residues. This protein contains at least"
+                     " one residue with no atoms.")
+
+
+def _check_atom_mask_is_ideal(prot):
+  """Sanity-check the atom mask is ideal, up to a possible OXT."""
+  atom_mask = prot.atom_mask
+  ideal_atom_mask = protein.ideal_atom_mask(prot)
+  utils.assert_equal_nonterminal_atom_types(atom_mask, ideal_atom_mask)
+
+
+def clean_protein(
+    prot: protein.Protein,
+    checks: bool = True):
+  """Adds missing atoms to Protein instance.
+
+  Args:
+    prot: A `protein.Protein` instance.
+    checks: A `bool` specifying whether to add additional checks to the cleaning
+      process.
+
+  Returns:
+    pdb_string: A string of the cleaned protein.
+  """
+  _check_atom_mask_is_ideal(prot)
+
+  # Clean pdb.
+  prot_pdb_string = protein.to_pdb(prot)
+  pdb_file = io.StringIO(prot_pdb_string)
+  alterations_info = {}
+  fixed_pdb = cleanup.fix_pdb(pdb_file, alterations_info)
+  fixed_pdb_file = io.StringIO(fixed_pdb)
+  pdb_structure = PdbStructure(fixed_pdb_file)
+  cleanup.clean_structure(pdb_structure, alterations_info)
+
+  logging.info("alterations info: %s", alterations_info)
+
+  # Write pdb file of cleaned structure.
+  as_file = openmm_app.PDBFile(pdb_structure)
+  pdb_string = _get_pdb_string(as_file.getTopology(), as_file.getPositions())
+  if checks:
+    _check_cleaned_atoms(pdb_string, prot_pdb_string)
+  return pdb_string
+
+
+def make_atom14_positions(prot):
+  """Constructs denser atom positions (14 dimensions instead of 37)."""
+  restype_atom14_to_atom37 = []  # mapping (restype, atom14) --> atom37
+  restype_atom37_to_atom14 = []  # mapping (restype, atom37) --> atom14
+  restype_atom14_mask = []
+
+  for rt in residue_constants.restypes:
+    atom_names = residue_constants.restype_name_to_atom14_names[
+        residue_constants.restype_1to3[rt]]
+
+    restype_atom14_to_atom37.append([
+        (residue_constants.atom_order[name] if name else 0)
+        for name in atom_names
+    ])
+
+    atom_name_to_idx14 = {name: i for i, name in enumerate(atom_names)}
+    restype_atom37_to_atom14.append([
+        (atom_name_to_idx14[name] if name in atom_name_to_idx14 else 0)
+        for name in residue_constants.atom_types
+    ])
+
+    restype_atom14_mask.append([(1. if name else 0.) for name in atom_names])
+
+  # Add dummy mapping for restype 'UNK'.
+  restype_atom14_to_atom37.append([0] * 14)
+  restype_atom37_to_atom14.append([0] * 37)
+  restype_atom14_mask.append([0.] * 14)
+
+  restype_atom14_to_atom37 = np.array(restype_atom14_to_atom37, dtype=np.int32)
+  restype_atom37_to_atom14 = np.array(restype_atom37_to_atom14, dtype=np.int32)
+  restype_atom14_mask = np.array(restype_atom14_mask, dtype=np.float32)
+
+  # Create the mapping for (residx, atom14) --> atom37, i.e. an array
+  # with shape (num_res, 14) containing the atom37 indices for this protein.
+  residx_atom14_to_atom37 = restype_atom14_to_atom37[prot["aatype"]]
+  residx_atom14_mask = restype_atom14_mask[prot["aatype"]]
+
+  # Create a mask for known ground truth positions.
+  residx_atom14_gt_mask = residx_atom14_mask * np.take_along_axis(
+      prot["all_atom_mask"], residx_atom14_to_atom37, axis=1).astype(np.float32)
+
+  # Gather the ground truth positions.
+  residx_atom14_gt_positions = residx_atom14_gt_mask[:, :, None] * (
+      np.take_along_axis(prot["all_atom_positions"],
+                         residx_atom14_to_atom37[..., None],
+                         axis=1))
+
+  prot["atom14_atom_exists"] = residx_atom14_mask
+  prot["atom14_gt_exists"] = residx_atom14_gt_mask
+  prot["atom14_gt_positions"] = residx_atom14_gt_positions
+
+  prot["residx_atom14_to_atom37"] = residx_atom14_to_atom37
+
+  # Create the gather indices for mapping back.
+  residx_atom37_to_atom14 = restype_atom37_to_atom14[prot["aatype"]]
+  prot["residx_atom37_to_atom14"] = residx_atom37_to_atom14
+
+  # Create the corresponding mask.
+  restype_atom37_mask = np.zeros([21, 37], dtype=np.float32)
+  for restype, restype_letter in enumerate(residue_constants.restypes):
+    restype_name = residue_constants.restype_1to3[restype_letter]
+    atom_names = residue_constants.residue_atoms[restype_name]
+    for atom_name in atom_names:
+      atom_type = residue_constants.atom_order[atom_name]
+      restype_atom37_mask[restype, atom_type] = 1
+
+  residx_atom37_mask = restype_atom37_mask[prot["aatype"]]
+  prot["atom37_atom_exists"] = residx_atom37_mask
+
+  # As the atom naming is ambiguous for 7 of the 20 amino acids, provide
+  # alternative ground truth coordinates where the naming is swapped
+  restype_3 = [
+      residue_constants.restype_1to3[res] for res in residue_constants.restypes
+  ]
+  restype_3 += ["UNK"]
+
+  # Matrices for renaming ambiguous atoms.
+  all_matrices = {res: np.eye(14, dtype=np.float32) for res in restype_3}
+  for resname, swap in residue_constants.residue_atom_renaming_swaps.items():
+    correspondences = np.arange(14)
+    for source_atom_swap, target_atom_swap in swap.items():
+      source_index = residue_constants.restype_name_to_atom14_names[
+          resname].index(source_atom_swap)
+      target_index = residue_constants.restype_name_to_atom14_names[
+          resname].index(target_atom_swap)
+      correspondences[source_index] = target_index
+      correspondences[target_index] = source_index
+      renaming_matrix = np.zeros((14, 14), dtype=np.float32)
+      for index, correspondence in enumerate(correspondences):
+        renaming_matrix[index, correspondence] = 1.
+    all_matrices[resname] = renaming_matrix.astype(np.float32)
+  renaming_matrices = np.stack([all_matrices[restype] for restype in restype_3])
+
+  # Pick the transformation matrices for the given residue sequence
+  # shape (num_res, 14, 14).
+  renaming_transform = renaming_matrices[prot["aatype"]]
+
+  # Apply it to the ground truth positions. shape (num_res, 14, 3).
+  alternative_gt_positions = np.einsum("rac,rab->rbc",
+                                       residx_atom14_gt_positions,
+                                       renaming_transform)
+  prot["atom14_alt_gt_positions"] = alternative_gt_positions
+
+  # Create the mask for the alternative ground truth (differs from the
+  # ground truth mask, if only one of the atoms in an ambiguous pair has a
+  # ground truth position).
+  alternative_gt_mask = np.einsum("ra,rab->rb",
+                                  residx_atom14_gt_mask,
+                                  renaming_transform)
+
+  prot["atom14_alt_gt_exists"] = alternative_gt_mask
+
+  # Create an ambiguous atoms mask.  shape: (21, 14).
+  restype_atom14_is_ambiguous = np.zeros((21, 14), dtype=np.float32)
+  for resname, swap in residue_constants.residue_atom_renaming_swaps.items():
+    for atom_name1, atom_name2 in swap.items():
+      restype = residue_constants.restype_order[
+          residue_constants.restype_3to1[resname]]
+      atom_idx1 = residue_constants.restype_name_to_atom14_names[resname].index(
+          atom_name1)
+      atom_idx2 = residue_constants.restype_name_to_atom14_names[resname].index(
+          atom_name2)
+      restype_atom14_is_ambiguous[restype, atom_idx1] = 1
+      restype_atom14_is_ambiguous[restype, atom_idx2] = 1
+
+  # From this create an ambiguous_mask for the given sequence.
+  prot["atom14_atom_is_ambiguous"] = (
+      restype_atom14_is_ambiguous[prot["aatype"]])
+
+  return prot
+
+
+def find_violations(prot_np: protein.Protein):
+  """Analyzes a protein and returns structural violation information.
+
+  Args:
+    prot_np: A protein.
+
+  Returns:
+    violations: A `dict` of structure components with structural violations.
+    violation_metrics: A `dict` of violation metrics.
+  """
+  batch = {
+      "aatype": prot_np.aatype,
+      "all_atom_positions": prot_np.atom_positions.astype(np.float32),
+      "all_atom_mask": prot_np.atom_mask.astype(np.float32),
+      "residue_index": prot_np.residue_index,
+  }
+
+  batch["seq_mask"] = np.ones_like(batch["aatype"], np.float32)
+  batch = make_atom14_positions(batch)
+
+  violations = folding.find_structural_violations(
+      batch=batch,
+      atom14_pred_positions=batch["atom14_gt_positions"],
+      config=ml_collections.ConfigDict(
+          {"violation_tolerance_factor": 12,  # Taken from model config.
+           "clash_overlap_tolerance": 1.5,  # Taken from model config.
+          }))
+  violation_metrics = folding.compute_violation_metrics(
+      batch=batch,
+      atom14_pred_positions=batch["atom14_gt_positions"],
+      violations=violations,
+  )
+
+  return violations, violation_metrics
+
+
+def get_violation_metrics(prot: protein.Protein):
+  """Computes violation and alignment metrics."""
+  structural_violations, struct_metrics = find_violations(prot)
+  violation_idx = np.flatnonzero(
+      structural_violations["total_per_residue_violations_mask"])
+
+  struct_metrics["residue_violations"] = violation_idx
+  struct_metrics["num_residue_violations"] = len(violation_idx)
+  struct_metrics["structural_violations"] = structural_violations
+  return struct_metrics
+
+
+def _run_one_iteration(
+    *,
+    pdb_string: str,
+    max_iterations: int,
+    tolerance: float,
+    stiffness: float,
+    restraint_set: str,
+    max_attempts: int,
+    exclude_residues: Optional[Collection[int]] = None):
+  """Runs the minimization pipeline.
+
+  Args:
+    pdb_string: A pdb string.
+    max_iterations: An `int` specifying the maximum number of L-BFGS iterations.
+    A value of 0 specifies no limit.
+    tolerance: kcal/mol, the energy tolerance of L-BFGS.
+    stiffness: kcal/mol A**2, spring constant of heavy atom restraining
+      potential.
+    restraint_set: The set of atoms to restrain.
+    max_attempts: The maximum number of minimization attempts.
+    exclude_residues: An optional list of zero-indexed residues to exclude from
+        restraints.
+
+  Returns:
+    A `dict` of minimization info.
+  """
+  exclude_residues = exclude_residues or []
+
+  # Assign physical dimensions.
+  tolerance = tolerance * ENERGY
+  stiffness = stiffness * ENERGY / (LENGTH**2)
+
+  start = time.time()
+  minimized = False
+  attempts = 0
+  while not minimized and attempts < max_attempts:
+    attempts += 1
+    try:
+      logging.info("Minimizing protein, attempt %d of %d.",
+                   attempts, max_attempts)
+      ret = _openmm_minimize(
+          pdb_string, max_iterations=max_iterations,
+          tolerance=tolerance, stiffness=stiffness,
+          restraint_set=restraint_set,
+          exclude_residues=exclude_residues)
+      minimized = True
+    except Exception as e:  # pylint: disable=broad-except
+      logging.info(e)
+  if not minimized:
+    raise ValueError(f"Minimization failed after {max_attempts} attempts.")
+  ret["opt_time"] = time.time() - start
+  ret["min_attempts"] = attempts
+  return ret
+
+
+def run_pipeline(
+    prot: protein.Protein,
+    stiffness: float,
+    max_outer_iterations: int = 1,
+    place_hydrogens_every_iteration: bool = True,
+    max_iterations: int = 0,
+    tolerance: float = 2.39,
+    restraint_set: str = "non_hydrogen",
+    max_attempts: int = 100,
+    checks: bool = True,
+    exclude_residues: Optional[Sequence[int]] = None):
+  """Run iterative amber relax.
+
+  Successive relax iterations are performed until all violations have been
+  resolved. Each iteration involves a restrained Amber minimization, with
+  restraint exclusions determined by violation-participating residues.
+
+  Args:
+    prot: A protein to be relaxed.
+    stiffness: kcal/mol A**2, the restraint stiffness.
+    max_outer_iterations: The maximum number of iterative minimization.
+    place_hydrogens_every_iteration: Whether hydrogens are re-initialized
+        prior to every minimization.
+    max_iterations: An `int` specifying the maximum number of L-BFGS steps
+        per relax iteration. A value of 0 specifies no limit.
+    tolerance: kcal/mol, the energy tolerance of L-BFGS.
+        The default value is the OpenMM default.
+    restraint_set: The set of atoms to restrain.
+    max_attempts: The maximum number of minimization attempts per iteration.
+    checks: Whether to perform cleaning checks.
+    exclude_residues: An optional list of zero-indexed residues to exclude from
+        restraints.
+
+  Returns:
+    out: A dictionary of output values.
+  """
+
+  # `protein.to_pdb` will strip any poorly-defined residues so we need to
+  # perform this check before `clean_protein`.
+  _check_residues_are_well_defined(prot)
+  pdb_string = clean_protein(prot, checks=checks)
+
+  exclude_residues = exclude_residues or []
+  exclude_residues = set(exclude_residues)
+  violations = np.inf
+  iteration = 0
+
+  while violations > 0 and iteration < max_outer_iterations:
+    ret = _run_one_iteration(
+        pdb_string=pdb_string,
+        exclude_residues=exclude_residues,
+        max_iterations=max_iterations,
+        tolerance=tolerance,
+        stiffness=stiffness,
+        restraint_set=restraint_set,
+        max_attempts=max_attempts)
+    prot = protein.from_pdb_string(ret["min_pdb"])
+    if place_hydrogens_every_iteration:
+      pdb_string = clean_protein(prot, checks=True)
+    else:
+      pdb_string = ret["min_pdb"]
+    ret.update(get_violation_metrics(prot))
+    ret.update({
+        "num_exclusions": len(exclude_residues),
+        "iteration": iteration,
+    })
+    violations = ret["violations_per_residue"]
+    exclude_residues = exclude_residues.union(ret["residue_violations"])
+
+    logging.info("Iteration completed: Einit %.2f Efinal %.2f Time %.2f s "
+                 "num residue violations %d num residue exclusions %d ",
+                 ret["einit"], ret["efinal"], ret["opt_time"],
+                 ret["num_residue_violations"], ret["num_exclusions"])
+    iteration += 1
+  return ret
+
+
+def get_initial_energies(pdb_strs: Sequence[str],
+                         stiffness: float = 0.0,
+                         restraint_set: str = "non_hydrogen",
+                         exclude_residues: Optional[Sequence[int]] = None):
+  """Returns initial potential energies for a sequence of PDBs.
+
+  Assumes the input PDBs are ready for minimization, and all have the same
+  topology.
+  Allows time to be saved by not pdbfixing / rebuilding the system.
+
+  Args:
+    pdb_strs: List of PDB strings.
+    stiffness: kcal/mol A**2, spring constant of heavy atom restraining
+        potential.
+    restraint_set: Which atom types to restrain.
+    exclude_residues: An optional list of zero-indexed residues to exclude from
+        restraints.
+
+  Returns:
+    A list of initial energies in the same order as pdb_strs.
+  """
+  exclude_residues = exclude_residues or []
+
+  openmm_pdbs = [openmm_app.PDBFile(PdbStructure(io.StringIO(p)))
+                 for p in pdb_strs]
+  force_field = openmm_app.ForceField("amber99sb.xml")
+  system = force_field.createSystem(openmm_pdbs[0].topology,
+                                    constraints=openmm_app.HBonds)
+  stiffness = stiffness * ENERGY / (LENGTH**2)
+  if stiffness > 0 * ENERGY / (LENGTH**2):
+    _add_restraints(system, openmm_pdbs[0], stiffness, restraint_set,
+                    exclude_residues)
+  simulation = openmm_app.Simulation(openmm_pdbs[0].topology,
+                                     system,
+                                     openmm.LangevinIntegrator(0, 0.01, 0.0),
+                                     openmm.Platform.getPlatformByName("CPU"))
+  energies = []
+  for pdb in openmm_pdbs:
+    try:
+      simulation.context.setPositions(pdb.positions)
+      state = simulation.context.getState(getEnergy=True)
+      energies.append(state.getPotentialEnergy().value_in_unit(ENERGY))
+    except Exception as e:  # pylint: disable=broad-except
+      logging.error("Error getting initial energy, returning large value %s", e)
+      energies.append(unit.Quantity(1e20, ENERGY))
+  return energies

alphafold/relax/amber_minimize_test.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for amber_minimize."""
+import os
+
+from absl.testing import absltest
+import numpy as np
+
+from alphafold.common import protein
+from alphafold.relax import amber_minimize
+# Internal import (7716).
+
+
+def _load_test_protein(data_path):
+  pdb_path = os.path.join(absltest.get_default_test_srcdir(), data_path)
+  with open(pdb_path, 'r') as f:
+    return protein.from_pdb_string(f.read())
+
+
+class AmberMinimizeTest(absltest.TestCase):
+
+  def test_multiple_disulfides_target(self):
+    prot = _load_test_protein(
+        'alphafold/relax/testdata/multiple_disulfides_target.pdb'
+        )
+    ret = amber_minimize.run_pipeline(prot, max_iterations=10, max_attempts=1,
+                                      stiffness=10.)
+    self.assertIn('opt_time', ret)
+    self.assertIn('min_attempts', ret)
+
+  def test_raises_invalid_protein_assertion(self):
+    prot = _load_test_protein(
+        'alphafold/relax/testdata/multiple_disulfides_target.pdb'
+        )
+    prot.atom_mask[4, :] = 0
+    with self.assertRaisesRegex(
+        ValueError,
+        'Amber minimization can only be performed on proteins with well-defined'
+        ' residues. This protein contains at least one residue with no atoms.'):
+      amber_minimize.run_pipeline(prot, max_iterations=10,
+                                  stiffness=1.,
+                                  max_attempts=1)
+
+  def test_iterative_relax(self):
+    # This test can occasionally fail because of nondeterminism in OpenMM.
+    prot = _load_test_protein(
+        'alphafold/relax/testdata/with_violations.pdb'
+        )
+    violations = amber_minimize.get_violation_metrics(prot)
+    self.assertGreater(violations['num_residue_violations'], 0)
+    out = amber_minimize.run_pipeline(
+        prot=prot, max_outer_iterations=10, stiffness=10.)
+    self.assertLess(out['efinal'], out['einit'])
+    self.assertEqual(0, out['num_residue_violations'])
+
+  def test_find_violations(self):
+    prot = _load_test_protein(
+        'alphafold/relax/testdata/multiple_disulfides_target.pdb'
+        )
+    viols, _ = amber_minimize.find_violations(prot)
+
+    expected_between_residues_connection_mask = np.zeros((191,), np.float32)
+    for residue in (42, 43, 59, 60, 135, 136):
+      expected_between_residues_connection_mask[residue] = 1.0
+
+    expected_clash_indices = np.array([
+        [8, 4],
+        [8, 5],
+        [13, 3],
+        [14, 1],
+        [14, 4],
+        [26, 4],
+        [26, 5],
+        [31, 8],
+        [31, 10],
+        [39, 0],
+        [39, 1],
+        [39, 2],
+        [39, 3],
+        [39, 4],
+        [42, 5],
+        [42, 6],
+        [42, 7],
+        [42, 8],
+        [47, 7],
+        [47, 8],
+        [47, 9],
+        [47, 10],
+        [64, 4],
+        [85, 5],
+        [102, 4],
+        [102, 5],
+        [109, 13],
+        [111, 5],
+        [118, 6],
+        [118, 7],
+        [118, 8],
+        [124, 4],
+        [124, 5],
+        [131, 5],
+        [139, 7],
+        [147, 4],
+        [152, 7]], dtype=np.int32)
+    expected_between_residues_clash_mask = np.zeros([191, 14])
+    expected_between_residues_clash_mask[expected_clash_indices[:, 0],
+                                         expected_clash_indices[:, 1]] += 1
+    expected_per_atom_violations = np.zeros([191, 14])
+    np.testing.assert_array_equal(
+        viols['between_residues']['connections_per_residue_violation_mask'],
+        expected_between_residues_connection_mask)
+    np.testing.assert_array_equal(
+        viols['between_residues']['clashes_per_atom_clash_mask'],
+        expected_between_residues_clash_mask)
+    np.testing.assert_array_equal(
+        viols['within_residues']['per_atom_violations'],
+        expected_per_atom_violations)
+
+
+if __name__ == '__main__':
+  absltest.main()

alphafold/relax/cleanup.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Cleans up a PDB file using pdbfixer in preparation for OpenMM simulations.
+
+fix_pdb uses a third-party tool. We also support fixing some additional edge
+cases like removing chains of length one (see clean_structure).
+"""
+import io
+
+import pdbfixer
+from simtk.openmm import app
+from simtk.openmm.app import element
+
+
+def fix_pdb(pdbfile, alterations_info):
+  """Apply pdbfixer to the contents of a PDB file; return a PDB string result.
+
+  1) Replaces nonstandard residues.
+  2) Removes heterogens (non protein residues) including water.
+  3) Adds missing residues and missing atoms within existing residues.
+  4) Adds hydrogens assuming pH=7.0.
+  5) KeepIds is currently true, so the fixer must keep the existing chain and
+     residue identifiers. This will fail for some files in wider PDB that have
+     invalid IDs.
+
+  Args:
+    pdbfile: Input PDB file handle.
+    alterations_info: A dict that will store details of changes made.
+
+  Returns:
+    A PDB string representing the fixed structure.
+  """
+  fixer = pdbfixer.PDBFixer(pdbfile=pdbfile)
+  fixer.findNonstandardResidues()
+  alterations_info['nonstandard_residues'] = fixer.nonstandardResidues
+  fixer.replaceNonstandardResidues()
+  _remove_heterogens(fixer, alterations_info, keep_water=False)
+  fixer.findMissingResidues()
+  alterations_info['missing_residues'] = fixer.missingResidues
+  fixer.findMissingAtoms()
+  alterations_info['missing_heavy_atoms'] = fixer.missingAtoms
+  alterations_info['missing_terminals'] = fixer.missingTerminals
+  fixer.addMissingAtoms(seed=0)
+  fixer.addMissingHydrogens()
+  out_handle = io.StringIO()
+  app.PDBFile.writeFile(fixer.topology, fixer.positions, out_handle,
+                        keepIds=True)
+  return out_handle.getvalue()
+
+
+def clean_structure(pdb_structure, alterations_info):
+  """Applies additional fixes to an OpenMM structure, to handle edge cases.
+
+  Args:
+    pdb_structure: An OpenMM structure to modify and fix.
+    alterations_info: A dict that will store details of changes made.
+  """
+  _replace_met_se(pdb_structure, alterations_info)
+  _remove_chains_of_length_one(pdb_structure, alterations_info)
+
+
+def _remove_heterogens(fixer, alterations_info, keep_water):
+  """Removes the residues that Pdbfixer considers to be heterogens.
+
+  Args:
+    fixer: A Pdbfixer instance.
+    alterations_info: A dict that will store details of changes made.
+    keep_water: If True, water (HOH) is not considered to be a heterogen.
+  """
+  initial_resnames = set()
+  for chain in fixer.topology.chains():
+    for residue in chain.residues():
+      initial_resnames.add(residue.name)
+  fixer.removeHeterogens(keepWater=keep_water)
+  final_resnames = set()
+  for chain in fixer.topology.chains():
+    for residue in chain.residues():
+      final_resnames.add(residue.name)
+  alterations_info['removed_heterogens'] = (
+      initial_resnames.difference(final_resnames))
+
+
+def _replace_met_se(pdb_structure, alterations_info):
+  """Replace the Se in any MET residues that were not marked as modified."""
+  modified_met_residues = []
+  for res in pdb_structure.iter_residues():
+    name = res.get_name_with_spaces().strip()
+    if name == 'MET':
+      s_atom = res.get_atom('SD')
+      if s_atom.element_symbol == 'Se':
+        s_atom.element_symbol = 'S'
+        s_atom.element = element.get_by_symbol('S')
+        modified_met_residues.append(s_atom.residue_number)
+  alterations_info['Se_in_MET'] = modified_met_residues
+
+
+def _remove_chains_of_length_one(pdb_structure, alterations_info):
+  """Removes chains that correspond to a single amino acid.
+
+  A single amino acid in a chain is both N and C terminus. There is no force
+  template for this case.
+
+  Args:
+    pdb_structure: An OpenMM pdb_structure to modify and fix.
+    alterations_info: A dict that will store details of changes made.
+  """
+  removed_chains = {}
+  for model in pdb_structure.iter_models():
+    valid_chains = [c for c in model.iter_chains() if len(c) > 1]
+    invalid_chain_ids = [c.chain_id for c in model.iter_chains() if len(c) <= 1]
+    model.chains = valid_chains
+    for chain_id in invalid_chain_ids:
+      model.chains_by_id.pop(chain_id)
+    removed_chains[model.number] = invalid_chain_ids
+  alterations_info['removed_chains'] = removed_chains

alphafold/relax/cleanup_test.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for relax.cleanup."""
+import io
+
+from absl.testing import absltest
+from simtk.openmm.app.internal import pdbstructure
+
+from alphafold.relax import cleanup
+
+
+def _pdb_to_structure(pdb_str):
+  handle = io.StringIO(pdb_str)
+  return pdbstructure.PdbStructure(handle)
+
+
+def _lines_to_structure(pdb_lines):
+  return _pdb_to_structure('\n'.join(pdb_lines))
+
+
+class CleanupTest(absltest.TestCase):
+
+  def test_missing_residues(self):
+    pdb_lines = ['SEQRES   1 C    3  CYS GLY LEU',
+                 'ATOM      1  N   CYS C   1     -12.262  20.115  60.959  1.00 '
+                 '19.08           N',
+                 'ATOM      2  CA  CYS C   1     -11.065  20.934  60.773  1.00 '
+                 '17.23           C',
+                 'ATOM      3  C   CYS C   1     -10.002  20.742  61.844  1.00 '
+                 '15.38           C',
+                 'ATOM      4  O   CYS C   1     -10.284  20.225  62.929  1.00 '
+                 '16.04           O',
+                 'ATOM      5  N   LEU C   3      -7.688  18.700  62.045  1.00 '
+                 '14.75           N',
+                 'ATOM      6  CA  LEU C   3      -7.256  17.320  62.234  1.00 '
+                 '16.81           C',
+                 'ATOM      7  C   LEU C   3      -6.380  16.864  61.070  1.00 '
+                 '16.95           C',
+                 'ATOM      8  O   LEU C   3      -6.551  17.332  59.947  1.00 '
+                 '16.97           O']
+    input_handle = io.StringIO('\n'.join(pdb_lines))
+    alterations = {}
+    result = cleanup.fix_pdb(input_handle, alterations)
+    structure = _pdb_to_structure(result)
+    residue_names = [r.get_name() for r in structure.iter_residues()]
+    self.assertCountEqual(residue_names, ['CYS', 'GLY', 'LEU'])
+    self.assertCountEqual(alterations['missing_residues'].values(), [['GLY']])
+
+  def test_missing_atoms(self):
+    pdb_lines = ['SEQRES   1 A    1  PRO',
+                 'ATOM      1  CA  PRO A   1       1.000   1.000   1.000  1.00 '
+                 ' 0.00           C']
+    input_handle = io.StringIO('\n'.join(pdb_lines))
+    alterations = {}
+    result = cleanup.fix_pdb(input_handle, alterations)
+    structure = _pdb_to_structure(result)
+    atom_names = [a.get_name() for a in structure.iter_atoms()]
+    self.assertCountEqual(atom_names, ['N', 'CD', 'HD2', 'HD3', 'CG', 'HG2',
+                                       'HG3', 'CB', 'HB2', 'HB3', 'CA', 'HA',
+                                       'C', 'O', 'H2', 'H3', 'OXT'])
+    missing_atoms_by_residue = list(alterations['missing_heavy_atoms'].values())
+    self.assertLen(missing_atoms_by_residue, 1)
+    atoms_added = [a.name for a in missing_atoms_by_residue[0]]
+    self.assertCountEqual(atoms_added, ['N', 'CD', 'CG', 'CB', 'C', 'O'])
+    missing_terminals_by_residue = alterations['missing_terminals']
+    self.assertLen(missing_terminals_by_residue, 1)
+    has_missing_terminal = [r.name for r in missing_terminals_by_residue.keys()]
+    self.assertCountEqual(has_missing_terminal, ['PRO'])
+    self.assertCountEqual([t for t in missing_terminals_by_residue.values()],
+                          [['OXT']])
+
+  def test_remove_heterogens(self):
+    pdb_lines = ['SEQRES   1 A    1  GLY',
+                 'ATOM      1  CA  GLY A   1       0.000   0.000   0.000  1.00 '
+                 ' 0.00           C',
+                 'ATOM      2   O  HOH A   2       0.000   0.000   0.000  1.00 '
+                 ' 0.00           O']
+    input_handle = io.StringIO('\n'.join(pdb_lines))
+    alterations = {}
+    result = cleanup.fix_pdb(input_handle, alterations)
+    structure = _pdb_to_structure(result)
+    self.assertCountEqual([res.get_name() for res in structure.iter_residues()],
+                          ['GLY'])
+    self.assertEqual(alterations['removed_heterogens'], set(['HOH']))
+
+  def test_fix_nonstandard_residues(self):
+    pdb_lines = ['SEQRES   1 A    1  DAL',
+                 'ATOM      1  CA  DAL A   1       0.000   0.000   0.000  1.00 '
+                 ' 0.00           C']
+    input_handle = io.StringIO('\n'.join(pdb_lines))
+    alterations = {}
+    result = cleanup.fix_pdb(input_handle, alterations)
+    structure = _pdb_to_structure(result)
+    residue_names = [res.get_name() for res in structure.iter_residues()]
+    self.assertCountEqual(residue_names, ['ALA'])
+    self.assertLen(alterations['nonstandard_residues'], 1)
+    original_res, new_name = alterations['nonstandard_residues'][0]
+    self.assertEqual(original_res.id, '1')
+    self.assertEqual(new_name, 'ALA')
+
+  def test_replace_met_se(self):
+    pdb_lines = ['SEQRES   1 A    1  MET',
+                 'ATOM      1  SD  MET A   1       0.000   0.000   0.000  1.00 '
+                 ' 0.00          Se']
+    structure = _lines_to_structure(pdb_lines)
+    alterations = {}
+    cleanup._replace_met_se(structure, alterations)
+    sd = [a for a in structure.iter_atoms() if a.get_name() == 'SD']
+    self.assertLen(sd, 1)
+    self.assertEqual(sd[0].element_symbol, 'S')
+    self.assertCountEqual(alterations['Se_in_MET'], [sd[0].residue_number])
+
+  def test_remove_chains_of_length_one(self):
+    pdb_lines = ['SEQRES   1 A    1  GLY',
+                 'ATOM      1  CA  GLY A   1       0.000   0.000   0.000  1.00 '
+                 ' 0.00           C']
+    structure = _lines_to_structure(pdb_lines)
+    alterations = {}
+    cleanup._remove_chains_of_length_one(structure, alterations)
+    chains = list(structure.iter_chains())
+    self.assertEmpty(chains)
+    self.assertCountEqual(alterations['removed_chains'].values(), [['A']])
+
+
+if __name__ == '__main__':
+  absltest.main()

alphafold/relax/relax.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Amber relaxation."""
+from typing import Any, Dict, Sequence, Tuple
+
+import numpy as np
+
+from alphafold.common import protein
+from alphafold.relax import amber_minimize
+from alphafold.relax import utils
+
+
+class AmberRelaxation(object):
+  """Amber relaxation."""
+
+  def __init__(self,
+               *,
+               max_iterations: int,
+               tolerance: float,
+               stiffness: float,
+               exclude_residues: Sequence[int],
+               max_outer_iterations: int):
+    """Initialize Amber Relaxer.
+
+    Args:
+      max_iterations: Maximum number of L-BFGS iterations. 0 means no max.
+      tolerance: kcal/mol, the energy tolerance of L-BFGS.
+      stiffness: kcal/mol A**2, spring constant of heavy atom restraining
+        potential.
+      exclude_residues: Residues to exclude from per-atom restraining.
+        Zero-indexed.
+      max_outer_iterations: Maximum number of violation-informed relax
+       iterations. A value of 1 will run the non-iterative procedure used in
+       CASP14. Use 20 so that >95% of the bad cases are relaxed. Relax finishes
+       as soon as there are no violations, hence in most cases this causes no
+       slowdown. In the worst case we do 20 outer iterations.
+    """
+
+    self._max_iterations = max_iterations
+    self._tolerance = tolerance
+    self._stiffness = stiffness
+    self._exclude_residues = exclude_residues
+    self._max_outer_iterations = max_outer_iterations
+
+  def process(self, *,
+              prot: protein.Protein) -> Tuple[str, Dict[str, Any], np.ndarray]:
+    """Runs Amber relax on a prediction, adds hydrogens, returns PDB string."""
+    out = amber_minimize.run_pipeline(
+        prot=prot, max_iterations=self._max_iterations,
+        tolerance=self._tolerance, stiffness=self._stiffness,
+        exclude_residues=self._exclude_residues,
+        max_outer_iterations=self._max_outer_iterations)
+    min_pos = out['pos']
+    start_pos = out['posinit']
+    rmsd = np.sqrt(np.sum((start_pos - min_pos)**2) / start_pos.shape[0])
+    debug_data = {
+        'initial_energy': out['einit'],
+        'final_energy': out['efinal'],
+        'attempts': out['min_attempts'],
+        'rmsd': rmsd
+    }
+    pdb_str = amber_minimize.clean_protein(prot)
+    min_pdb = utils.overwrite_pdb_coordinates(pdb_str, min_pos)
+    min_pdb = utils.overwrite_b_factors(min_pdb, prot.b_factors)
+    utils.assert_equal_nonterminal_atom_types(
+        protein.from_pdb_string(min_pdb).atom_mask,
+        prot.atom_mask)
+    violations = out['structural_violations'][
+        'total_per_residue_violations_mask']
+    return min_pdb, debug_data, violations
+

alphafold/relax/relax_test.py

+# Copyright 2021 DeepMind Technologies Limited
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+"""Tests for relax."""
+import os
+
+from absl.testing import absltest
+import numpy as np
+from alphafold.common import protein
+from alphafold.relax import relax
+# Internal import (7716).
+
+
+class RunAmberRelaxTest(absltest.TestCase):
+
+  def setUp(self):
+    super().setUp()
+    self.test_dir = os.path.join(
+        absltest.get_default_test_srcdir(),
+        'alphafold/relax/testdata/')
+    self.test_config = {
+        'max_iterations': 1,
+        'tolerance': 2.39,
+        'stiffness': 10.0,
+        'exclude_residues': [],
+        'max_outer_iterations': 1}
+
+  def test_process(self):
+    amber_relax = relax.AmberRelaxation(**self.test_config)
+
+    with open(os.path.join(self.test_dir, 'model_output.pdb')) as f:
+      test_prot = protein.from_pdb_string(f.read())
+    pdb_min, debug_info, num_violations = amber_relax.process(prot=test_prot)
+
+    self.assertCountEqual(debug_info.keys(),
+                          set({'initial_energy', 'final_energy',
+                               'attempts', 'rmsd'}))
+    self.assertLess(debug_info['final_energy'], debug_info['initial_energy'])
+    self.assertGreater(debug_info['rmsd'], 0)
+
+    prot_min = protein.from_pdb_string(pdb_min)
+    # Most protein properties should be unchanged.
+    np.testing.assert_almost_equal(test_prot.aatype, prot_min.aatype)
+    np.testing.assert_almost_equal(test_prot.residue_index,
+                                   prot_min.residue_index)
+    # Atom mask and bfactors identical except for terminal OXT of last residue.
+    np.testing.assert_almost_equal(test_prot.atom_mask[:-1, :],
+                                   prot_min.atom_mask[:-1, :])
+    np.testing.assert_almost_equal(test_prot.b_factors[:-1, :],
+                                   prot_min.b_factors[:-1, :])
+    np.testing.assert_almost_equal(test_prot.atom_mask[:, :-1],
+                                   prot_min.atom_mask[:, :-1])
+    np.testing.assert_almost_equal(test_prot.b_factors[:, :-1],
+                                   prot_min.b_factors[:, :-1])
+    # There are no residues with violations.
+    np.testing.assert_equal(num_violations, np.zeros_like(num_violations))
+
+  def test_unresolved_violations(self):
+    amber_relax = relax.AmberRelaxation(**self.test_config)
+    with open(os.path.join(self.test_dir,
+                                 'with_violations_casp14.pdb')) as f:
+      test_prot = protein.from_pdb_string(f.read())
+    _, _, num_violations = amber_relax.process(prot=test_prot)
+    exp_num_violations = np.array(
+        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1,
+         1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0,
+         0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
+         0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 0,
+         0, 0, 0, 0])
+    # Check no violations were added. Can't check exactly due to stochasticity.
+    self.assertTrue(np.all(num_violations <= exp_num_violations))
+
+
+if __name__ == '__main__':
+  absltest.main()

alphafold/relax/testdata/model_output.pdb

+ATOM      1  C   MET A   1       1.921 -46.152   7.786  1.00  4.39           C  
+ATOM      2  CA  MET A   1       1.631 -46.829   9.131  1.00  4.39           C  
+ATOM      3  CB  MET A   1       2.759 -47.768   9.578  1.00  4.39           C  
+ATOM      4  CE  MET A   1       3.466 -49.770  13.198  1.00  4.39           C  
+ATOM      5  CG  MET A   1       2.581 -48.221  11.034  1.00  4.39           C  
+ATOM      6  H   MET A   1       0.234 -48.249   8.549  1.00  4.39           H  
+ATOM      7  H2  MET A   1      -0.424 -46.789   8.952  1.00  4.39           H  
+ATOM      8  H3  MET A   1       0.111 -47.796  10.118  1.00  4.39           H  
+ATOM      9  HA  MET A   1       1.628 -46.009   9.849  1.00  4.39           H  
+ATOM     10  HB2 MET A   1       3.701 -47.225   9.500  1.00  4.39           H  
+ATOM     11  HB3 MET A   1       2.807 -48.640   8.926  1.00  4.39           H  
+ATOM     12  HE1 MET A   1       2.747 -50.537  12.910  1.00  4.39           H  
+ATOM     13  HE2 MET A   1       4.296 -50.241  13.725  1.00  4.39           H  
+ATOM     14  HE3 MET A   1       2.988 -49.052  13.864  1.00  4.39           H  
+ATOM     15  HG2 MET A   1       1.791 -48.971  11.083  1.00  4.39           H  
+ATOM     16  HG3 MET A   1       2.295 -47.368  11.650  1.00  4.39           H  
+ATOM     17  N   MET A   1       0.291 -47.464   9.182  1.00  4.39           N  
+ATOM     18  O   MET A   1       2.091 -44.945   7.799  1.00  4.39           O  
+ATOM     19  SD  MET A   1       4.096 -48.921  11.725  1.00  4.39           S  
+ATOM     20  C   LYS A   2       1.366 -45.033   4.898  1.00  2.92           C  
+ATOM     21  CA  LYS A   2       2.235 -46.242   5.308  1.00  2.92           C  
+ATOM     22  CB  LYS A   2       2.206 -47.314   4.196  1.00  2.92           C  
+ATOM     23  CD  LYS A   2       3.331 -49.342   3.134  1.00  2.92           C  
+ATOM     24  CE  LYS A   2       4.434 -50.403   3.293  1.00  2.92           C  
+ATOM     25  CG  LYS A   2       3.294 -48.395   4.349  1.00  2.92           C  
+ATOM     26  H   LYS A   2       1.832 -47.853   6.656  1.00  2.92           H  
+ATOM     27  HA  LYS A   2       3.248 -45.841   5.355  1.00  2.92           H  
+ATOM     28  HB2 LYS A   2       1.223 -47.785   4.167  1.00  2.92           H  
+ATOM     29  HB3 LYS A   2       2.363 -46.812   3.241  1.00  2.92           H  
+ATOM     30  HD2 LYS A   2       3.524 -48.754   2.237  1.00  2.92           H  
+ATOM     31  HD3 LYS A   2       2.364 -49.833   3.031  1.00  2.92           H  
+ATOM     32  HE2 LYS A   2       5.383 -49.891   3.455  1.00  2.92           H  
+ATOM     33  HE3 LYS A   2       4.225 -51.000   4.180  1.00  2.92           H  
+ATOM     34  HG2 LYS A   2       3.102 -48.977   5.250  1.00  2.92           H  
+ATOM     35  HG3 LYS A   2       4.264 -47.909   4.446  1.00  2.92           H  
+ATOM     36  HZ1 LYS A   2       4.763 -50.747   1.274  1.00  2.92           H  
+ATOM     37  HZ2 LYS A   2       3.681 -51.785   1.931  1.00  2.92           H  
+ATOM     38  HZ3 LYS A   2       5.280 -51.965   2.224  1.00  2.92           H  
+ATOM     39  N   LYS A   2       1.907 -46.846   6.629  1.00  2.92           N  
+ATOM     40  NZ  LYS A   2       4.542 -51.286   2.100  1.00  2.92           N  
+ATOM     41  O   LYS A   2       1.882 -44.093   4.312  1.00  2.92           O  
+ATOM     42  C   PHE A   3      -0.511 -42.597   5.624  1.00  4.39           C  
+ATOM     43  CA  PHE A   3      -0.853 -43.933   4.929  1.00  4.39           C  
+ATOM     44  CB  PHE A   3      -2.271 -44.408   5.285  1.00  4.39           C  
+ATOM     45  CD1 PHE A   3      -3.760 -43.542   3.432  1.00  4.39           C  
+ATOM     46  CD2 PHE A   3      -4.050 -42.638   5.675  1.00  4.39           C  
+ATOM     47  CE1 PHE A   3      -4.797 -42.715   2.965  1.00  4.39           C  
+ATOM     48  CE2 PHE A   3      -5.091 -41.818   5.207  1.00  4.39           C  
+ATOM     49  CG  PHE A   3      -3.382 -43.505   4.788  1.00  4.39           C  
+ATOM     50  CZ  PHE A   3      -5.463 -41.853   3.853  1.00  4.39           C  
+ATOM     51  H   PHE A   3      -0.311 -45.868   5.655  1.00  4.39           H  
+ATOM     52  HA  PHE A   3      -0.817 -43.746   3.856  1.00  4.39           H  
+ATOM     53  HB2 PHE A   3      -2.353 -44.512   6.367  1.00  4.39           H  
+ATOM     54  HB3 PHE A   3      -2.432 -45.393   4.848  1.00  4.39           H  
+ATOM     55  HD1 PHE A   3      -3.255 -44.198   2.739  1.00  4.39           H  
+ATOM     56  HD2 PHE A   3      -3.768 -42.590   6.716  1.00  4.39           H  
+ATOM     57  HE1 PHE A   3      -5.083 -42.735   1.923  1.00  4.39           H  
+ATOM     58  HE2 PHE A   3      -5.604 -41.151   5.885  1.00  4.39           H  
+ATOM     59  HZ  PHE A   3      -6.257 -41.215   3.493  1.00  4.39           H  
+ATOM     60  N   PHE A   3       0.079 -45.027   5.253  1.00  4.39           N  
+ATOM     61  O   PHE A   3      -0.633 -41.541   5.014  1.00  4.39           O  
+ATOM     62  C   LEU A   4       1.598 -40.732   7.042  1.00  4.39           C  
+ATOM     63  CA  LEU A   4       0.367 -41.437   7.633  1.00  4.39           C  
+ATOM     64  CB  LEU A   4       0.628 -41.823   9.104  1.00  4.39           C  
+ATOM     65  CD1 LEU A   4      -0.319 -42.778  11.228  1.00  4.39           C  
+ATOM     66  CD2 LEU A   4      -1.300 -40.694  10.309  1.00  4.39           C  
+ATOM     67  CG  LEU A   4      -0.650 -42.027   9.937  1.00  4.39           C  
+ATOM     68  H   LEU A   4       0.163 -43.538   7.292  1.00  4.39           H  
+ATOM     69  HA  LEU A   4      -0.445 -40.712   7.588  1.00  4.39           H  
+ATOM     70  HB2 LEU A   4       1.213 -41.034   9.576  1.00  4.39           H  
+ATOM     71  HB3 LEU A   4       1.235 -42.728   9.127  1.00  4.39           H  
+ATOM     72 HD11 LEU A   4       0.380 -42.191  11.824  1.00  4.39           H  
+ATOM     73 HD12 LEU A   4       0.127 -43.747  11.002  1.00  4.39           H  
+ATOM     74 HD13 LEU A   4      -1.230 -42.927  11.808  1.00  4.39           H  
+ATOM     75 HD21 LEU A   4      -0.606 -40.080  10.883  1.00  4.39           H  
+ATOM     76 HD22 LEU A   4      -2.193 -40.869  10.909  1.00  4.39           H  
+ATOM     77 HD23 LEU A   4      -1.593 -40.147   9.413  1.00  4.39           H  
+ATOM     78  HG  LEU A   4      -1.359 -42.630   9.370  1.00  4.39           H  
+ATOM     79  N   LEU A   4      -0.012 -42.638   6.869  1.00  4.39           N  
+ATOM     80  O   LEU A   4       1.655 -39.508   7.028  1.00  4.39           O  
+ATOM     81  C   VAL A   5       3.372 -40.190   4.573  1.00  4.39           C  
+ATOM     82  CA  VAL A   5       3.752 -40.956   5.845  1.00  4.39           C  
+ATOM     83  CB  VAL A   5       4.757 -42.083   5.528  1.00  4.39           C  
+ATOM     84  CG1 VAL A   5       6.019 -41.568   4.827  1.00  4.39           C  
+ATOM     85  CG2 VAL A   5       5.199 -42.807   6.810  1.00  4.39           C  
+ATOM     86  H   VAL A   5       2.440 -42.503   6.548  1.00  4.39           H  
+ATOM     87  HA  VAL A   5       4.234 -40.242   6.512  1.00  4.39           H  
+ATOM     88  HB  VAL A   5       4.279 -42.813   4.875  1.00  4.39           H  
+ATOM     89 HG11 VAL A   5       6.494 -40.795   5.431  1.00  4.39           H  
+ATOM     90 HG12 VAL A   5       5.770 -41.145   3.853  1.00  4.39           H  
+ATOM     91 HG13 VAL A   5       6.725 -42.383   4.670  1.00  4.39           H  
+ATOM     92 HG21 VAL A   5       4.347 -43.283   7.297  1.00  4.39           H  
+ATOM     93 HG22 VAL A   5       5.933 -43.575   6.568  1.00  4.39           H  
+ATOM     94 HG23 VAL A   5       5.651 -42.093   7.498  1.00  4.39           H  
+ATOM     95  N   VAL A   5       2.554 -41.501   6.509  1.00  4.39           N  
+ATOM     96  O   VAL A   5       3.937 -39.138   4.297  1.00  4.39           O  
+TER      96      VAL A   5                                                      
+END

alphafold/relax/testdata/multiple_disulfides_target.pdb

+MODEL        0
+ATOM      1  N   MET A   1      19.164 -28.457  26.130  1.00  0.00          N   
+ATOM      2  CA  MET A   1      19.746 -27.299  25.456  1.00  0.00          C   
+ATOM      3  C   MET A   1      19.080 -26.008  25.921  1.00  0.00          C   
+ATOM      4  CB  MET A   1      19.615 -27.438  23.938  1.00  0.00          C   
+ATOM      5  O   MET A   1      17.853 -25.899  25.913  1.00  0.00          O   
+ATOM      6  CG  MET A   1      19.873 -28.846  23.427  1.00  0.00          C   
+ATOM      7  SD  MET A   1      21.636 -29.126  23.002  1.00  0.00          S   
+ATOM      8  CE  MET A   1      22.302 -27.462  23.284  1.00  0.00          C   
+ATOM      9  N   ALA A   2      19.679 -25.354  27.019  1.00  0.00          N   
+ATOM     10  CA  ALA A   2      19.241 -24.061  27.539  1.00  0.00          C   
+ATOM     11  C   ALA A   2      18.629 -23.204  26.434  1.00  0.00          C   
+ATOM     12  CB  ALA A   2      20.410 -23.326  28.192  1.00  0.00          C   
+ATOM     13  O   ALA A   2      19.158 -23.145  25.322  1.00  0.00          O   
+ATOM     14  N   HIS A   3      17.369 -23.382  26.161  1.00  0.00          N   
+ATOM     15  CA  HIS A   3      16.748 -22.427  25.250  1.00  0.00          C   
+ATOM     16  C   HIS A   3      17.419 -21.061  25.342  1.00  0.00          C   
+ATOM     17  CB  HIS A   3      15.252 -22.299  25.547  1.00  0.00          C   
+ATOM     18  O   HIS A   3      17.896 -20.669  26.409  1.00  0.00          O   
+ATOM     19  CG  HIS A   3      14.464 -23.520  25.196  1.00  0.00          C   
+ATOM     20  CD2 HIS A   3      13.848 -24.436  25.979  1.00  0.00          C   
+ATOM     21  ND1 HIS A   3      14.242 -23.914  23.894  1.00  0.00          N   
+ATOM     22  CE1 HIS A   3      13.520 -25.022  23.892  1.00  0.00          C   
+ATOM     23  NE2 HIS A   3      13.268 -25.360  25.145  1.00  0.00          N   
+ATOM     24  N   GLU A   4      18.306 -20.798  24.429  1.00  0.00          N   
+ATOM     25  CA  GLU A   4      18.907 -19.505  24.115  1.00  0.00          C   
+ATOM     26  C   GLU A   4      18.392 -18.415  25.050  1.00  0.00          C   
+ATOM     27  CB  GLU A   4      18.631 -19.123  22.659  1.00  0.00          C   
+ATOM     28  O   GLU A   4      17.240 -18.458  25.486  1.00  0.00          O   
+ATOM     29  CG  GLU A   4      19.253 -20.072  21.645  1.00  0.00          C   
+ATOM     30  CD  GLU A   4      20.767 -19.956  21.564  1.00  0.00          C   
+ATOM     31  OE1 GLU A   4      21.330 -18.981  22.111  1.00  0.00          O   
+ATOM     32  OE2 GLU A   4      21.394 -20.846  20.948  1.00  0.00          O   
+ATOM     33  N   GLU A   5      19.093 -18.090  26.026  1.00  0.00          N   
+ATOM     34  CA  GLU A   5      19.080 -16.885  26.849  1.00  0.00          C   
+ATOM     35  C   GLU A   5      17.938 -15.956  26.449  1.00  0.00          C   
+ATOM     36  CB  GLU A   5      20.418 -16.148  26.746  1.00  0.00          C   
+ATOM     37  O   GLU A   5      17.774 -15.636  25.269  1.00  0.00          O   
+ATOM     38  CG  GLU A   5      21.604 -16.952  27.257  1.00  0.00          C   
+ATOM     39  CD  GLU A   5      21.641 -17.070  28.772  1.00  0.00          C   
+ATOM     40  OE1 GLU A   5      20.899 -16.330  29.457  1.00  0.00          O   
+ATOM     41  OE2 GLU A   5      22.419 -17.909  29.279  1.00  0.00          O   
+ATOM     42  N   ASP A   6      16.721 -16.161  26.857  1.00  0.00          N   
+ATOM     43  CA  ASP A   6      15.629 -15.196  26.948  1.00  0.00          C   
+ATOM     44  C   ASP A   6      16.107 -13.791  26.591  1.00  0.00          C   
+ATOM     45  CB  ASP A   6      15.022 -15.204  28.353  1.00  0.00          C   
+ATOM     46  O   ASP A   6      17.144 -13.339  27.079  1.00  0.00          O   
+ATOM     47  CG  ASP A   6      14.317 -16.507  28.687  1.00  0.00          C   
+ATOM     48  OD1 ASP A   6      14.123 -16.805  29.885  1.00  0.00          O   
+ATOM     49  OD2 ASP A   6      13.956 -17.243  27.744  1.00  0.00          O   
+ATOM     50  N   GLY A   7      16.251 -13.433  25.339  1.00  0.00          N   
+ATOM     51  CA  GLY A   7      16.311 -11.996  25.123  1.00  0.00          C   
+ATOM     52  C   GLY A   7      15.833 -11.192  26.317  1.00  0.00          C   
+ATOM     53  O   GLY A   7      15.023 -11.674  27.112  1.00  0.00          O   
+ATOM     54  N   VAL A   8      16.762 -10.664  27.143  1.00  0.00          N   
+ATOM     55  CA  VAL A   8      16.521  -9.756  28.260  1.00  0.00          C   
+ATOM     56  C   VAL A   8      15.307  -8.880  27.960  1.00  0.00          C   
+ATOM     57  CB  VAL A   8      17.755  -8.875  28.552  1.00  0.00          C   
+ATOM     58  O   VAL A   8      15.173  -8.351  26.854  1.00  0.00          O   
+ATOM     59  CG1 VAL A   8      17.461  -7.891  29.683  1.00  0.00          C   
+ATOM     60  CG2 VAL A   8      18.962  -9.745  28.898  1.00  0.00          C   
+ATOM     61  N   CYS A   9      14.157  -9.255  28.398  1.00  0.00          N   
+ATOM     62  CA  CYS A   9      13.010  -8.353  28.403  1.00  0.00          C   
+ATOM     63  C   CYS A   9      13.310  -7.095  29.209  1.00  0.00          C   
+ATOM     64  CB  CYS A   9      11.779  -9.055  28.975  1.00  0.00          C   
+ATOM     65  O   CYS A   9      14.058  -7.142  30.187  1.00  0.00          O   
+ATOM     66  SG  CYS A   9      11.197 -10.439  27.970  1.00  0.00          S   
+ATOM     67  N   ASN A  10      13.304  -5.993  28.589  1.00  0.00          N   
+ATOM     68  CA  ASN A  10      13.371  -4.703  29.267  1.00  0.00          C   
+ATOM     69  C   ASN A  10      12.018  -3.997  29.264  1.00  0.00          C   
+ATOM     70  CB  ASN A  10      14.436  -3.812  28.624  1.00  0.00          C   
+ATOM     71  O   ASN A  10      11.047  -4.510  28.706  1.00  0.00          O   
+ATOM     72  CG  ASN A  10      14.149  -3.521  27.164  1.00  0.00          C   
+ATOM     73  ND2 ASN A  10      15.189  -3.547  26.338  1.00  0.00          N   
+ATOM     74  OD1 ASN A  10      13.003  -3.275  26.781  1.00  0.00          O   
+ATOM     75  N   SER A  11      11.830  -2.986  30.142  1.00  0.00          N   
+ATOM     76  CA  SER A  11      10.597  -2.233  30.343  1.00  0.00          C   
+ATOM     77  C   SER A  11      10.027  -1.741  29.017  1.00  0.00          C   
+ATOM     78  CB  SER A  11      10.840  -1.044  31.274  1.00  0.00          C   
+ATOM     79  O   SER A  11       8.847  -1.392  28.933  1.00  0.00          O   
+ATOM     80  OG  SER A  11      11.841  -0.190  30.748  1.00  0.00          O   
+ATOM     81  N   ASN A  12      10.789  -1.874  27.933  1.00  0.00          N   
+ATOM     82  CA  ASN A  12      10.334  -1.422  26.622  1.00  0.00          C   
+ATOM     83  C   ASN A  12       9.775  -2.576  25.795  1.00  0.00          C   
+ATOM     84  CB  ASN A  12      11.472  -0.730  25.868  1.00  0.00          C   
+ATOM     85  O   ASN A  12       9.262  -2.365  24.694  1.00  0.00          O   
+ATOM     86  CG  ASN A  12      11.875   0.587  26.501  1.00  0.00          C   
+ATOM     87  ND2 ASN A  12      13.170   0.882  26.482  1.00  0.00          N   
+ATOM     88  OD1 ASN A  12      11.031   1.333  27.004  1.00  0.00          O   
+ATOM     89  N   ALA A  13      10.045  -3.775  26.303  1.00  0.00          N   
+ATOM     90  CA  ALA A  13       9.523  -4.930  25.578  1.00  0.00          C   
+ATOM     91  C   ALA A  13       8.001  -4.994  25.671  1.00  0.00          C   
+ATOM     92  CB  ALA A  13      10.140  -6.219  26.115  1.00  0.00          C   
+ATOM     93  O   ALA A  13       7.423  -4.684  26.715  1.00  0.00          O   
+ATOM     94  N   PRO A  14       7.310  -5.193  24.591  1.00  0.00          N   
+ATOM     95  CA  PRO A  14       5.846  -5.238  24.577  1.00  0.00          C   
+ATOM     96  C   PRO A  14       5.280  -6.316  25.499  1.00  0.00          C   
+ATOM     97  CB  PRO A  14       5.517  -5.544  23.113  1.00  0.00          C   
+ATOM     98  O   PRO A  14       4.127  -6.222  25.929  1.00  0.00          O   
+ATOM     99  CG  PRO A  14       6.757  -6.177  22.568  1.00  0.00          C   
+ATOM    100  CD  PRO A  14       7.941  -5.617  23.303  1.00  0.00          C   
+ATOM    101  N   CYS A  15       6.076  -7.229  25.793  1.00  0.00          N   
+ATOM    102  CA  CYS A  15       5.597  -8.339  26.610  1.00  0.00          C   
+ATOM    103  C   CYS A  15       6.142  -8.245  28.030  1.00  0.00          C   
+ATOM    104  CB  CYS A  15       5.999  -9.676  25.987  1.00  0.00          C   
+ATOM    105  O   CYS A  15       6.205  -9.249  28.743  1.00  0.00          O   
+ATOM    106  SG  CYS A  15       7.766  -9.813  25.636  1.00  0.00          S   
+ATOM    107  N   TYR A  16       6.510  -6.994  28.366  1.00  0.00          N   
+ATOM    108  CA  TYR A  16       7.076  -6.735  29.685  1.00  0.00          C   
+ATOM    109  C   TYR A  16       5.978  -6.589  30.731  1.00  0.00          C   
+ATOM    110  CB  TYR A  16       7.944  -5.473  29.659  1.00  0.00          C   
+ATOM    111  O   TYR A  16       5.053  -5.791  30.563  1.00  0.00          O   
+ATOM    112  CG  TYR A  16       8.545  -5.122  30.998  1.00  0.00          C   
+ATOM    113  CD1 TYR A  16       8.126  -3.993  31.698  1.00  0.00          C   
+ATOM    114  CD2 TYR A  16       9.534  -5.918  31.566  1.00  0.00          C   
+ATOM    115  CE1 TYR A  16       8.678  -3.665  32.932  1.00  0.00          C   
+ATOM    116  CE2 TYR A  16      10.093  -5.600  32.799  1.00  0.00          C   
+ATOM    117  OH  TYR A  16      10.210  -4.153  34.695  1.00  0.00          O   
+ATOM    118  CZ  TYR A  16       9.660  -4.473  33.474  1.00  0.00          C   
+ATOM    119  N   HIS A  17       5.834  -7.548  31.703  1.00  0.00          N   
+ATOM    120  CA  HIS A  17       4.846  -7.504  32.775  1.00  0.00          C   
+ATOM    121  C   HIS A  17       5.518  -7.493  34.143  1.00  0.00          C   
+ATOM    122  CB  HIS A  17       3.888  -8.692  32.669  1.00  0.00          C   
+ATOM    123  O   HIS A  17       6.482  -8.228  34.372  1.00  0.00          O   
+ATOM    124  CG  HIS A  17       2.782  -8.661  33.675  1.00  0.00          C   
+ATOM    125  CD2 HIS A  17       2.548  -9.432  34.764  1.00  0.00          C   
+ATOM    126  ND1 HIS A  17       1.748  -7.752  33.617  1.00  0.00          N   
+ATOM    127  CE1 HIS A  17       0.924  -7.965  34.630  1.00  0.00          C   
+ATOM    128  NE2 HIS A  17       1.387  -8.979  35.341  1.00  0.00          N   
+ATOM    129  N   CYS A  18       5.067  -6.579  34.995  1.00  0.00          N   
+ATOM    130  CA  CYS A  18       5.599  -6.487  36.350  1.00  0.00          C   
+ATOM    131  C   CYS A  18       4.501  -6.711  37.383  1.00  0.00          C   
+ATOM    132  CB  CYS A  18       6.255  -5.126  36.577  1.00  0.00          C   
+ATOM    133  O   CYS A  18       3.325  -6.465  37.109  1.00  0.00          O   
+ATOM    134  SG  CYS A  18       7.757  -4.870  35.607  1.00  0.00          S   
+ATOM    135  N   ASP A  19       4.791  -7.344  38.476  1.00  0.00          N   
+ATOM    136  CA  ASP A  19       3.829  -7.460  39.568  1.00  0.00          C   
+ATOM    137  C   ASP A  19       3.430  -6.084  40.096  1.00  0.00          C   
+ATOM    138  CB  ASP A  19       4.403  -8.313  40.701  1.00  0.00          C   
+ATOM    139  O   ASP A  19       3.960  -5.064  39.651  1.00  0.00          O   
+ATOM    140  CG  ASP A  19       5.572  -7.650  41.408  1.00  0.00          C   
+ATOM    141  OD1 ASP A  19       6.325  -8.345  42.124  1.00  0.00          O   
+ATOM    142  OD2 ASP A  19       5.741  -6.422  41.250  1.00  0.00          O   
+ATOM    143  N   ALA A  20       2.383  -5.908  40.933  1.00  0.00          N   
+ATOM    144  CA  ALA A  20       1.776  -4.676  41.429  1.00  0.00          C   
+ATOM    145  C   ALA A  20       2.806  -3.807  42.144  1.00  0.00          C   
+ATOM    146  CB  ALA A  20       0.612  -4.995  42.363  1.00  0.00          C   
+ATOM    147  O   ALA A  20       2.714  -2.577  42.119  1.00  0.00          O   
+ATOM    148  N   ASN A  21       3.841  -4.457  42.638  1.00  0.00          N   
+ATOM    149  CA  ASN A  21       4.863  -3.719  43.373  1.00  0.00          C   
+ATOM    150  C   ASN A  21       6.048  -3.362  42.480  1.00  0.00          C   
+ATOM    151  CB  ASN A  21       5.335  -4.521  44.588  1.00  0.00          C   
+ATOM    152  O   ASN A  21       6.980  -2.686  42.919  1.00  0.00          O   
+ATOM    153  CG  ASN A  21       4.246  -4.704  45.626  1.00  0.00          C   
+ATOM    154  ND2 ASN A  21       4.183  -5.892  46.216  1.00  0.00          N   
+ATOM    155  OD1 ASN A  21       3.467  -3.786  45.895  1.00  0.00          O   
+ATOM    156  N   GLY A  22       5.989  -3.893  41.230  1.00  0.00          N   
+ATOM    157  CA  GLY A  22       7.093  -3.614  40.325  1.00  0.00          C   
+ATOM    158  C   GLY A  22       8.376  -4.324  40.712  1.00  0.00          C   
+ATOM    159  O   GLY A  22       9.456  -3.972  40.234  1.00  0.00          O   
+ATOM    160  N   GLU A  23       8.305  -5.221  41.664  1.00  0.00          N   
+ATOM    161  CA  GLU A  23       9.501  -5.877  42.183  1.00  0.00          C   
+ATOM    162  C   GLU A  23       9.861  -7.105  41.352  1.00  0.00          C   
+ATOM    163  CB  GLU A  23       9.306  -6.272  43.649  1.00  0.00          C   
+ATOM    164  O   GLU A  23      11.038  -7.361  41.089  1.00  0.00          O   
+ATOM    165  CG  GLU A  23       9.200  -5.085  44.596  1.00  0.00          C   
+ATOM    166  CD  GLU A  23       9.074  -5.493  46.055  1.00  0.00          C   
+ATOM    167  OE1 GLU A  23       9.075  -6.710  46.348  1.00  0.00          O   
+ATOM    168  OE2 GLU A  23       8.972  -4.587  46.913  1.00  0.00          O   
+ATOM    169  N   ASN A  24       8.853  -7.853  40.844  1.00  0.00          N   
+ATOM    170  CA  ASN A  24       9.050  -9.077  40.075  1.00  0.00          C   
+ATOM    171  C   ASN A  24       8.522  -8.936  38.651  1.00  0.00          C   
+ATOM    172  CB  ASN A  24       8.381 -10.263  40.774  1.00  0.00          C   
+ATOM    173  O   ASN A  24       7.317  -9.045  38.417  1.00  0.00          O   
+ATOM    174  CG  ASN A  24       8.973 -10.546  42.140  1.00  0.00          C   
+ATOM    175  ND2 ASN A  24       8.125 -10.569  43.162  1.00  0.00          N   
+ATOM    176  OD1 ASN A  24      10.184 -10.741  42.277  1.00  0.00          O   
+ATOM    177  N   CYS A  25       9.371  -8.554  37.764  1.00  0.00          N   
+ATOM    178  CA  CYS A  25       8.978  -8.390  36.369  1.00  0.00          C   
+ATOM    179  C   CYS A  25       9.448  -9.572  35.529  1.00  0.00          C   
+ATOM    180  CB  CYS A  25       9.548  -7.091  35.800  1.00  0.00          C   
+ATOM    181  O   CYS A  25      10.486 -10.171  35.816  1.00  0.00          O   
+ATOM    182  SG  CYS A  25       8.933  -5.605  36.623  1.00  0.00          S   
+ATOM    183  N   SER A  26       8.561 -10.102  34.701  1.00  0.00          N   
+ATOM    184  CA  SER A  26       8.921 -11.145  33.746  1.00  0.00          C   
+ATOM    185  C   SER A  26       8.422 -10.808  32.345  1.00  0.00          C   
+ATOM    186  CB  SER A  26       8.353 -12.495  34.187  1.00  0.00          C   
+ATOM    187  O   SER A  26       7.563  -9.940  32.178  1.00  0.00          O   
+ATOM    188  OG  SER A  26       6.936 -12.470  34.186  1.00  0.00          O   
+ATOM    189  N   CYS A  27       9.208 -11.265  31.277  1.00  0.00          N   
+ATOM    190  CA  CYS A  27       8.779 -11.211  29.884  1.00  0.00          C   
+ATOM    191  C   CYS A  27       7.948 -12.436  29.521  1.00  0.00          C   
+ATOM    192  CB  CYS A  27       9.988 -11.110  28.954  1.00  0.00          C   
+ATOM    193  O   CYS A  27       8.470 -13.551  29.464  1.00  0.00          O   
+ATOM    194  SG  CYS A  27      10.970  -9.614  29.197  1.00  0.00          S   
+ATOM    195  N   ASN A  28       6.768 -12.360  29.728  1.00  0.00          N   
+ATOM    196  CA  ASN A  28       5.905 -13.476  29.355  1.00  0.00          C   
+ATOM    197  C   ASN A  28       5.123 -13.178  28.079  1.00  0.00          C   
+ATOM    198  CB  ASN A  28       4.946 -13.817  30.498  1.00  0.00          C   
+ATOM    199  O   ASN A  28       4.074 -12.532  28.125  1.00  0.00          O   
+ATOM    200  CG  ASN A  28       4.239 -15.142  30.291  1.00  0.00          C   
+ATOM    201  ND2 ASN A  28       3.472 -15.568  31.288  1.00  0.00          N   
+ATOM    202  OD1 ASN A  28       4.381 -15.779  29.243  1.00  0.00          O   
+ATOM    203  N   CYS A  29       5.741 -13.488  26.787  1.00  0.00          N   
+ATOM    204  CA  CYS A  29       5.086 -13.282  25.500  1.00  0.00          C   
+ATOM    205  C   CYS A  29       3.880 -14.201  25.348  1.00  0.00          C   
+ATOM    206  CB  CYS A  29       6.070 -13.522  24.355  1.00  0.00          C   
+ATOM    207  O   CYS A  29       3.011 -13.958  24.510  1.00  0.00          O   
+ATOM    208  SG  CYS A  29       7.446 -12.353  24.319  1.00  0.00          S   
+ATOM    209  N   GLU A  30       3.849 -15.077  26.140  1.00  0.00          N   
+ATOM    210  CA  GLU A  30       2.725 -16.005  26.063  1.00  0.00          C   
+ATOM    211  C   GLU A  30       1.452 -15.379  26.627  1.00  0.00          C   
+ATOM    212  CB  GLU A  30       3.047 -17.303  26.808  1.00  0.00          C   
+ATOM    213  O   GLU A  30       0.344 -15.770  26.255  1.00  0.00          O   
+ATOM    214  CG  GLU A  30       4.161 -18.119  26.169  1.00  0.00          C   
+ATOM    215  CD  GLU A  30       4.469 -19.405  26.919  1.00  0.00          C   
+ATOM    216  OE1 GLU A  30       3.822 -19.672  27.957  1.00  0.00          O   
+ATOM    217  OE2 GLU A  30       5.366 -20.150  26.466  1.00  0.00          O   
+ATOM    218  N   LEU A  31       1.743 -14.305  27.387  1.00  0.00          N   
+ATOM    219  CA  LEU A  31       0.622 -13.672  28.074  1.00  0.00          C   
+ATOM    220  C   LEU A  31       0.044 -12.536  27.237  1.00  0.00          C   
+ATOM    221  CB  LEU A  31       1.061 -13.142  29.441  1.00  0.00          C   
+ATOM    222  O   LEU A  31      -0.996 -11.971  27.584  1.00  0.00          O   
+ATOM    223  CG  LEU A  31       1.437 -14.194  30.487  1.00  0.00          C   
+ATOM    224  CD1 LEU A  31       1.920 -13.520  31.766  1.00  0.00          C   
+ATOM    225  CD2 LEU A  31       0.252 -15.110  30.774  1.00  0.00          C   
+ATOM    226  N   PHE A  32       0.769 -12.166  26.008  1.00  0.00          N   
+ATOM    227  CA  PHE A  32       0.157 -11.063  25.278  1.00  0.00          C   
+ATOM    228  C   PHE A  32      -1.020 -11.553  24.443  1.00  0.00          C   
+ATOM    229  CB  PHE A  32       1.188 -10.374  24.378  1.00  0.00          C   
+ATOM    230  O   PHE A  32      -0.898 -12.531  23.702  1.00  0.00          O   
+ATOM    231  CG  PHE A  32       2.115  -9.447  25.117  1.00  0.00          C   
+ATOM    232  CD1 PHE A  32       3.383  -9.869  25.499  1.00  0.00          C   
+ATOM    233  CD2 PHE A  32       1.719  -8.153  25.429  1.00  0.00          C   
+ATOM    234  CE1 PHE A  32       4.243  -9.014  26.183  1.00  0.00          C   
+ATOM    235  CE2 PHE A  32       2.574  -7.293  26.112  1.00  0.00          C   
+ATOM    236  CZ  PHE A  32       3.835  -7.725  26.489  1.00  0.00          C   
+ATOM    237  N   ASP A  33      -2.070 -11.361  25.097  1.00  0.00          N   
+ATOM    238  CA  ASP A  33      -3.364 -11.602  24.466  1.00  0.00          C   
+ATOM    239  C   ASP A  33      -3.423 -10.975  23.075  1.00  0.00          C   
+ATOM    240  CB  ASP A  33      -4.496 -11.055  25.339  1.00  0.00          C   
+ATOM    241  O   ASP A  33      -3.225  -9.767  22.924  1.00  0.00          O   
+ATOM    242  CG  ASP A  33      -5.861 -11.590  24.943  1.00  0.00          C   
+ATOM    243  OD1 ASP A  33      -6.769 -11.638  25.800  1.00  0.00          O   
+ATOM    244  OD2 ASP A  33      -6.029 -11.969  23.764  1.00  0.00          O   
+ATOM    245  N   CYS A  34      -3.021 -11.756  22.063  1.00  0.00          N   
+ATOM    246  CA  CYS A  34      -3.371 -11.337  20.711  1.00  0.00          C   
+ATOM    247  C   CYS A  34      -4.691 -10.576  20.700  1.00  0.00          C   
+ATOM    248  CB  CYS A  34      -3.461 -12.547  19.781  1.00  0.00          C   
+ATOM    249  O   CYS A  34      -4.986  -9.851  19.748  1.00  0.00          O   
+ATOM    250  SG  CYS A  34      -1.909 -13.455  19.615  1.00  0.00          S   
+ATOM    251  N   GLU A  35      -5.284 -10.672  21.987  1.00  0.00          N   
+ATOM    252  CA  GLU A  35      -6.617 -10.086  22.085  1.00  0.00          C   
+ATOM    253  C   GLU A  35      -6.556  -8.667  22.644  1.00  0.00          C   
+ATOM    254  CB  GLU A  35      -7.525 -10.956  22.958  1.00  0.00          C   
+ATOM    255  O   GLU A  35      -7.592  -8.032  22.853  1.00  0.00          O   
+ATOM    256  CG  GLU A  35      -7.790 -12.339  22.381  1.00  0.00          C   
+ATOM    257  CD  GLU A  35      -8.779 -13.152  23.202  1.00  0.00          C   
+ATOM    258  OE1 GLU A  35      -9.290 -12.636  24.222  1.00  0.00          O   
+ATOM    259  OE2 GLU A  35      -9.046 -14.314  22.821  1.00  0.00          O   
+ATOM    260  N   ALA A  36      -5.315  -8.202  22.860  1.00  0.00          N   
+ATOM    261  CA  ALA A  36      -5.282  -6.884  23.489  1.00  0.00          C   
+ATOM    262  C   ALA A  36      -5.714  -5.797  22.509  1.00  0.00          C   
+ATOM    263  CB  ALA A  36      -3.884  -6.586  24.027  1.00  0.00          C   
+ATOM    264  O   ALA A  36      -5.299  -5.799  21.348  1.00  0.00          O   
+ATOM    265  N   LYS A  37      -6.942  -5.271  22.819  1.00  0.00          N   
+ATOM    266  CA  LYS A  37      -7.519  -4.143  22.094  1.00  0.00          C   
+ATOM    267  C   LYS A  37      -6.974  -2.817  22.617  1.00  0.00          C   
+ATOM    268  CB  LYS A  37      -9.045  -4.160  22.200  1.00  0.00          C   
+ATOM    269  O   LYS A  37      -6.897  -2.606  23.829  1.00  0.00          O   
+ATOM    270  CG  LYS A  37      -9.701  -5.341  21.499  1.00  0.00          C   
+ATOM    271  CD  LYS A  37     -11.220  -5.239  21.536  1.00  0.00          C   
+ATOM    272  CE  LYS A  37     -11.877  -6.385  20.778  1.00  0.00          C   
+ATOM    273  NZ  LYS A  37     -13.353  -6.194  20.656  1.00  0.00          N   
+ATOM    274  N   LYS A  38      -6.207  -2.111  21.604  1.00  0.00          N   
+ATOM    275  CA  LYS A  38      -5.876  -0.745  21.998  1.00  0.00          C   
+ATOM    276  C   LYS A  38      -7.131   0.118  22.100  1.00  0.00          C   
+ATOM    277  CB  LYS A  38      -4.892  -0.123  21.007  1.00  0.00          C   
+ATOM    278  O   LYS A  38      -8.188  -0.253  21.585  1.00  0.00          O   
+ATOM    279  CG  LYS A  38      -3.518  -0.776  21.006  1.00  0.00          C   
+ATOM    280  CD  LYS A  38      -2.564  -0.072  20.049  1.00  0.00          C   
+ATOM    281  CE  LYS A  38      -1.196  -0.740  20.029  1.00  0.00          C   
+ATOM    282  NZ  LYS A  38      -0.234  -0.007  19.153  1.00  0.00          N   
+ATOM    283  N   PRO A  39      -7.175   1.097  22.994  1.00  0.00          N   
+ATOM    284  CA  PRO A  39      -8.319   2.000  23.133  1.00  0.00          C   
+ATOM    285  C   PRO A  39      -8.863   2.474  21.787  1.00  0.00          C   
+ATOM    286  CB  PRO A  39      -7.748   3.173  23.934  1.00  0.00          C   
+ATOM    287  O   PRO A  39     -10.057   2.762  21.666  1.00  0.00          O   
+ATOM    288  CG  PRO A  39      -6.594   2.594  24.688  1.00  0.00          C   
+ATOM    289  CD  PRO A  39      -6.004   1.478  23.874  1.00  0.00          C   
+ATOM    290  N   ASP A  40      -8.068   2.468  20.731  1.00  0.00          N   
+ATOM    291  CA  ASP A  40      -8.452   2.969  19.415  1.00  0.00          C   
+ATOM    292  C   ASP A  40      -9.034   1.852  18.551  1.00  0.00          C   
+ATOM    293  CB  ASP A  40      -7.252   3.607  18.712  1.00  0.00          C   
+ATOM    294  O   ASP A  40      -9.337   2.064  17.375  1.00  0.00          O   
+ATOM    295  CG  ASP A  40      -6.113   2.630  18.480  1.00  0.00          C   
+ATOM    296  OD1 ASP A  40      -5.040   3.049  17.994  1.00  0.00          O   
+ATOM    297  OD2 ASP A  40      -6.290   1.431  18.784  1.00  0.00          O   
+ATOM    298  N   GLY A  41      -9.199   0.638  19.013  1.00  0.00          N   
+ATOM    299  CA  GLY A  41      -9.761  -0.484  18.279  1.00  0.00          C   
+ATOM    300  C   GLY A  41      -8.723  -1.268  17.500  1.00  0.00          C   
+ATOM    301  O   GLY A  41      -9.019  -2.338  16.963  1.00  0.00          O   
+ATOM    302  N   SER A  42      -7.510  -0.651  17.403  1.00  0.00          N   
+ATOM    303  CA  SER A  42      -6.433  -1.355  16.714  1.00  0.00          C   
+ATOM    304  C   SER A  42      -5.824  -2.436  17.601  1.00  0.00          C   
+ATOM    305  CB  SER A  42      -5.346  -0.373  16.274  1.00  0.00          C   
+ATOM    306  O   SER A  42      -6.031  -2.440  18.816  1.00  0.00          O   
+ATOM    307  OG  SER A  42      -4.758   0.262  17.396  1.00  0.00          O   
+ATOM    308  N   TYR A  43      -5.412  -3.575  16.938  1.00  0.00          N   
+ATOM    309  CA  TYR A  43      -4.705  -4.628  17.660  1.00  0.00          C   
+ATOM    310  C   TYR A  43      -3.244  -4.254  17.877  1.00  0.00          C   
+ATOM    311  CB  TYR A  43      -4.798  -5.955  16.901  1.00  0.00          C   
+ATOM    312  O   TYR A  43      -2.651  -3.542  17.063  1.00  0.00          O   
+ATOM    313  CG  TYR A  43      -6.184  -6.551  16.887  1.00  0.00          C   
+ATOM    314  CD1 TYR A  43      -7.022  -6.388  15.786  1.00  0.00          C   
+ATOM    315  CD2 TYR A  43      -6.659  -7.277  17.974  1.00  0.00          C   
+ATOM    316  CE1 TYR A  43      -8.302  -6.934  15.769  1.00  0.00          C   
+ATOM    317  CE2 TYR A  43      -7.937  -7.827  17.968  1.00  0.00          C   
+ATOM    318  OH  TYR A  43     -10.015  -8.194  16.852  1.00  0.00          O   
+ATOM    319  CZ  TYR A  43      -8.749  -7.651  16.863  1.00  0.00          C   
+ATOM    320  N   ALA A  44      -3.024  -4.415  19.155  1.00  0.00          N   
+ATOM    321  CA  ALA A  44      -1.659  -4.137  19.595  1.00  0.00          C   
+ATOM    322  C   ALA A  44      -0.642  -4.865  18.721  1.00  0.00          C   
+ATOM    323  CB  ALA A  44      -1.480  -4.536  21.058  1.00  0.00          C   
+ATOM    324  O   ALA A  44       0.477  -4.383  18.527  1.00  0.00          O   
+ATOM    325  N   HIS A  45      -1.081  -5.938  17.989  1.00  0.00          N   
+ATOM    326  CA  HIS A  45      -0.065  -6.665  17.236  1.00  0.00          C   
+ATOM    327  C   HIS A  45      -0.455  -6.795  15.768  1.00  0.00          C   
+ATOM    328  CB  HIS A  45       0.163  -8.051  17.843  1.00  0.00          C   
+ATOM    329  O   HIS A  45      -1.558  -7.246  15.452  1.00  0.00          O   
+ATOM    330  CG  HIS A  45       1.501  -8.634  17.520  1.00  0.00          C   
+ATOM    331  CD2 HIS A  45       2.577  -8.880  18.304  1.00  0.00          C   
+ATOM    332  ND1 HIS A  45       1.850  -9.037  16.249  1.00  0.00          N   
+ATOM    333  CE1 HIS A  45       3.086  -9.508  16.266  1.00  0.00          C   
+ATOM    334  NE2 HIS A  45       3.550  -9.423  17.502  1.00  0.00          N   
+ATOM    335  N   PRO A  46       0.267  -6.191  14.776  1.00  0.00          N   
+ATOM    336  CA  PRO A  46       0.007  -6.193  13.334  1.00  0.00          C   
+ATOM    337  C   PRO A  46      -0.224  -7.596  12.778  1.00  0.00          C   
+ATOM    338  CB  PRO A  46       1.278  -5.574  12.747  1.00  0.00          C   
+ATOM    339  O   PRO A  46      -0.835  -7.750  11.717  1.00  0.00          O   
+ATOM    340  CG  PRO A  46       2.320  -5.770  13.800  1.00  0.00          C   
+ATOM    341  CD  PRO A  46       1.648  -5.768  15.143  1.00  0.00          C   
+ATOM    342  N   CYS A  47       0.238  -8.592  13.354  1.00  0.00          N   
+ATOM    343  CA  CYS A  47       0.115  -9.950  12.835  1.00  0.00          C   
+ATOM    344  C   CYS A  47      -1.253 -10.537  13.163  1.00  0.00          C   
+ATOM    345  CB  CYS A  47       1.214 -10.844  13.408  1.00  0.00          C   
+ATOM    346  O   CYS A  47      -1.515 -11.707  12.880  1.00  0.00          O   
+ATOM    347  SG  CYS A  47       1.222 -10.923  15.212  1.00  0.00          S   
+ATOM    348  N   ARG A  48      -2.155  -9.724  13.452  1.00  0.00          N   
+ATOM    349  CA  ARG A  48      -3.422 -10.192  14.005  1.00  0.00          C   
+ATOM    350  C   ARG A  48      -4.542 -10.086  12.974  1.00  0.00          C   
+ATOM    351  CB  ARG A  48      -3.788  -9.396  15.260  1.00  0.00          C   
+ATOM    352  O   ARG A  48      -4.649  -9.082  12.268  1.00  0.00          O   
+ATOM    353  CG  ARG A  48      -5.032  -9.905  15.970  1.00  0.00          C   
+ATOM    354  CD  ARG A  48      -5.909  -8.761  16.460  1.00  0.00          C   
+ATOM    355  NE  ARG A  48      -6.344  -7.906  15.359  1.00  0.00          N   
+ATOM    356  NH1 ARG A  48      -6.885  -6.103  16.700  1.00  0.00          N   
+ATOM    357  NH2 ARG A  48      -7.167  -5.974  14.429  1.00  0.00          N   
+ATOM    358  CZ  ARG A  48      -6.798  -6.663  15.499  1.00  0.00          C   
+ATOM    359  N   ARG A  49      -5.146 -11.174  12.527  1.00  0.00          N   
+ATOM    360  CA  ARG A  49      -6.391 -11.158  11.765  1.00  0.00          C   
+ATOM    361  C   ARG A  49      -7.546 -11.713  12.593  1.00  0.00          C   
+ATOM    362  CB  ARG A  49      -6.241 -11.962  10.472  1.00  0.00          C   
+ATOM    363  O   ARG A  49      -7.402 -12.739  13.261  1.00  0.00          O   
+ATOM    364  CG  ARG A  49      -5.303 -11.327   9.458  1.00  0.00          C   
+ATOM    365  CD  ARG A  49      -5.887 -10.048   8.873  1.00  0.00          C   
+ATOM    366  NE  ARG A  49      -5.349  -9.769   7.544  1.00  0.00          N   
+ATOM    367  NH1 ARG A  49      -6.902  -8.137   7.033  1.00  0.00          N   
+ATOM    368  NH2 ARG A  49      -5.276  -8.694   5.516  1.00  0.00          N   
+ATOM    369  CZ  ARG A  49      -5.843  -8.867   6.701  1.00  0.00          C   
+ATOM    370  N   CYS A  50      -8.427 -10.800  12.832  1.00  0.00          N   
+ATOM    371  CA  CYS A  50      -9.591 -11.226  13.601  1.00  0.00          C   
+ATOM    372  C   CYS A  50     -10.795 -11.442  12.692  1.00  0.00          C   
+ATOM    373  CB  CYS A  50      -9.931 -10.193  14.675  1.00  0.00          C   
+ATOM    374  O   CYS A  50     -11.034 -10.657  11.773  1.00  0.00          O   
+ATOM    375  SG  CYS A  50      -8.684 -10.057  15.975  1.00  0.00          S   
+ATOM    376  N   ASP A  51     -11.409 -12.618  12.691  1.00  0.00          N   
+ATOM    377  CA  ASP A  51     -12.641 -12.851  11.943  1.00  0.00          C   
+ATOM    378  C   ASP A  51     -13.818 -12.115  12.580  1.00  0.00          C   
+ATOM    379  CB  ASP A  51     -12.942 -14.349  11.858  1.00  0.00          C   
+ATOM    380  O   ASP A  51     -13.640 -11.361  13.539  1.00  0.00          O   
+ATOM    381  CG  ASP A  51     -13.232 -14.974  13.211  1.00  0.00          C   
+ATOM    382  OD1 ASP A  51     -13.125 -16.212  13.347  1.00  0.00          O   
+ATOM    383  OD2 ASP A  51     -13.573 -14.221  14.150  1.00  0.00          O   
+ATOM    384  N   ALA A  52     -15.076 -12.051  11.991  1.00  0.00          N   
+ATOM    385  CA  ALA A  52     -16.275 -11.314  12.381  1.00  0.00          C   
+ATOM    386  C   ALA A  52     -16.730 -11.710  13.783  1.00  0.00          C   
+ATOM    387  CB  ALA A  52     -17.397 -11.550  11.374  1.00  0.00          C   
+ATOM    388  O   ALA A  52     -17.439 -10.952  14.450  1.00  0.00          O   
+ATOM    389  N   ASN A  53     -16.263 -12.790  14.290  1.00  0.00          N   
+ATOM    390  CA  ASN A  53     -16.638 -13.257  15.620  1.00  0.00          C   
+ATOM    391  C   ASN A  53     -15.557 -12.943  16.650  1.00  0.00          C   
+ATOM    392  CB  ASN A  53     -16.930 -14.759  15.599  1.00  0.00          C   
+ATOM    393  O   ASN A  53     -15.602 -13.442  17.776  1.00  0.00          O   
+ATOM    394  CG  ASN A  53     -18.169 -15.101  14.795  1.00  0.00          C   
+ATOM    395  ND2 ASN A  53     -18.098 -16.183  14.029  1.00  0.00          N   
+ATOM    396  OD1 ASN A  53     -19.181 -14.399  14.862  1.00  0.00          O   
+ATOM    397  N   ASN A  54     -14.551 -12.153  16.191  1.00  0.00          N   
+ATOM    398  CA  ASN A  54     -13.470 -11.666  17.041  1.00  0.00          C   
+ATOM    399  C   ASN A  54     -12.543 -12.798  17.474  1.00  0.00          C   
+ATOM    400  CB  ASN A  54     -14.034 -10.943  18.266  1.00  0.00          C   
+ATOM    401  O   ASN A  54     -11.968 -12.753  18.563  1.00  0.00          O   
+ATOM    402  CG  ASN A  54     -14.752  -9.657  17.906  1.00  0.00          C   
+ATOM    403  ND2 ASN A  54     -15.894  -9.418  18.540  1.00  0.00          N   
+ATOM    404  OD1 ASN A  54     -14.285  -8.885  17.065  1.00  0.00          O   
+ATOM    405  N   ILE A  55     -12.428 -13.839  16.751  1.00  0.00          N   
+ATOM    406  CA  ILE A  55     -11.423 -14.875  16.963  1.00  0.00          C   
+ATOM    407  C   ILE A  55     -10.158 -14.536  16.179  1.00  0.00          C   
+ATOM    408  CB  ILE A  55     -11.952 -16.268  16.552  1.00  0.00          C   
+ATOM    409  O   ILE A  55     -10.162 -14.552  14.946  1.00  0.00          O   
+ATOM    410  CG1 ILE A  55     -13.233 -16.602  17.325  1.00  0.00          C   
+ATOM    411  CG2 ILE A  55     -10.881 -17.340  16.777  1.00  0.00          C   
+ATOM    412  CD1 ILE A  55     -13.942 -17.857  16.834  1.00  0.00          C   
+ATOM    413  N   CYS A  56      -9.197 -14.050  16.887  1.00  0.00          N   
+ATOM    414  CA  CYS A  56      -7.960 -13.587  16.266  1.00  0.00          C   
+ATOM    415  C   CYS A  56      -6.914 -14.694  16.244  1.00  0.00          C   
+ATOM    416  CB  CYS A  56      -7.411 -12.369  17.009  1.00  0.00          C   
+ATOM    417  O   CYS A  56      -6.807 -15.473  17.192  1.00  0.00          O   
+ATOM    418  SG  CYS A  56      -8.495 -10.925  16.941  1.00  0.00          S   
+ATOM    419  N   LYS A  57      -6.417 -14.976  15.112  1.00  0.00          N   
+ATOM    420  CA  LYS A  57      -5.263 -15.861  14.977  1.00  0.00          C   
+ATOM    421  C   LYS A  57      -4.007 -15.075  14.612  1.00  0.00          C   
+ATOM    422  CB  LYS A  57      -5.532 -16.937  13.924  1.00  0.00          C   
+ATOM    423  O   LYS A  57      -4.077 -14.092  13.873  1.00  0.00          O   
+ATOM    424  CG  LYS A  57      -6.672 -17.880  14.280  1.00  0.00          C   
+ATOM    425  CD  LYS A  57      -6.811 -19.000  13.257  1.00  0.00          C   
+ATOM    426  CE  LYS A  57      -7.903 -19.986  13.651  1.00  0.00          C   
+ATOM    427  NZ  LYS A  57      -7.947 -21.161  12.730  1.00  0.00          N   
+ATOM    428  N   CYS A  58      -2.976 -15.105  15.608  1.00  0.00          N   
+ATOM    429  CA  CYS A  58      -1.644 -14.583  15.328  1.00  0.00          C   
+ATOM    430  C   CYS A  58      -0.938 -15.425  14.272  1.00  0.00          C   
+ATOM    431  CB  CYS A  58      -0.804 -14.543  16.605  1.00  0.00          C   
+ATOM    432  O   CYS A  58      -0.662 -16.605  14.495  1.00  0.00          O   
+ATOM    433  SG  CYS A  58      -1.471 -13.452  17.881  1.00  0.00          S   
+ATOM    434  N   SER A  59      -1.100 -15.266  13.105  1.00  0.00          N   
+ATOM    435  CA  SER A  59      -0.317 -16.194  12.296  1.00  0.00          C   
+ATOM    436  C   SER A  59       0.363 -15.475  11.135  1.00  0.00          C   
+ATOM    437  CB  SER A  59      -1.204 -17.319  11.760  1.00  0.00          C   
+ATOM    438  O   SER A  59      -0.281 -15.151  10.135  1.00  0.00          O   
+ATOM    439  OG  SER A  59      -0.425 -18.302  11.100  1.00  0.00          O   
+ATOM    440  N   CYS A  60       1.699 -14.861  11.329  1.00  0.00          N   
+ATOM    441  CA  CYS A  60       2.405 -14.577  10.084  1.00  0.00          C   
+ATOM    442  C   CYS A  60       2.585 -15.845   9.258  1.00  0.00          C   
+ATOM    443  CB  CYS A  60       3.768 -13.947  10.372  1.00  0.00          C   
+ATOM    444  O   CYS A  60       2.717 -15.781   8.035  1.00  0.00          O   
+ATOM    445  SG  CYS A  60       4.863 -14.997  11.352  1.00  0.00          S   
+ATOM    446  N   THR A  61       2.370 -16.747  10.083  1.00  0.00          N   
+ATOM    447  CA  THR A  61       2.549 -18.025   9.403  1.00  0.00          C   
+ATOM    448  C   THR A  61       1.237 -18.493   8.779  1.00  0.00          C   
+ATOM    449  CB  THR A  61       3.075 -19.103  10.369  1.00  0.00          C   
+ATOM    450  O   THR A  61       1.241 -19.301   7.848  1.00  0.00          O   
+ATOM    451  CG2 THR A  61       4.474 -18.758  10.869  1.00  0.00          C   
+ATOM    452  OG1 THR A  61       2.190 -19.204  11.491  1.00  0.00          O   
+ATOM    453  N   ALA A  62       0.127 -17.759   9.279  1.00  0.00          N   
+ATOM    454  CA  ALA A  62      -1.157 -18.259   8.792  1.00  0.00          C   
+ATOM    455  C   ALA A  62      -1.490 -17.673   7.423  1.00  0.00          C   
+ATOM    456  CB  ALA A  62      -2.266 -17.936   9.790  1.00  0.00          C   
+ATOM    457  O   ALA A  62      -2.183 -18.305   6.623  1.00  0.00          O   
+ATOM    458  N   ILE A  63      -0.953 -16.508   7.207  1.00  0.00          N   
+ATOM    459  CA  ILE A  63      -1.310 -15.966   5.900  1.00  0.00          C   
+ATOM    460  C   ILE A  63      -0.123 -16.091   4.948  1.00  0.00          C   
+ATOM    461  CB  ILE A  63      -1.761 -14.492   6.004  1.00  0.00          C   
+ATOM    462  O   ILE A  63       0.973 -15.611   5.246  1.00  0.00          O   
+ATOM    463  CG1 ILE A  63      -2.978 -14.369   6.929  1.00  0.00          C   
+ATOM    464  CG2 ILE A  63      -2.068 -13.922   4.616  1.00  0.00          C   
+ATOM    465  CD1 ILE A  63      -3.430 -12.936   7.171  1.00  0.00          C   
+ATOM    466  N   PRO A  64      -0.261 -17.160   4.081  1.00  0.00          N   
+ATOM    467  CA  PRO A  64       0.812 -17.254   3.088  1.00  0.00          C   
+ATOM    468  C   PRO A  64       1.182 -15.899   2.489  1.00  0.00          C   
+ATOM    469  CB  PRO A  64       0.224 -18.181   2.021  1.00  0.00          C   
+ATOM    470  O   PRO A  64       0.304 -15.069   2.242  1.00  0.00          O   
+ATOM    471  CG  PRO A  64      -1.257 -18.050   2.175  1.00  0.00          C   
+ATOM    472  CD  PRO A  64      -1.560 -17.707   3.605  1.00  0.00          C   
+ATOM    473  N   CYS A  65       2.470 -15.492   2.721  1.00  0.00          N   
+ATOM    474  CA  CYS A  65       2.970 -14.283   2.076  1.00  0.00          C   
+ATOM    475  C   CYS A  65       2.884 -14.399   0.559  1.00  0.00          C   
+ATOM    476  CB  CYS A  65       4.415 -14.011   2.494  1.00  0.00          C   
+ATOM    477  O   CYS A  65       3.627 -15.170  -0.052  1.00  0.00          O   
+ATOM    478  SG  CYS A  65       4.983 -12.341   2.107  1.00  0.00          S   
+ATOM    479  N   ASN A  66       1.810 -14.008   0.034  1.00  0.00          N   
+ATOM    480  CA  ASN A  66       1.657 -13.952  -1.416  1.00  0.00          C   
+ATOM    481  C   ASN A  66       1.636 -12.512  -1.922  1.00  0.00          C   
+ATOM    482  CB  ASN A  66       0.388 -14.686  -1.851  1.00  0.00          C   
+ATOM    483  O   ASN A  66       1.843 -11.575  -1.149  1.00  0.00          O   
+ATOM    484  CG  ASN A  66      -0.864 -14.121  -1.209  1.00  0.00          C   
+ATOM    485  ND2 ASN A  66      -1.787 -14.999  -0.835  1.00  0.00          N   
+ATOM    486  OD1 ASN A  66      -0.999 -12.905  -1.050  1.00  0.00          O   
+ATOM    487  N   GLU A  67       1.630 -12.346  -3.214  1.00  0.00          N   
+ATOM    488  CA  GLU A  67       1.700 -11.038  -3.857  1.00  0.00          C   
+ATOM    489  C   GLU A  67       0.657 -10.083  -3.284  1.00  0.00          C   
+ATOM    490  CB  GLU A  67       1.515 -11.172  -5.371  1.00  0.00          C   
+ATOM    491  O   GLU A  67       0.820  -8.863  -3.353  1.00  0.00          O   
+ATOM    492  CG  GLU A  67       0.220 -11.863  -5.773  1.00  0.00          C   
+ATOM    493  CD  GLU A  67       0.104 -12.095  -7.271  1.00  0.00          C   
+ATOM    494  OE1 GLU A  67      -1.026 -12.040  -7.808  1.00  0.00          O   
+ATOM    495  OE2 GLU A  67       1.151 -12.333  -7.914  1.00  0.00          O   
+ATOM    496  N   ASP A  68      -0.317 -10.492  -2.553  1.00  0.00          N   
+ATOM    497  CA  ASP A  68      -1.388  -9.666  -2.004  1.00  0.00          C   
+ATOM    498  C   ASP A  68      -1.103  -9.292  -0.551  1.00  0.00          C   
+ATOM    499  CB  ASP A  68      -2.731 -10.391  -2.108  1.00  0.00          C   
+ATOM    500  O   ASP A  68      -1.847  -8.517   0.053  1.00  0.00          O   
+ATOM    501  CG  ASP A  68      -3.195 -10.578  -3.541  1.00  0.00          C   
+ATOM    502  OD1 ASP A  68      -3.828 -11.611  -3.848  1.00  0.00          O   
+ATOM    503  OD2 ASP A  68      -2.923  -9.685  -4.373  1.00  0.00          O   
+ATOM    504  N   HIS A  69      -0.167  -9.956   0.090  1.00  0.00          N   
+ATOM    505  CA  HIS A  69       0.211  -9.683   1.472  1.00  0.00          C   
+ATOM    506  C   HIS A  69       1.044  -8.410   1.574  1.00  0.00          C   
+ATOM    507  CB  HIS A  69       0.985 -10.865   2.059  1.00  0.00          C   
+ATOM    508  O   HIS A  69       2.031  -8.249   0.852  1.00  0.00          O   
+ATOM    509  CG  HIS A  69       1.021 -10.875   3.555  1.00  0.00          C   
+ATOM    510  CD2 HIS A  69       0.448 -11.711   4.452  1.00  0.00          C   
+ATOM    511  ND1 HIS A  69       1.712  -9.936   4.288  1.00  0.00          N   
+ATOM    512  CE1 HIS A  69       1.562 -10.195   5.577  1.00  0.00          C   
+ATOM    513  NE2 HIS A  69       0.800 -11.267   5.703  1.00  0.00          N   
+ATOM    514  N   PRO A  70       0.701  -7.489   2.427  1.00  0.00          N   
+ATOM    515  CA  PRO A  70       1.384  -6.197   2.516  1.00  0.00          C   
+ATOM    516  C   PRO A  70       2.882  -6.337   2.776  1.00  0.00          C   
+ATOM    517  CB  PRO A  70       0.687  -5.510   3.693  1.00  0.00          C   
+ATOM    518  O   PRO A  70       3.663  -5.461   2.397  1.00  0.00          O   
+ATOM    519  CG  PRO A  70      -0.046  -6.606   4.396  1.00  0.00          C   
+ATOM    520  CD  PRO A  70      -0.242  -7.742   3.433  1.00  0.00          C   
+ATOM    521  N   CYS A  71       3.295  -7.400   3.302  1.00  0.00          N   
+ATOM    522  CA  CYS A  71       4.698  -7.619   3.633  1.00  0.00          C   
+ATOM    523  C   CYS A  71       5.402  -8.407   2.534  1.00  0.00          C   
+ATOM    524  CB  CYS A  71       4.825  -8.359   4.965  1.00  0.00          C   
+ATOM    525  O   CYS A  71       6.576  -8.754   2.669  1.00  0.00          O   
+ATOM    526  SG  CYS A  71       4.149  -7.448   6.371  1.00  0.00          S   
+ATOM    527  N   HIS A  72       4.559  -8.757   1.576  1.00  0.00          N   
+ATOM    528  CA  HIS A  72       5.119  -9.541   0.482  1.00  0.00          C   
+ATOM    529  C   HIS A  72       6.010  -8.684  -0.411  1.00  0.00          C   
+ATOM    530  CB  HIS A  72       4.003 -10.179  -0.347  1.00  0.00          C   
+ATOM    531  O   HIS A  72       5.596  -7.614  -0.864  1.00  0.00          O   
+ATOM    532  CG  HIS A  72       4.498 -10.942  -1.534  1.00  0.00          C   
+ATOM    533  CD2 HIS A  72       4.508 -10.627  -2.851  1.00  0.00          C   
+ATOM    534  ND1 HIS A  72       5.064 -12.194  -1.431  1.00  0.00          N   
+ATOM    535  CE1 HIS A  72       5.402 -12.618  -2.638  1.00  0.00          C   
+ATOM    536  NE2 HIS A  72       5.076 -11.686  -3.517  1.00  0.00          N   
+ATOM    537  N   HIS A  73       7.276  -9.193  -0.608  1.00  0.00          N   
+ATOM    538  CA  HIS A  73       8.219  -8.528  -1.500  1.00  0.00          C   
+ATOM    539  C   HIS A  73       8.888  -9.527  -2.439  1.00  0.00          C   
+ATOM    540  CB  HIS A  73       9.278  -7.774  -0.695  1.00  0.00          C   
+ATOM    541  O   HIS A  73       9.246 -10.632  -2.024  1.00  0.00          O   
+ATOM    542  CG  HIS A  73       8.715  -6.693   0.172  1.00  0.00          C   
+ATOM    543  CD2 HIS A  73       8.550  -6.625   1.514  1.00  0.00          C   
+ATOM    544  ND1 HIS A  73       8.240  -5.504  -0.336  1.00  0.00          N   
+ATOM    545  CE1 HIS A  73       7.806  -4.749   0.660  1.00  0.00          C   
+ATOM    546  NE2 HIS A  73       7.983  -5.406   1.793  1.00  0.00          N   
+ATOM    547  N   CYS A  74       8.907  -9.137  -3.729  1.00  0.00          N   
+ATOM    548  CA  CYS A  74       9.582  -9.976  -4.713  1.00  0.00          C   
+ATOM    549  C   CYS A  74      10.677  -9.199  -5.433  1.00  0.00          C   
+ATOM    550  CB  CYS A  74       8.580 -10.523  -5.729  1.00  0.00          C   
+ATOM    551  O   CYS A  74      10.529  -8.003  -5.689  1.00  0.00          O   
+ATOM    552  SG  CYS A  74       7.391 -11.686  -5.025  1.00  0.00          S   
+ATOM    553  N   HIS A  75      11.715  -9.738  -5.575  1.00  0.00          N   
+ATOM    554  CA  HIS A  75      12.772  -9.115  -6.364  1.00  0.00          C   
+ATOM    555  C   HIS A  75      13.308 -10.074  -7.422  1.00  0.00          C   
+ATOM    556  CB  HIS A  75      13.910  -8.643  -5.458  1.00  0.00          C   
+ATOM    557  O   HIS A  75      13.275 -11.292  -7.235  1.00  0.00          O   
+ATOM    558  CG  HIS A  75      14.605  -9.755  -4.740  1.00  0.00          C   
+ATOM    559  CD2 HIS A  75      15.789 -10.366  -4.981  1.00  0.00          C   
+ATOM    560  ND1 HIS A  75      14.075 -10.368  -3.625  1.00  0.00          N   
+ATOM    561  CE1 HIS A  75      14.905 -11.310  -3.211  1.00  0.00          C   
+ATOM    562  NE2 HIS A  75      15.954 -11.330  -4.016  1.00  0.00          N   
+ATOM    563  N   GLU A  76      13.647  -9.546  -8.538  1.00  0.00          N   
+ATOM    564  CA  GLU A  76      14.228 -10.322  -9.630  1.00  0.00          C   
+ATOM    565  C   GLU A  76      15.753 -10.283  -9.585  1.00  0.00          C   
+ATOM    566  CB  GLU A  76      13.727  -9.806 -10.981  1.00  0.00          C   
+ATOM    567  O   GLU A  76      16.350  -9.205  -9.546  1.00  0.00          O   
+ATOM    568  CG  GLU A  76      14.060 -10.722 -12.150  1.00  0.00          C   
+ATOM    569  CD  GLU A  76      13.399 -10.297 -13.452  1.00  0.00          C   
+ATOM    570  OE1 GLU A  76      12.554  -9.373 -13.430  1.00  0.00          O   
+ATOM    571  OE2 GLU A  76      13.727 -10.894 -14.501  1.00  0.00          O   
+ATOM    572  N   GLU A  77      16.313 -11.414  -9.551  1.00  0.00          N   
+ATOM    573  CA  GLU A  77      17.769 -11.510  -9.570  1.00  0.00          C   
+ATOM    574  C   GLU A  77      18.310 -11.423 -10.994  1.00  0.00          C   
+ATOM    575  CB  GLU A  77      18.231 -12.812  -8.911  1.00  0.00          C   
+ATOM    576  O   GLU A  77      17.548 -11.510 -11.959  1.00  0.00          O   
+ATOM    577  CG  GLU A  77      17.844 -12.929  -7.444  1.00  0.00          C   
+ATOM    578  CD  GLU A  77      18.639 -12.003  -6.537  1.00  0.00          C   
+ATOM    579  OE1 GLU A  77      19.776 -11.626  -6.901  1.00  0.00          O   
+ATOM    580  OE2 GLU A  77      18.120 -11.651  -5.454  1.00  0.00          O   
+ATOM    581  N   ASP A  78      19.573 -11.066 -11.091  1.00  0.00          N   
+ATOM    582  CA  ASP A  78      20.266 -10.915 -12.367  1.00  0.00          C   
+ATOM    583  C   ASP A  78      20.084 -12.153 -13.241  1.00  0.00          C   
+ATOM    584  CB  ASP A  78      21.755 -10.645 -12.140  1.00  0.00          C   
+ATOM    585  O   ASP A  78      20.095 -12.059 -14.470  1.00  0.00          O   
+ATOM    586  CG  ASP A  78      22.029  -9.254 -11.597  1.00  0.00          C   
+ATOM    587  OD1 ASP A  78      23.114  -9.028 -11.018  1.00  0.00          O   
+ATOM    588  OD2 ASP A  78      21.152  -8.376 -11.747  1.00  0.00          O   
+ATOM    589  N   ASP A  79      19.875 -13.279 -12.572  1.00  0.00          N   
+ATOM    590  CA  ASP A  79      19.730 -14.515 -13.335  1.00  0.00          C   
+ATOM    591  C   ASP A  79      18.288 -14.708 -13.799  1.00  0.00          C   
+ATOM    592  CB  ASP A  79      20.180 -15.716 -12.501  1.00  0.00          C   
+ATOM    593  O   ASP A  79      17.946 -15.750 -14.363  1.00  0.00          O   
+ATOM    594  CG  ASP A  79      19.357 -15.903 -11.238  1.00  0.00          C   
+ATOM    595  OD1 ASP A  79      19.656 -16.822 -10.446  1.00  0.00          O   
+ATOM    596  OD2 ASP A  79      18.399 -15.127 -11.036  1.00  0.00          O   
+ATOM    597  N   GLY A  80      17.414 -13.715 -13.581  1.00  0.00          N   
+ATOM    598  CA  GLY A  80      16.044 -13.776 -14.063  1.00  0.00          C   
+ATOM    599  C   GLY A  80      15.095 -14.439 -13.081  1.00  0.00          C   
+ATOM    600  O   GLY A  80      13.881 -14.444 -13.291  1.00  0.00          O   
+ATOM    601  N   ASP A  81      15.662 -15.063 -12.040  1.00  0.00          N   
+ATOM    602  CA  ASP A  81      14.823 -15.721 -11.043  1.00  0.00          C   
+ATOM    603  C   ASP A  81      14.161 -14.699 -10.121  1.00  0.00          C   
+ATOM    604  CB  ASP A  81      15.646 -16.715 -10.221  1.00  0.00          C   
+ATOM    605  O   ASP A  81      14.715 -13.625  -9.878  1.00  0.00          O   
+ATOM    606  CG  ASP A  81      16.113 -17.911 -11.031  1.00  0.00          C   
+ATOM    607  OD1 ASP A  81      17.118 -18.550 -10.652  1.00  0.00          O   
+ATOM    608  OD2 ASP A  81      15.472 -18.216 -12.060  1.00  0.00          O   
+ATOM    609  N   THR A  82      12.968 -14.929  -9.764  1.00  0.00          N   
+ATOM    610  CA  THR A  82      12.231 -14.082  -8.832  1.00  0.00          C   
+ATOM    611  C   THR A  82      12.233 -14.689  -7.432  1.00  0.00          C   
+ATOM    612  CB  THR A  82      10.780 -13.868  -9.299  1.00  0.00          C   
+ATOM    613  O   THR A  82      11.931 -15.872  -7.262  1.00  0.00          O   
+ATOM    614  CG2 THR A  82      10.028 -12.938  -8.352  1.00  0.00          C   
+ATOM    615  OG1 THR A  82      10.786 -13.291 -10.611  1.00  0.00          O   
+ATOM    616  N   HIS A  83      12.679 -13.936  -6.510  1.00  0.00          N   
+ATOM    617  CA  HIS A  83      12.653 -14.347  -5.110  1.00  0.00          C   
+ATOM    618  C   HIS A  83      11.661 -13.511  -4.309  1.00  0.00          C   
+ATOM    619  CB  HIS A  83      14.049 -14.239  -4.494  1.00  0.00          C   
+ATOM    620  O   HIS A  83      11.675 -12.280  -4.387  1.00  0.00          O   
+ATOM    621  CG  HIS A  83      15.047 -15.170  -5.104  1.00  0.00          C   
+ATOM    622  CD2 HIS A  83      15.925 -14.991  -6.119  1.00  0.00          C   
+ATOM    623  ND1 HIS A  83      15.219 -16.466  -4.669  1.00  0.00          N   
+ATOM    624  CE1 HIS A  83      16.163 -17.046  -5.391  1.00  0.00          C   
+ATOM    625  NE2 HIS A  83      16.608 -16.172  -6.279  1.00  0.00          N   
+ATOM    626  N   CYS A  84      10.791 -14.185  -3.722  1.00  0.00          N   
+ATOM    627  CA  CYS A  84       9.793 -13.514  -2.896  1.00  0.00          C   
+ATOM    628  C   CYS A  84      10.017 -13.813  -1.419  1.00  0.00          C   
+ATOM    629  CB  CYS A  84       8.384 -13.942  -3.305  1.00  0.00          C   
+ATOM    630  O   CYS A  84      10.408 -14.924  -1.059  1.00  0.00          O   
+ATOM    631  SG  CYS A  84       7.968 -13.539  -5.016  1.00  0.00          S   
+ATOM    632  N   HIS A  85       9.909 -12.859  -0.708  1.00  0.00          N   
+ATOM    633  CA  HIS A  85       9.975 -13.070   0.733  1.00  0.00          C   
+ATOM    634  C   HIS A  85       8.927 -12.236   1.461  1.00  0.00          C   
+ATOM    635  CB  HIS A  85      11.372 -12.734   1.260  1.00  0.00          C   
+ATOM    636  O   HIS A  85       8.377 -11.289   0.894  1.00  0.00          O   
+ATOM    637  CG  HIS A  85      11.748 -11.296   1.089  1.00  0.00          C   
+ATOM    638  CD2 HIS A  85      11.777 -10.273   1.975  1.00  0.00          C   
+ATOM    639  ND1 HIS A  85      12.152 -10.772  -0.120  1.00  0.00          N   
+ATOM    640  CE1 HIS A  85      12.415  -9.485   0.031  1.00  0.00          C   
+ATOM    641  NE2 HIS A  85      12.196  -9.157   1.293  1.00  0.00          N   
+ATOM    642  N   CYS A  86       8.500 -12.728   2.583  1.00  0.00          N   
+ATOM    643  CA  CYS A  86       7.596 -12.021   3.484  1.00  0.00          C   
+ATOM    644  C   CYS A  86       8.373 -11.290   4.572  1.00  0.00          C   
+ATOM    645  CB  CYS A  86       6.603 -12.993   4.119  1.00  0.00          C   
+ATOM    646  O   CYS A  86       8.939 -11.920   5.467  1.00  0.00          O   
+ATOM    647  SG  CYS A  86       5.473 -13.757   2.934  1.00  0.00          S   
+ATOM    648  N   SER A  87       8.541 -10.143   4.355  1.00  0.00          N   
+ATOM    649  CA  SER A  87       9.296  -9.406   5.363  1.00  0.00          C   
+ATOM    650  C   SER A  87       8.570  -8.129   5.774  1.00  0.00          C   
+ATOM    651  CB  SER A  87      10.692  -9.064   4.843  1.00  0.00          C   
+ATOM    652  O   SER A  87       8.018  -7.424   4.927  1.00  0.00          O   
+ATOM    653  OG  SER A  87      11.410  -8.297   5.794  1.00  0.00          O   
+ATOM    654  N   CYS A  88       8.324  -8.020   6.956  1.00  0.00          N   
+ATOM    655  CA  CYS A  88       7.764  -6.786   7.497  1.00  0.00          C   
+ATOM    656  C   CYS A  88       8.869  -5.829   7.928  1.00  0.00          C   
+ATOM    657  CB  CYS A  88       6.847  -7.088   8.681  1.00  0.00          C   
+ATOM    658  O   CYS A  88       8.600  -4.816   8.576  1.00  0.00          O   
+ATOM    659  SG  CYS A  88       5.414  -8.102   8.253  1.00  0.00          S   
+ATOM    660  N   GLU A  89       9.941  -6.277   7.427  1.00  0.00          N   
+ATOM    661  CA  GLU A  89      11.079  -5.417   7.736  1.00  0.00          C   
+ATOM    662  C   GLU A  89      11.164  -4.244   6.763  1.00  0.00          C   
+ATOM    663  CB  GLU A  89      12.382  -6.219   7.709  1.00  0.00          C   
+ATOM    664  O   GLU A  89      10.884  -4.397   5.572  1.00  0.00          O   
+ATOM    665  CG  GLU A  89      12.497  -7.244   8.828  1.00  0.00          C   
+ATOM    666  CD  GLU A  89      12.821  -6.626  10.178  1.00  0.00          C   
+ATOM    667  OE1 GLU A  89      13.318  -5.477  10.216  1.00  0.00          O   
+ATOM    668  OE2 GLU A  89      12.577  -7.295  11.207  1.00  0.00          O   
+ATOM    669  N   HIS A  90      10.877  -2.882   7.151  1.00  0.00          N   
+ATOM    670  CA  HIS A  90      11.037  -1.634   6.414  1.00  0.00          C   
+ATOM    671  C   HIS A  90      12.477  -1.452   5.945  1.00  0.00          C   
+ATOM    672  CB  HIS A  90      10.611  -0.444   7.276  1.00  0.00          C   
+ATOM    673  O   HIS A  90      13.291  -0.847   6.647  1.00  0.00          O   
+ATOM    674  CG  HIS A  90       9.172  -0.482   7.682  1.00  0.00          C   
+ATOM    675  CD2 HIS A  90       8.592  -0.729   8.880  1.00  0.00          C   
+ATOM    676  ND1 HIS A  90       8.143  -0.249   6.795  1.00  0.00          N   
+ATOM    677  CE1 HIS A  90       6.989  -0.350   7.434  1.00  0.00          C   
+ATOM    678  NE2 HIS A  90       7.234  -0.641   8.700  1.00  0.00          N   
+ATOM    679  N   SER A  91      13.113  -2.415   5.257  1.00  0.00          N   
+ATOM    680  CA  SER A  91      14.468  -1.999   4.909  1.00  0.00          C   
+ATOM    681  C   SER A  91      14.482  -1.180   3.623  1.00  0.00          C   
+ATOM    682  CB  SER A  91      15.380  -3.217   4.758  1.00  0.00          C   
+ATOM    683  O   SER A  91      13.868  -1.568   2.627  1.00  0.00          O   
+ATOM    684  OG  SER A  91      15.023  -3.974   3.614  1.00  0.00          O   
+ATOM    685  N   HIS A  92      14.296   0.148   3.642  1.00  0.00          N   
+ATOM    686  CA  HIS A  92      14.603   1.170   2.647  1.00  0.00          C   
+ATOM    687  C   HIS A  92      15.930   0.882   1.953  1.00  0.00          C   
+ATOM    688  CB  HIS A  92      14.638   2.555   3.295  1.00  0.00          C   
+ATOM    689  O   HIS A  92      16.284   1.551   0.979  1.00  0.00          O   
+ATOM    690  CG  HIS A  92      13.324   2.984   3.866  1.00  0.00          C   
+ATOM    691  CD2 HIS A  92      12.943   3.213   5.145  1.00  0.00          C   
+ATOM    692  ND1 HIS A  92      12.216   3.224   3.084  1.00  0.00          N   
+ATOM    693  CE1 HIS A  92      11.207   3.584   3.859  1.00  0.00          C   
+ATOM    694  NE2 HIS A  92      11.621   3.585   5.114  1.00  0.00          N   
+ATOM    695  N   ASP A  93      16.676  -0.193   2.168  1.00  0.00          N   
+ATOM    696  CA  ASP A  93      18.015  -0.132   1.589  1.00  0.00          C   
+ATOM    697  C   ASP A  93      18.097  -0.954   0.305  1.00  0.00          C   
+ATOM    698  CB  ASP A  93      19.058  -0.622   2.596  1.00  0.00          C   
+ATOM    699  O   ASP A  93      19.179  -1.132  -0.256  1.00  0.00          O   
+ATOM    700  CG  ASP A  93      19.487   0.454   3.577  1.00  0.00          C   
+ATOM    701  OD1 ASP A  93      20.370   0.192   4.423  1.00  0.00          O   
+ATOM    702  OD2 ASP A  93      18.935   1.573   3.507  1.00  0.00          O   
+ATOM    703  N   HIS A  94      17.467  -0.634  -0.758  1.00  0.00          N   
+ATOM    704  CA  HIS A  94      18.140  -1.057  -1.982  1.00  0.00          C   
+ATOM    705  C   HIS A  94      17.627  -0.280  -3.189  1.00  0.00          C   
+ATOM    706  CB  HIS A  94      17.951  -2.559  -2.205  1.00  0.00          C   
+ATOM    707  O   HIS A  94      16.419  -0.075  -3.334  1.00  0.00          O   
+ATOM    708  CG  HIS A  94      18.800  -3.409  -1.315  1.00  0.00          C   
+ATOM    709  CD2 HIS A  94      18.467  -4.255  -0.312  1.00  0.00          C   
+ATOM    710  ND1 HIS A  94      20.175  -3.442  -1.407  1.00  0.00          N   
+ATOM    711  CE1 HIS A  94      20.651  -4.276  -0.497  1.00  0.00          C   
+ATOM    712  NE2 HIS A  94      19.635  -4.782   0.181  1.00  0.00          N   
+ATOM    713  N   HIS A  95      18.249   0.957  -3.481  1.00  0.00          N   
+ATOM    714  CA  HIS A  95      18.496   1.578  -4.778  1.00  0.00          C   
+ATOM    715  C   HIS A  95      18.041   0.672  -5.918  1.00  0.00          C   
+ATOM    716  CB  HIS A  95      19.979   1.916  -4.936  1.00  0.00          C   
+ATOM    717  O   HIS A  95      18.521   0.799  -7.046  1.00  0.00          O   
+ATOM    718  CG  HIS A  95      20.458   2.973  -3.992  1.00  0.00          C   
+ATOM    719  CD2 HIS A  95      21.388   2.932  -3.010  1.00  0.00          C   
+ATOM    720  ND1 HIS A  95      19.959   4.258  -3.999  1.00  0.00          N   
+ATOM    721  CE1 HIS A  95      20.565   4.963  -3.059  1.00  0.00          C   
+ATOM    722  NE2 HIS A  95      21.437   4.182  -2.444  1.00  0.00          N   
+ATOM    723  N   ASP A  96      16.923   0.136  -5.980  1.00  0.00          N   
+ATOM    724  CA  ASP A  96      16.554  -0.218  -7.347  1.00  0.00          C   
+ATOM    725  C   ASP A  96      15.459   0.705  -7.877  1.00  0.00          C   
+ATOM    726  CB  ASP A  96      16.093  -1.676  -7.418  1.00  0.00          C   
+ATOM    727  O   ASP A  96      14.655   1.230  -7.104  1.00  0.00          O   
+ATOM    728  CG  ASP A  96      17.246  -2.663  -7.414  1.00  0.00          C   
+ATOM    729  OD1 ASP A  96      17.024  -3.859  -7.125  1.00  0.00          O   
+ATOM    730  OD2 ASP A  96      18.388  -2.242  -7.699  1.00  0.00          O   
+ATOM    731  N   ASP A  97      15.890   1.837  -8.509  1.00  0.00          N   
+ATOM    732  CA  ASP A  97      15.081   2.551  -9.491  1.00  0.00          C   
+ATOM    733  C   ASP A  97      13.874   1.718  -9.918  1.00  0.00          C   
+ATOM    734  CB  ASP A  97      15.923   2.923 -10.713  1.00  0.00          C   
+ATOM    735  O   ASP A  97      13.369   1.874 -11.032  1.00  0.00          O   
+ATOM    736  CG  ASP A  97      16.981   3.969 -10.409  1.00  0.00          C   
+ATOM    737  OD1 ASP A  97      18.049   3.963 -11.058  1.00  0.00          O   
+ATOM    738  OD2 ASP A  97      16.746   4.804  -9.509  1.00  0.00          O   
+ATOM    739  N   ASP A  98      13.468   0.802  -9.181  1.00  0.00          N   
+ATOM    740  CA  ASP A  98      12.224   0.241  -9.699  1.00  0.00          C   
+ATOM    741  C   ASP A  98      11.093   1.266  -9.639  1.00  0.00          C   
+ATOM    742  CB  ASP A  98      11.837  -1.017  -8.920  1.00  0.00          C   
+ATOM    743  O   ASP A  98      10.974   2.010  -8.663  1.00  0.00          O   
+ATOM    744  CG  ASP A  98      12.688  -2.222  -9.278  1.00  0.00          C   
+ATOM    745  OD1 ASP A  98      12.775  -3.170  -8.468  1.00  0.00          O   
+ATOM    746  OD2 ASP A  98      13.280  -2.223 -10.379  1.00  0.00          O   
+ATOM    747  N   THR A  99      11.132   2.146 -10.695  1.00  0.00          N   
+ATOM    748  CA  THR A  99       9.998   2.959 -11.120  1.00  0.00          C   
+ATOM    749  C   THR A  99       8.685   2.355 -10.628  1.00  0.00          C   
+ATOM    750  CB  THR A  99       9.957   3.102 -12.653  1.00  0.00          C   
+ATOM    751  O   THR A  99       7.730   2.223 -11.396  1.00  0.00          O   
+ATOM    752  CG2 THR A  99      11.214   3.791 -13.174  1.00  0.00          C   
+ATOM    753  OG1 THR A  99       9.857   1.802 -13.246  1.00  0.00          O   
+ATOM    754  N   HIS A 100       8.653   1.675  -9.540  1.00  0.00          N   
+ATOM    755  CA  HIS A 100       7.234   1.548  -9.228  1.00  0.00          C   
+ATOM    756  C   HIS A 100       6.625   2.899  -8.870  1.00  0.00          C   
+ATOM    757  CB  HIS A 100       7.024   0.557  -8.082  1.00  0.00          C   
+ATOM    758  O   HIS A 100       7.154   3.617  -8.019  1.00  0.00          O   
+ATOM    759  CG  HIS A 100       7.437  -0.842  -8.414  1.00  0.00          C   
+ATOM    760  CD2 HIS A 100       8.446  -1.607  -7.937  1.00  0.00          C   
+ATOM    761  ND1 HIS A 100       6.777  -1.610  -9.349  1.00  0.00          N   
+ATOM    762  CE1 HIS A 100       7.365  -2.793  -9.431  1.00  0.00          C   
+ATOM    763  NE2 HIS A 100       8.380  -2.816  -8.585  1.00  0.00          N   
+ATOM    764  N   GLY A 101       6.381   3.654  -9.900  1.00  0.00          N   
+ATOM    765  CA  GLY A 101       5.487   4.753  -9.574  1.00  0.00          C   
+ATOM    766  C   GLY A 101       4.744   4.550  -8.267  1.00  0.00          C   
+ATOM    767  O   GLY A 101       3.522   4.386  -8.261  1.00  0.00          O   
+ATOM    768  N   GLU A 102       5.430   3.707  -7.432  1.00  0.00          N   
+ATOM    769  CA  GLU A 102       4.594   3.693  -6.235  1.00  0.00          C   
+ATOM    770  C   GLU A 102       4.478   5.087  -5.627  1.00  0.00          C   
+ATOM    771  CB  GLU A 102       5.153   2.712  -5.201  1.00  0.00          C   
+ATOM    772  O   GLU A 102       5.392   5.905  -5.757  1.00  0.00          O   
+ATOM    773  CG  GLU A 102       5.195   1.269  -5.681  1.00  0.00          C   
+ATOM    774  CD  GLU A 102       3.815   0.668  -5.897  1.00  0.00          C   
+ATOM    775  OE1 GLU A 102       2.810   1.292  -5.486  1.00  0.00          O   
+ATOM    776  OE2 GLU A 102       3.738  -0.436  -6.481  1.00  0.00          O   
+ATOM    777  N   CYS A 103       3.304   5.585  -5.881  1.00  0.00          N   
+ATOM    778  CA  CYS A 103       2.937   6.733  -5.061  1.00  0.00          C   
+ATOM    779  C   CYS A 103       3.767   6.778  -3.783  1.00  0.00          C   
+ATOM    780  CB  CYS A 103       1.449   6.690  -4.712  1.00  0.00          C   
+ATOM    781  O   CYS A 103       3.803   5.806  -3.027  1.00  0.00          O   
+ATOM    782  SG  CYS A 103       0.362   6.999  -6.121  1.00  0.00          S   
+ATOM    783  N   THR A 104       4.856   7.423  -3.910  1.00  0.00          N   
+ATOM    784  CA  THR A 104       5.617   7.650  -2.686  1.00  0.00          C   
+ATOM    785  C   THR A 104       5.025   8.808  -1.888  1.00  0.00          C   
+ATOM    786  CB  THR A 104       7.098   7.939  -2.995  1.00  0.00          C   
+ATOM    787  O   THR A 104       4.142   9.517  -2.375  1.00  0.00          O   
+ATOM    788  CG2 THR A 104       7.686   6.875  -3.916  1.00  0.00          C   
+ATOM    789  OG1 THR A 104       7.206   9.219  -3.631  1.00  0.00          O   
+ATOM    790  N   LYS A 105       5.301   8.726  -0.683  1.00  0.00          N   
+ATOM    791  CA  LYS A 105       4.870   9.830   0.169  1.00  0.00          C   
+ATOM    792  C   LYS A 105       5.196  11.178  -0.469  1.00  0.00          C   
+ATOM    793  CB  LYS A 105       5.523   9.731   1.548  1.00  0.00          C   
+ATOM    794  O   LYS A 105       4.534  12.179  -0.190  1.00  0.00          O   
+ATOM    795  CG  LYS A 105       4.955   8.625   2.425  1.00  0.00          C   
+ATOM    796  CD  LYS A 105       5.514   8.690   3.840  1.00  0.00          C   
+ATOM    797  CE  LYS A 105       4.894   7.627   4.736  1.00  0.00          C   
+ATOM    798  NZ  LYS A 105       5.487   7.643   6.107  1.00  0.00          N   
+ATOM    799  N   LYS A 106       6.132  11.170  -1.417  1.00  0.00          N   
+ATOM    800  CA  LYS A 106       6.565  12.408  -2.059  1.00  0.00          C   
+ATOM    801  C   LYS A 106       5.727  12.707  -3.298  1.00  0.00          C   
+ATOM    802  CB  LYS A 106       8.046  12.329  -2.434  1.00  0.00          C   
+ATOM    803  O   LYS A 106       5.794  13.808  -3.849  1.00  0.00          O   
+ATOM    804  CG  LYS A 106       8.986  12.274  -1.239  1.00  0.00          C   
+ATOM    805  CD  LYS A 106      10.445  12.262  -1.676  1.00  0.00          C   
+ATOM    806  CE  LYS A 106      11.387  12.222  -0.480  1.00  0.00          C   
+ATOM    807  NZ  LYS A 106      12.817  12.151  -0.903  1.00  0.00          N   
+ATOM    808  N   ALA A 107       5.009  11.655  -3.672  1.00  0.00          N   
+ATOM    809  CA  ALA A 107       4.208  11.854  -4.877  1.00  0.00          C   
+ATOM    810  C   ALA A 107       3.004  12.748  -4.594  1.00  0.00          C   
+ATOM    811  CB  ALA A 107       3.749  10.511  -5.439  1.00  0.00          C   
+ATOM    812  O   ALA A 107       2.358  12.618  -3.552  1.00  0.00          O   
+ATOM    813  N   PRO A 108       2.750  13.735  -5.350  1.00  0.00          N   
+ATOM    814  CA  PRO A 108       1.593  14.609  -5.140  1.00  0.00          C   
+ATOM    815  C   PRO A 108       0.271  13.845  -5.124  1.00  0.00          C   
+ATOM    816  CB  PRO A 108       1.656  15.568  -6.331  1.00  0.00          C   
+ATOM    817  O   PRO A 108      -0.730  14.348  -4.607  1.00  0.00          O   
+ATOM    818  CG  PRO A 108       2.473  14.851  -7.356  1.00  0.00          C   
+ATOM    819  CD  PRO A 108       3.398  13.901  -6.650  1.00  0.00          C   
+ATOM    820  N   CYS A 109       0.245  12.652  -5.681  1.00  0.00          N   
+ATOM    821  CA  CYS A 109      -1.009  11.911  -5.770  1.00  0.00          C   
+ATOM    822  C   CYS A 109      -1.162  10.954  -4.594  1.00  0.00          C   
+ATOM    823  CB  CYS A 109      -1.079  11.134  -7.084  1.00  0.00          C   
+ATOM    824  O   CYS A 109      -2.174  10.261  -4.480  1.00  0.00          O   
+ATOM    825  SG  CYS A 109       0.290   9.980  -7.322  1.00  0.00          S   
+ATOM    826  N   TRP A 110      -0.068  10.925  -3.822  1.00  0.00          N   
+ATOM    827  CA  TRP A 110      -0.125  10.100  -2.621  1.00  0.00          C   
+ATOM    828  C   TRP A 110      -1.071  10.704  -1.589  1.00  0.00          C   
+ATOM    829  CB  TRP A 110       1.272   9.934  -2.016  1.00  0.00          C   
+ATOM    830  O   TRP A 110      -0.962  11.887  -1.255  1.00  0.00          O   
+ATOM    831  CG  TRP A 110       1.322   8.997  -0.846  1.00  0.00          C   
+ATOM    832  CD1 TRP A 110       1.696   7.682  -0.859  1.00  0.00          C   
+ATOM    833  CD2 TRP A 110       0.980   9.304   0.509  1.00  0.00          C   
+ATOM    834  CE2 TRP A 110       1.172   8.127   1.266  1.00  0.00          C   
+ATOM    835  CE3 TRP A 110       0.531  10.462   1.158  1.00  0.00          C   
+ATOM    836  NE1 TRP A 110       1.608   7.153   0.408  1.00  0.00          N   
+ATOM    837  CH2 TRP A 110       0.491   9.222   3.250  1.00  0.00          C   
+ATOM    838  CZ2 TRP A 110       0.929   8.075   2.640  1.00  0.00          C   
+ATOM    839  CZ3 TRP A 110       0.290  10.409   2.526  1.00  0.00          C   
+ATOM    840  N   ARG A 111      -2.102   9.880  -1.162  1.00  0.00          N   
+ATOM    841  CA  ARG A 111      -3.086  10.357  -0.197  1.00  0.00          C   
+ATOM    842  C   ARG A 111      -3.345   9.313   0.884  1.00  0.00          C   
+ATOM    843  CB  ARG A 111      -4.397  10.720  -0.899  1.00  0.00          C   
+ATOM    844  O   ARG A 111      -3.329   8.111   0.610  1.00  0.00          O   
+ATOM    845  CG  ARG A 111      -5.466  11.263   0.034  1.00  0.00          C   
+ATOM    846  CD  ARG A 111      -5.180  12.701   0.443  1.00  0.00          C   
+ATOM    847  NE  ARG A 111      -6.289  13.277   1.200  1.00  0.00          N   
+ATOM    848  NH1 ARG A 111      -5.313  15.357   1.444  1.00  0.00          N   
+ATOM    849  NH2 ARG A 111      -7.384  14.946   2.335  1.00  0.00          N   
+ATOM    850  CZ  ARG A 111      -6.326  14.525   1.658  1.00  0.00          C   
+ATOM    851  N   CYS A 112      -3.365   9.888   2.033  1.00  0.00          N   
+ATOM    852  CA  CYS A 112      -3.705   9.030   3.162  1.00  0.00          C   
+ATOM    853  C   CYS A 112      -5.019   9.463   3.801  1.00  0.00          C   
+ATOM    854  CB  CYS A 112      -2.589   9.051   4.206  1.00  0.00          C   
+ATOM    855  O   CYS A 112      -5.318  10.657   3.866  1.00  0.00          O   
+ATOM    856  SG  CYS A 112      -1.031   8.349   3.621  1.00  0.00          S   
+ATOM    857  N   GLU A 113      -5.830   8.580   3.951  1.00  0.00          N   
+ATOM    858  CA  GLU A 113      -7.053   8.822   4.710  1.00  0.00          C   
+ATOM    859  C   GLU A 113      -7.031   8.080   6.044  1.00  0.00          C   
+ATOM    860  CB  GLU A 113      -8.282   8.407   3.897  1.00  0.00          C   
+ATOM    861  O   GLU A 113      -6.553   6.947   6.122  1.00  0.00          O   
+ATOM    862  CG  GLU A 113      -8.500   9.241   2.643  1.00  0.00          C   
+ATOM    863  CD  GLU A 113      -9.731   8.826   1.853  1.00  0.00          C   
+ATOM    864  OE1 GLU A 113     -10.458   7.909   2.299  1.00  0.00          O   
+ATOM    865  OE2 GLU A 113      -9.971   9.422   0.780  1.00  0.00          O   
+ATOM    866  N   TYR A 114      -7.305   8.869   7.059  1.00  0.00          N   
+ATOM    867  CA  TYR A 114      -7.411   8.262   8.381  1.00  0.00          C   
+ATOM    868  C   TYR A 114      -8.671   7.412   8.491  1.00  0.00          C   
+ATOM    869  CB  TYR A 114      -7.412   9.340   9.469  1.00  0.00          C   
+ATOM    870  O   TYR A 114      -9.775   7.889   8.219  1.00  0.00          O   
+ATOM    871  CG  TYR A 114      -7.392   8.785  10.872  1.00  0.00          C   
+ATOM    872  CD1 TYR A 114      -8.527   8.834  11.678  1.00  0.00          C   
+ATOM    873  CD2 TYR A 114      -6.238   8.213  11.396  1.00  0.00          C   
+ATOM    874  CE1 TYR A 114      -8.513   8.326  12.973  1.00  0.00          C   
+ATOM    875  CE2 TYR A 114      -6.212   7.702  12.690  1.00  0.00          C   
+ATOM    876  OH  TYR A 114      -7.333   7.258  14.750  1.00  0.00          O   
+ATOM    877  CZ  TYR A 114      -7.353   7.762  13.469  1.00  0.00          C   
+ATOM    878  N   ASN A 115      -8.439   6.137   8.704  1.00  0.00          N   
+ATOM    879  CA  ASN A 115      -9.527   5.202   8.972  1.00  0.00          C   
+ATOM    880  C   ASN A 115      -9.770   5.039  10.469  1.00  0.00          C   
+ATOM    881  CB  ASN A 115      -9.238   3.844   8.330  1.00  0.00          C   
+ATOM    882  O   ASN A 115      -8.953   4.443  11.174  1.00  0.00          O   
+ATOM    883  CG  ASN A 115     -10.442   2.922   8.345  1.00  0.00          C   
+ATOM    884  ND2 ASN A 115     -10.511   2.021   7.373  1.00  0.00          N   
+ATOM    885  OD1 ASN A 115     -11.302   3.020   9.224  1.00  0.00          O   
+ATOM    886  N   ALA A 116     -10.796   5.699  10.920  1.00  0.00          N   
+ATOM    887  CA  ALA A 116     -11.108   5.723  12.347  1.00  0.00          C   
+ATOM    888  C   ALA A 116     -11.283   4.310  12.894  1.00  0.00          C   
+ATOM    889  CB  ALA A 116     -12.366   6.549  12.603  1.00  0.00          C   
+ATOM    890  O   ALA A 116     -10.898   4.025  14.031  1.00  0.00          O   
+ATOM    891  N   ASP A 117     -11.725   3.414  12.007  1.00  0.00          N   
+ATOM    892  CA  ASP A 117     -11.929   2.033  12.433  1.00  0.00          C   
+ATOM    893  C   ASP A 117     -10.595   1.313  12.619  1.00  0.00          C   
+ATOM    894  CB  ASP A 117     -12.796   1.281  11.421  1.00  0.00          C   
+ATOM    895  O   ASP A 117     -10.432   0.529  13.557  1.00  0.00          O   
+ATOM    896  CG  ASP A 117     -14.225   1.793  11.369  1.00  0.00          C   
+ATOM    897  OD1 ASP A 117     -14.898   1.618  10.331  1.00  0.00          O   
+ATOM    898  OD2 ASP A 117     -14.681   2.378  12.375  1.00  0.00          O   
+ATOM    899  N   LEU A 118      -9.664   1.666  11.738  1.00  0.00          N   
+ATOM    900  CA  LEU A 118      -8.349   1.035  11.785  1.00  0.00          C   
+ATOM    901  C   LEU A 118      -7.364   1.891  12.575  1.00  0.00          C   
+ATOM    902  CB  LEU A 118      -7.816   0.800  10.369  1.00  0.00          C   
+ATOM    903  O   LEU A 118      -6.231   1.472  12.822  1.00  0.00          O   
+ATOM    904  CG  LEU A 118      -8.639  -0.135   9.481  1.00  0.00          C   
+ATOM    905  CD1 LEU A 118      -8.022  -0.225   8.090  1.00  0.00          C   
+ATOM    906  CD2 LEU A 118      -8.746  -1.518  10.115  1.00  0.00          C   
+ATOM    907  N   LYS A 119      -7.828   3.091  12.895  1.00  0.00          N   
+ATOM    908  CA  LYS A 119      -6.988   4.069  13.580  1.00  0.00          C   
+ATOM    909  C   LYS A 119      -5.640   4.222  12.882  1.00  0.00          C   
+ATOM    910  CB  LYS A 119      -6.780   3.668  15.041  1.00  0.00          C   
+ATOM    911  O   LYS A 119      -4.596   4.257  13.537  1.00  0.00          O   
+ATOM    912  CG  LYS A 119      -8.064   3.604  15.855  1.00  0.00          C   
+ATOM    913  CD  LYS A 119      -7.786   3.255  17.311  1.00  0.00          C   
+ATOM    914  CE  LYS A 119      -9.062   3.263  18.143  1.00  0.00          C   
+ATOM    915  NZ  LYS A 119      -8.786   2.979  19.583  1.00  0.00          N   
+ATOM    916  N   HIS A 120      -5.544   4.099  11.731  1.00  0.00          N   
+ATOM    917  CA  HIS A 120      -4.341   4.353  10.946  1.00  0.00          C   
+ATOM    918  C   HIS A 120      -4.690   4.898   9.565  1.00  0.00          C   
+ATOM    919  CB  HIS A 120      -3.510   3.075  10.811  1.00  0.00          C   
+ATOM    920  O   HIS A 120      -5.853   4.869   9.156  1.00  0.00          O   
+ATOM    921  CG  HIS A 120      -4.217   1.973  10.089  1.00  0.00          C   
+ATOM    922  CD2 HIS A 120      -4.107   1.532   8.813  1.00  0.00          C   
+ATOM    923  ND1 HIS A 120      -5.174   1.183  10.689  1.00  0.00          N   
+ATOM    924  CE1 HIS A 120      -5.622   0.301   9.811  1.00  0.00          C   
+ATOM    925  NE2 HIS A 120      -4.990   0.491   8.666  1.00  0.00          N   
+ATOM    926  N   ASP A 121      -3.704   5.475   9.017  1.00  0.00          N   
+ATOM    927  CA  ASP A 121      -3.873   6.009   7.669  1.00  0.00          C   
+ATOM    928  C   ASP A 121      -3.838   4.892   6.628  1.00  0.00          C   
+ATOM    929  CB  ASP A 121      -2.792   7.047   7.363  1.00  0.00          C   
+ATOM    930  O   ASP A 121      -3.053   3.949   6.747  1.00  0.00          O   
+ATOM    931  CG  ASP A 121      -2.917   8.301   8.210  1.00  0.00          C   
+ATOM    932  OD1 ASP A 121      -1.936   9.069   8.312  1.00  0.00          O   
+ATOM    933  OD2 ASP A 121      -4.006   8.521   8.784  1.00  0.00          O   
+ATOM    934  N   VAL A 122      -4.829   4.935   5.875  1.00  0.00          N   
+ATOM    935  CA  VAL A 122      -4.775   4.123   4.663  1.00  0.00          C   
+ATOM    936  C   VAL A 122      -4.276   4.971   3.495  1.00  0.00          C   
+ATOM    937  CB  VAL A 122      -6.154   3.511   4.328  1.00  0.00          C   
+ATOM    938  O   VAL A 122      -4.857   6.013   3.184  1.00  0.00          O   
+ATOM    939  CG1 VAL A 122      -6.063   2.625   3.087  1.00  0.00          C   
+ATOM    940  CG2 VAL A 122      -6.688   2.717   5.518  1.00  0.00          C   
+ATOM    941  N   CYS A 123      -3.142   4.531   3.102  1.00  0.00          N   
+ATOM    942  CA  CYS A 123      -2.472   5.318   2.073  1.00  0.00          C   
+ATOM    943  C   CYS A 123      -2.628   4.669   0.702  1.00  0.00          C   
+ATOM    944  CB  CYS A 123      -0.988   5.481   2.403  1.00  0.00          C   
+ATOM    945  O   CYS A 123      -2.671   3.443   0.593  1.00  0.00          O   
+ATOM    946  SG  CYS A 123      -0.681   6.285   3.991  1.00  0.00          S   
+ATOM    947  N   GLY A 124      -2.924   5.462  -0.260  1.00  0.00          N   
+ATOM    948  CA  GLY A 124      -2.940   5.028  -1.648  1.00  0.00          C   
+ATOM    949  C   GLY A 124      -2.699   6.159  -2.630  1.00  0.00          C   
+ATOM    950  O   GLY A 124      -2.463   7.299  -2.225  1.00  0.00          O   
+ATOM    951  N   CYS A 125      -2.378   5.820  -3.813  1.00  0.00          N   
+ATOM    952  CA  CYS A 125      -2.283   6.770  -4.916  1.00  0.00          C   
+ATOM    953  C   CYS A 125      -3.667   7.160  -5.421  1.00  0.00          C   
+ATOM    954  CB  CYS A 125      -1.458   6.183  -6.061  1.00  0.00          C   
+ATOM    955  O   CYS A 125      -4.425   6.307  -5.886  1.00  0.00          O   
+ATOM    956  SG  CYS A 125       0.275   5.900  -5.639  1.00  0.00          S   
+ATOM    957  N   GLU A 126      -4.004   8.323  -5.203  1.00  0.00          N   
+ATOM    958  CA  GLU A 126      -5.332   8.779  -5.604  1.00  0.00          C   
+ATOM    959  C   GLU A 126      -5.243   9.988  -6.530  1.00  0.00          C   
+ATOM    960  CB  GLU A 126      -6.177   9.119  -4.374  1.00  0.00          C   
+ATOM    961  O   GLU A 126      -5.752  11.064  -6.206  1.00  0.00          O   
+ATOM    962  CG  GLU A 126      -6.467   7.924  -3.478  1.00  0.00          C   
+ATOM    963  CD  GLU A 126      -7.488   6.964  -4.068  1.00  0.00          C   
+ATOM    964  OE1 GLU A 126      -8.228   7.361  -4.997  1.00  0.00          O   
+ATOM    965  OE2 GLU A 126      -7.550   5.807  -3.597  1.00  0.00          O   
+ATOM    966  N   CYS A 127      -4.822   9.841  -7.699  1.00  0.00          N   
+ATOM    967  CA  CYS A 127      -4.615  10.948  -8.626  1.00  0.00          C   
+ATOM    968  C   CYS A 127      -5.940  11.598  -9.005  1.00  0.00          C   
+ATOM    969  CB  CYS A 127      -3.895  10.466  -9.885  1.00  0.00          C   
+ATOM    970  O   CYS A 127      -5.987  12.790  -9.312  1.00  0.00          O   
+ATOM    971  SG  CYS A 127      -2.217   9.868  -9.581  1.00  0.00          S   
+ATOM    972  N   SER A 128      -6.846  10.833  -8.955  1.00  0.00          N   
+ATOM    973  CA  SER A 128      -8.150  11.305  -9.408  1.00  0.00          C   
+ATOM    974  C   SER A 128      -8.755  12.293  -8.417  1.00  0.00          C   
+ATOM    975  CB  SER A 128      -9.104  10.128  -9.616  1.00  0.00          C   
+ATOM    976  O   SER A 128      -9.642  13.073  -8.772  1.00  0.00          O   
+ATOM    977  OG  SER A 128      -9.249   9.381  -8.420  1.00  0.00          O   
+ATOM    978  N   LYS A 129      -8.286  12.254  -7.213  1.00  0.00          N   
+ATOM    979  CA  LYS A 129      -8.887  13.076  -6.166  1.00  0.00          C   
+ATOM    980  C   LYS A 129      -8.020  14.294  -5.859  1.00  0.00          C   
+ATOM    981  CB  LYS A 129      -9.104  12.253  -4.896  1.00  0.00          C   
+ATOM    982  O   LYS A 129      -8.420  15.169  -5.089  1.00  0.00          O   
+ATOM    983  CG  LYS A 129     -10.151  11.158  -5.039  1.00  0.00          C   
+ATOM    984  CD  LYS A 129     -10.395  10.441  -3.717  1.00  0.00          C   
+ATOM    985  CE  LYS A 129     -11.490   9.392  -3.843  1.00  0.00          C   
+ATOM    986  NZ  LYS A 129     -11.820   8.774  -2.524  1.00  0.00          N   
+ATOM    987  N   LEU A 130      -6.820  14.391  -6.394  1.00  0.00          N   
+ATOM    988  CA  LEU A 130      -5.922  15.506  -6.110  1.00  0.00          C   
+ATOM    989  C   LEU A 130      -6.255  16.708  -6.987  1.00  0.00          C   
+ATOM    990  CB  LEU A 130      -4.465  15.089  -6.326  1.00  0.00          C   
+ATOM    991  O   LEU A 130      -6.713  16.548  -8.120  1.00  0.00          O   
+ATOM    992  CG  LEU A 130      -3.879  14.117  -5.300  1.00  0.00          C   
+ATOM    993  CD1 LEU A 130      -2.476  13.689  -5.718  1.00  0.00          C   
+ATOM    994  CD2 LEU A 130      -3.859  14.751  -3.913  1.00  0.00          C   
+ATOM    995  N   PRO A 131      -6.218  17.878  -6.321  1.00  0.00          N   
+ATOM    996  CA  PRO A 131      -6.403  19.088  -7.125  1.00  0.00          C   
+ATOM    997  C   PRO A 131      -5.423  19.176  -8.293  1.00  0.00          C   
+ATOM    998  CB  PRO A 131      -6.159  20.219  -6.123  1.00  0.00          C   
+ATOM    999  O   PRO A 131      -4.287  18.706  -8.188  1.00  0.00          O   
+ATOM   1000  CG  PRO A 131      -5.279  19.617  -5.075  1.00  0.00          C   
+ATOM   1001  CD  PRO A 131      -5.586  18.150  -4.979  1.00  0.00          C   
+ATOM   1002  N   CYS A 132      -5.915  19.530  -9.527  1.00  0.00          N   
+ATOM   1003  CA  CYS A 132      -5.087  19.711 -10.714  1.00  0.00          C   
+ATOM   1004  C   CYS A 132      -4.132  20.886 -10.540  1.00  0.00          C   
+ATOM   1005  CB  CYS A 132      -5.960  19.930 -11.949  1.00  0.00          C   
+ATOM   1006  O   CYS A 132      -4.531  22.042 -10.690  1.00  0.00          O   
+ATOM   1007  SG  CYS A 132      -6.896  18.468 -12.448  1.00  0.00          S   
+ATOM   1008  N   ASN A 133      -3.080  20.705  -9.927  1.00  0.00          N   
+ATOM   1009  CA  ASN A 133      -2.027  21.708  -9.810  1.00  0.00          C   
+ATOM   1010  C   ASN A 133      -0.764  21.283 -10.553  1.00  0.00          C   
+ATOM   1011  CB  ASN A 133      -1.710  21.986  -8.339  1.00  0.00          C   
+ATOM   1012  O   ASN A 133      -0.740  20.230 -11.194  1.00  0.00          O   
+ATOM   1013  CG  ASN A 133      -1.260  20.744  -7.595  1.00  0.00          C   
+ATOM   1014  ND2 ASN A 133      -1.758  20.570  -6.376  1.00  0.00          N   
+ATOM   1015  OD1 ASN A 133      -0.470  19.949  -8.110  1.00  0.00          O   
+ATOM   1016  N   ASP A 134       0.201  22.148 -10.651  1.00  0.00          N   
+ATOM   1017  CA  ASP A 134       1.408  21.962 -11.451  1.00  0.00          C   
+ATOM   1018  C   ASP A 134       2.162  20.705 -11.023  1.00  0.00          C   
+ATOM   1019  CB  ASP A 134       2.320  23.185 -11.338  1.00  0.00          C   
+ATOM   1020  O   ASP A 134       2.999  20.192 -11.768  1.00  0.00          O   
+ATOM   1021  CG  ASP A 134       1.789  24.392 -12.091  1.00  0.00          C   
+ATOM   1022  OD1 ASP A 134       2.250  25.525 -11.832  1.00  0.00          O   
+ATOM   1023  OD2 ASP A 134       0.898  24.210 -12.950  1.00  0.00          O   
+ATOM   1024  N   GLU A 135       1.732  20.132  -9.899  1.00  0.00          N   
+ATOM   1025  CA  GLU A 135       2.429  18.946  -9.410  1.00  0.00          C   
+ATOM   1026  C   GLU A 135       1.714  17.669  -9.840  1.00  0.00          C   
+ATOM   1027  CB  GLU A 135       2.559  18.988  -7.885  1.00  0.00          C   
+ATOM   1028  O   GLU A 135       2.282  16.577  -9.766  1.00  0.00          O   
+ATOM   1029  CG  GLU A 135       3.439  20.120  -7.374  1.00  0.00          C   
+ATOM   1030  CD  GLU A 135       3.561  20.146  -5.859  1.00  0.00          C   
+ATOM   1031  OE1 GLU A 135       2.885  19.340  -5.181  1.00  0.00          O   
+ATOM   1032  OE2 GLU A 135       4.339  20.981  -5.346  1.00  0.00          O   
+ATOM   1033  N   HIS A 136       0.480  17.885 -10.293  1.00  0.00          N   
+ATOM   1034  CA  HIS A 136      -0.314  16.733 -10.704  1.00  0.00          C   
+ATOM   1035  C   HIS A 136       0.053  16.287 -12.116  1.00  0.00          C   
+ATOM   1036  CB  HIS A 136      -1.807  17.057 -10.628  1.00  0.00          C   
+ATOM   1037  O   HIS A 136       0.114  17.107 -13.035  1.00  0.00          O   
+ATOM   1038  CG  HIS A 136      -2.685  15.846 -10.645  1.00  0.00          C   
+ATOM   1039  CD2 HIS A 136      -3.469  15.303  -9.684  1.00  0.00          C   
+ATOM   1040  ND1 HIS A 136      -2.822  15.042 -11.756  1.00  0.00          N   
+ATOM   1041  CE1 HIS A 136      -3.655  14.054 -11.476  1.00  0.00          C   
+ATOM   1042  NE2 HIS A 136      -4.062  14.189 -10.225  1.00  0.00          N   
+ATOM   1043  N   PRO A 137       0.226  15.184 -12.322  1.00  0.00          N   
+ATOM   1044  CA  PRO A 137       0.690  14.688 -13.619  1.00  0.00          C   
+ATOM   1045  C   PRO A 137      -0.331  14.908 -14.734  1.00  0.00          C   
+ATOM   1046  CB  PRO A 137       0.910  13.194 -13.368  1.00  0.00          C   
+ATOM   1047  O   PRO A 137       0.032  14.929 -15.913  1.00  0.00          O   
+ATOM   1048  CG  PRO A 137       0.170  12.907 -12.101  1.00  0.00          C   
+ATOM   1049  CD  PRO A 137       0.003  14.193 -11.344  1.00  0.00          C   
+ATOM   1050  N   CYS A 138      -1.650  15.096 -14.399  1.00  0.00          N   
+ATOM   1051  CA  CYS A 138      -2.702  15.293 -15.390  1.00  0.00          C   
+ATOM   1052  C   CYS A 138      -2.947  16.776 -15.639  1.00  0.00          C   
+ATOM   1053  CB  CYS A 138      -3.998  14.621 -14.937  1.00  0.00          C   
+ATOM   1054  O   CYS A 138      -3.870  17.144 -16.368  1.00  0.00          O   
+ATOM   1055  SG  CYS A 138      -3.887  12.822 -14.830  1.00  0.00          S   
+ATOM   1056  N   TYR A 139      -2.050  17.530 -14.923  1.00  0.00          N   
+ATOM   1057  CA  TYR A 139      -2.147  18.977 -15.082  1.00  0.00          C   
+ATOM   1058  C   TYR A 139      -1.580  19.417 -16.427  1.00  0.00          C   
+ATOM   1059  CB  TYR A 139      -1.411  19.693 -13.946  1.00  0.00          C   
+ATOM   1060  O   TYR A 139      -0.470  19.029 -16.796  1.00  0.00          O   
+ATOM   1061  CG  TYR A 139      -1.400  21.197 -14.083  1.00  0.00          C   
+ATOM   1062  CD1 TYR A 139      -0.320  21.854 -14.668  1.00  0.00          C   
+ATOM   1063  CD2 TYR A 139      -2.468  21.962 -13.627  1.00  0.00          C   
+ATOM   1064  CE1 TYR A 139      -0.305  23.239 -14.795  1.00  0.00          C   
+ATOM   1065  CE2 TYR A 139      -2.463  23.348 -13.748  1.00  0.00          C   
+ATOM   1066  OH  TYR A 139      -1.369  25.348 -14.456  1.00  0.00          O   
+ATOM   1067  CZ  TYR A 139      -1.379  23.976 -14.333  1.00  0.00          C   
+ATOM   1068  N   ARG A 140      -2.489  20.100 -17.284  1.00  0.00          N   
+ATOM   1069  CA  ARG A 140      -2.036  20.668 -18.550  1.00  0.00          C   
+ATOM   1070  C   ARG A 140      -2.355  22.157 -18.626  1.00  0.00          C   
+ATOM   1071  CB  ARG A 140      -2.678  19.934 -19.729  1.00  0.00          C   
+ATOM   1072  O   ARG A 140      -3.435  22.589 -18.217  1.00  0.00          O   
+ATOM   1073  CG  ARG A 140      -2.260  18.477 -19.849  1.00  0.00          C   
+ATOM   1074  CD  ARG A 140      -2.856  17.819 -21.086  1.00  0.00          C   
+ATOM   1075  NE  ARG A 140      -2.303  16.486 -21.307  1.00  0.00          N   
+ATOM   1076  NH1 ARG A 140      -1.510  16.942 -23.429  1.00  0.00          N   
+ATOM   1077  NH2 ARG A 140      -1.212  14.863 -22.510  1.00  0.00          N   
+ATOM   1078  CZ  ARG A 140      -1.676  16.100 -22.415  1.00  0.00          C   
+ATOM   1079  N   LYS A 141      -1.270  22.911 -18.875  1.00  0.00          N   
+ATOM   1080  CA  LYS A 141      -1.432  24.343 -19.105  1.00  0.00          C   
+ATOM   1081  C   LYS A 141      -1.210  24.693 -20.574  1.00  0.00          C   
+ATOM   1082  CB  LYS A 141      -0.468  25.141 -18.226  1.00  0.00          C   
+ATOM   1083  O   LYS A 141      -0.111  24.513 -21.101  1.00  0.00          O   
+ATOM   1084  CG  LYS A 141      -0.749  26.636 -18.196  1.00  0.00          C   
+ATOM   1085  CD  LYS A 141       0.167  27.359 -17.217  1.00  0.00          C   
+ATOM   1086  CE  LYS A 141      -0.124  28.853 -17.175  1.00  0.00          C   
+ATOM   1087  NZ  LYS A 141       0.783  29.568 -16.230  1.00  0.00          N   
+ATOM   1088  N   GLU A 142      -2.285  24.849 -21.311  1.00  0.00          N   
+ATOM   1089  CA  GLU A 142      -2.217  25.247 -22.713  1.00  0.00          C   
+ATOM   1090  C   GLU A 142      -2.920  26.583 -22.942  1.00  0.00          C   
+ATOM   1091  CB  GLU A 142      -2.832  24.169 -23.609  1.00  0.00          C   
+ATOM   1092  O   GLU A 142      -4.113  26.718 -22.665  1.00  0.00          O   
+ATOM   1093  CG  GLU A 142      -2.588  24.391 -25.095  1.00  0.00          C   
+ATOM   1094  CD  GLU A 142      -3.160  23.287 -25.969  1.00  0.00          C   
+ATOM   1095  OE1 GLU A 142      -3.890  22.415 -25.445  1.00  0.00          O   
+ATOM   1096  OE2 GLU A 142      -2.875  23.292 -27.187  1.00  0.00          O   
+ATOM   1097  N   GLY A 143      -2.182  27.579 -23.469  1.00  0.00          N   
+ATOM   1098  CA  GLY A 143      -2.758  28.882 -23.764  1.00  0.00          C   
+ATOM   1099  C   GLY A 143      -3.342  29.566 -22.543  1.00  0.00          C   
+ATOM   1100  O   GLY A 143      -4.385  30.217 -22.629  1.00  0.00          O   
+ATOM   1101  N   GLY A 144      -2.777  29.290 -21.354  1.00  0.00          N   
+ATOM   1102  CA  GLY A 144      -3.245  29.947 -20.144  1.00  0.00          C   
+ATOM   1103  C   GLY A 144      -4.395  29.217 -19.476  1.00  0.00          C   
+ATOM   1104  O   GLY A 144      -4.892  29.651 -18.435  1.00  0.00          O   
+ATOM   1105  N   VAL A 145      -4.936  28.140 -20.164  1.00  0.00          N   
+ATOM   1106  CA  VAL A 145      -6.039  27.365 -19.605  1.00  0.00          C   
+ATOM   1107  C   VAL A 145      -5.504  26.079 -18.980  1.00  0.00          C   
+ATOM   1108  CB  VAL A 145      -7.101  27.035 -20.678  1.00  0.00          C   
+ATOM   1109  O   VAL A 145      -4.666  25.395 -19.573  1.00  0.00          O   
+ATOM   1110  CG1 VAL A 145      -8.253  26.236 -20.071  1.00  0.00          C   
+ATOM   1111  CG2 VAL A 145      -7.619  28.316 -21.328  1.00  0.00          C   
+ATOM   1112  N   VAL A 146      -5.959  25.837 -17.763  1.00  0.00          N   
+ATOM   1113  CA  VAL A 146      -5.574  24.626 -17.045  1.00  0.00          C   
+ATOM   1114  C   VAL A 146      -6.593  23.521 -17.311  1.00  0.00          C   
+ATOM   1115  CB  VAL A 146      -5.450  24.882 -15.526  1.00  0.00          C   
+ATOM   1116  O   VAL A 146      -7.803  23.758 -17.264  1.00  0.00          O   
+ATOM   1117  CG1 VAL A 146      -5.098  23.592 -14.788  1.00  0.00          C   
+ATOM   1118  CG2 VAL A 146      -4.405  25.962 -15.251  1.00  0.00          C   
+ATOM   1119  N   SER A 147      -6.150  22.494 -17.818  1.00  0.00          N   
+ATOM   1120  CA  SER A 147      -7.007  21.324 -17.979  1.00  0.00          C   
+ATOM   1121  C   SER A 147      -6.522  20.161 -17.121  1.00  0.00          C   
+ATOM   1122  CB  SER A 147      -7.062  20.898 -19.447  1.00  0.00          C   
+ATOM   1123  O   SER A 147      -5.316  19.946 -16.982  1.00  0.00          O   
+ATOM   1124  OG  SER A 147      -7.912  19.776 -19.614  1.00  0.00          O   
+ATOM   1125  N   CYS A 148      -7.409  19.637 -16.271  1.00  0.00          N   
+ATOM   1126  CA  CYS A 148      -7.135  18.448 -15.471  1.00  0.00          C   
+ATOM   1127  C   CYS A 148      -7.876  17.237 -16.024  1.00  0.00          C   
+ATOM   1128  CB  CYS A 148      -7.534  18.680 -14.014  1.00  0.00          C   
+ATOM   1129  O   CYS A 148      -8.941  16.873 -15.523  1.00  0.00          O   
+ATOM   1130  SG  CYS A 148      -6.884  17.438 -12.875  1.00  0.00          S   
+ATOM   1131  N   ASP A 149      -7.699  16.869 -17.159  1.00  0.00          N   
+ATOM   1132  CA  ASP A 149      -8.393  15.760 -17.806  1.00  0.00          C   
+ATOM   1133  C   ASP A 149      -7.445  14.590 -18.056  1.00  0.00          C   
+ATOM   1134  CB  ASP A 149      -9.023  16.217 -19.124  1.00  0.00          C   
+ATOM   1135  O   ASP A 149      -6.548  14.679 -18.896  1.00  0.00          O   
+ATOM   1136  CG  ASP A 149      -9.976  15.192 -19.713  1.00  0.00          C   
+ATOM   1137  OD1 ASP A 149     -10.762  15.540 -20.620  1.00  0.00          O   
+ATOM   1138  OD2 ASP A 149      -9.941  14.025 -19.265  1.00  0.00          O   
+ATOM   1139  N   CYS A 150      -7.567  13.519 -17.222  1.00  0.00          N   
+ATOM   1140  CA  CYS A 150      -6.727  12.334 -17.354  1.00  0.00          C   
+ATOM   1141  C   CYS A 150      -7.054  11.573 -18.634  1.00  0.00          C   
+ATOM   1142  CB  CYS A 150      -6.900  11.416 -16.145  1.00  0.00          C   
+ATOM   1143  O   CYS A 150      -6.244  10.777 -19.112  1.00  0.00          O   
+ATOM   1144  SG  CYS A 150      -6.406  12.171 -14.581  1.00  0.00          S   
+ATOM   1145  N   LYS A 151      -8.188  11.835 -19.161  1.00  0.00          N   
+ATOM   1146  CA  LYS A 151      -8.679  11.063 -20.298  1.00  0.00          C   
+ATOM   1147  C   LYS A 151      -8.050  11.543 -21.603  1.00  0.00          C   
+ATOM   1148  CB  LYS A 151     -10.204  11.151 -20.388  1.00  0.00          C   
+ATOM   1149  O   LYS A 151      -7.990  10.796 -22.581  1.00  0.00          O   
+ATOM   1150  CG  LYS A 151     -10.931  10.505 -19.219  1.00  0.00          C   
+ATOM   1151  CD  LYS A 151     -12.443  10.620 -19.368  1.00  0.00          C   
+ATOM   1152  CE  LYS A 151     -13.172   9.972 -18.199  1.00  0.00          C   
+ATOM   1153  NZ  LYS A 151     -14.653  10.132 -18.313  1.00  0.00          N   
+ATOM   1154  N   THR A 152      -7.674  12.782 -21.597  1.00  0.00          N   
+ATOM   1155  CA  THR A 152      -7.207  13.367 -22.850  1.00  0.00          C   
+ATOM   1156  C   THR A 152      -5.688  13.279 -22.954  1.00  0.00          C   
+ATOM   1157  CB  THR A 152      -7.649  14.836 -22.979  1.00  0.00          C   
+ATOM   1158  O   THR A 152      -5.115  13.562 -24.008  1.00  0.00          O   
+ATOM   1159  CG2 THR A 152      -9.168  14.950 -23.052  1.00  0.00          C   
+ATOM   1160  OG1 THR A 152      -7.180  15.572 -21.843  1.00  0.00          O   
+ATOM   1161  N   ILE A 153      -5.064  12.924 -21.810  1.00  0.00          N   
+ATOM   1162  CA  ILE A 153      -3.608  12.834 -21.820  1.00  0.00          C   
+ATOM   1163  C   ILE A 153      -3.181  11.435 -22.259  1.00  0.00          C   
+ATOM   1164  CB  ILE A 153      -3.011  13.167 -20.435  1.00  0.00          C   
+ATOM   1165  O   ILE A 153      -3.826  10.444 -21.909  1.00  0.00          O   
+ATOM   1166  CG1 ILE A 153      -3.390  14.593 -20.018  1.00  0.00          C   
+ATOM   1167  CG2 ILE A 153      -1.490  12.986 -20.444  1.00  0.00          C   
+ATOM   1168  CD1 ILE A 153      -2.744  15.679 -20.868  1.00  0.00          C   
+ATOM   1169  N   THR A 154      -2.270  11.363 -23.110  1.00  0.00          N   
+ATOM   1170  CA  THR A 154      -1.713  10.090 -23.553  1.00  0.00          C   
+ATOM   1171  C   THR A 154      -1.160   9.301 -22.370  1.00  0.00          C   
+ATOM   1172  CB  THR A 154      -0.603  10.299 -24.599  1.00  0.00          C   
+ATOM   1173  O   THR A 154      -0.336   9.812 -21.607  1.00  0.00          O   
+ATOM   1174  CG2 THR A 154      -0.102   8.965 -25.144  1.00  0.00          C   
+ATOM   1175  OG1 THR A 154      -1.117  11.082 -25.683  1.00  0.00          O   
+ATOM   1176  N   CYS A 155      -1.859   8.148 -22.092  1.00  0.00          N   
+ATOM   1177  CA  CYS A 155      -1.409   7.282 -21.008  1.00  0.00          C   
+ATOM   1178  C   CYS A 155      -0.060   6.653 -21.338  1.00  0.00          C   
+ATOM   1179  CB  CYS A 155      -2.439   6.187 -20.734  1.00  0.00          C   
+ATOM   1180  O   CYS A 155       0.086   5.991 -22.367  1.00  0.00          O   
+ATOM   1181  SG  CYS A 155      -4.010   6.809 -20.095  1.00  0.00          S   
+ATOM   1182  N   ASN A 156       0.893   7.176 -20.743  1.00  0.00          N   
+ATOM   1183  CA  ASN A 156       2.201   6.536 -20.836  1.00  0.00          C   
+ATOM   1184  C   ASN A 156       2.611   5.904 -19.509  1.00  0.00          C   
+ATOM   1185  CB  ASN A 156       3.259   7.541 -21.294  1.00  0.00          C   
+ATOM   1186  O   ASN A 156       1.841   5.916 -18.546  1.00  0.00          O   
+ATOM   1187  CG  ASN A 156       3.393   8.721 -20.351  1.00  0.00          C   
+ATOM   1188  ND2 ASN A 156       3.554   9.913 -20.912  1.00  0.00          N   
+ATOM   1189  OD1 ASN A 156       3.352   8.561 -19.128  1.00  0.00          O   
+ATOM   1190  N   GLU A 157       3.624   5.165 -19.538  1.00  0.00          N   
+ATOM   1191  CA  GLU A 157       4.078   4.402 -18.379  1.00  0.00          C   
+ATOM   1192  C   GLU A 157       4.196   5.291 -17.145  1.00  0.00          C   
+ATOM   1193  CB  GLU A 157       5.421   3.727 -18.672  1.00  0.00          C   
+ATOM   1194  O   GLU A 157       4.169   4.799 -16.014  1.00  0.00          O   
+ATOM   1195  CG  GLU A 157       5.336   2.611 -19.703  1.00  0.00          C   
+ATOM   1196  CD  GLU A 157       6.670   1.925 -19.955  1.00  0.00          C   
+ATOM   1197  OE1 GLU A 157       7.660   2.250 -19.261  1.00  0.00          O   
+ATOM   1198  OE2 GLU A 157       6.725   1.058 -20.855  1.00  0.00          O   
+ATOM   1199  N   ASP A 158       4.203   6.614 -17.357  1.00  0.00          N   
+ATOM   1200  CA  ASP A 158       4.344   7.540 -16.237  1.00  0.00          C   
+ATOM   1201  C   ASP A 158       2.979   8.001 -15.731  1.00  0.00          C   
+ATOM   1202  CB  ASP A 158       5.190   8.748 -16.643  1.00  0.00          C   
+ATOM   1203  O   ASP A 158       2.882   8.629 -14.675  1.00  0.00          O   
+ATOM   1204  CG  ASP A 158       6.638   8.390 -16.927  1.00  0.00          C   
+ATOM   1205  OD1 ASP A 158       7.251   8.999 -17.830  1.00  0.00          O   
+ATOM   1206  OD2 ASP A 158       7.169   7.487 -16.244  1.00  0.00          O   
+ATOM   1207  N   HIS A 159       2.048   7.688 -16.589  1.00  0.00          N   
+ATOM   1208  CA  HIS A 159       0.697   8.104 -16.230  1.00  0.00          C   
+ATOM   1209  C   HIS A 159       0.098   7.180 -15.176  1.00  0.00          C   
+ATOM   1210  CB  HIS A 159      -0.199   8.139 -17.469  1.00  0.00          C   
+ATOM   1211  O   HIS A 159       0.148   5.956 -15.317  1.00  0.00          O   
+ATOM   1212  CG  HIS A 159      -1.463   8.914 -17.273  1.00  0.00          C   
+ATOM   1213  CD2 HIS A 159      -1.859  10.110 -17.769  1.00  0.00          C   
+ATOM   1214  ND1 HIS A 159      -2.495   8.466 -16.477  1.00  0.00          N   
+ATOM   1215  CE1 HIS A 159      -3.474   9.356 -16.493  1.00  0.00          C   
+ATOM   1216  NE2 HIS A 159      -3.113  10.363 -17.270  1.00  0.00          N   
+ATOM   1217  N   PRO A 160      -0.393   7.607 -14.171  1.00  0.00          N   
+ATOM   1218  CA  PRO A 160      -0.882   6.789 -13.059  1.00  0.00          C   
+ATOM   1219  C   PRO A 160      -2.041   5.880 -13.461  1.00  0.00          C   
+ATOM   1220  CB  PRO A 160      -1.334   7.828 -12.030  1.00  0.00          C   
+ATOM   1221  O   PRO A 160      -2.326   4.896 -12.773  1.00  0.00          O   
+ATOM   1222  CG  PRO A 160      -1.619   9.058 -12.828  1.00  0.00          C   
+ATOM   1223  CD  PRO A 160      -0.678   9.096 -13.998  1.00  0.00          C   
+ATOM   1224  N   CYS A 161      -2.737   6.193 -14.475  1.00  0.00          N   
+ATOM   1225  CA  CYS A 161      -3.885   5.408 -14.913  1.00  0.00          C   
+ATOM   1226  C   CYS A 161      -3.470   4.357 -15.936  1.00  0.00          C   
+ATOM   1227  CB  CYS A 161      -4.960   6.317 -15.509  1.00  0.00          C   
+ATOM   1228  O   CYS A 161      -4.312   3.621 -16.453  1.00  0.00          O   
+ATOM   1229  SG  CYS A 161      -5.656   7.493 -14.328  1.00  0.00          S   
+ATOM   1230  N   TYR A 162      -2.132   4.465 -16.183  1.00  0.00          N   
+ATOM   1231  CA  TYR A 162      -1.573   3.516 -17.140  1.00  0.00          C   
+ATOM   1232  C   TYR A 162      -1.452   2.127 -16.525  1.00  0.00          C   
+ATOM   1233  CB  TYR A 162      -0.201   3.992 -17.629  1.00  0.00          C   
+ATOM   1234  O   TYR A 162      -0.908   1.972 -15.429  1.00  0.00          O   
+ATOM   1235  CG  TYR A 162       0.469   3.033 -18.583  1.00  0.00          C   
+ATOM   1236  CD1 TYR A 162       1.424   2.124 -18.131  1.00  0.00          C   
+ATOM   1237  CD2 TYR A 162       0.151   3.035 -19.936  1.00  0.00          C   
+ATOM   1238  CE1 TYR A 162       2.046   1.240 -19.007  1.00  0.00          C   
+ATOM   1239  CE2 TYR A 162       0.766   2.155 -20.821  1.00  0.00          C   
+ATOM   1240  OH  TYR A 162       2.323   0.390 -21.219  1.00  0.00          O   
+ATOM   1241  CZ  TYR A 162       1.710   1.263 -20.348  1.00  0.00          C   
+ATOM   1242  N   HIS A 163      -2.235   1.147 -17.118  1.00  0.00          N   
+ATOM   1243  CA  HIS A 163      -2.129  -0.243 -16.689  1.00  0.00          C   
+ATOM   1244  C   HIS A 163      -1.553  -1.119 -17.797  1.00  0.00          C   
+ATOM   1245  CB  HIS A 163      -3.496  -0.776 -16.256  1.00  0.00          C   
+ATOM   1246  O   HIS A 163      -1.953  -1.002 -18.957  1.00  0.00          O   
+ATOM   1247  CG  HIS A 163      -4.058  -0.081 -15.057  1.00  0.00          C   
+ATOM   1248  CD2 HIS A 163      -5.018   0.867 -14.948  1.00  0.00          C   
+ATOM   1249  ND1 HIS A 163      -3.625  -0.342 -13.775  1.00  0.00          N   
+ATOM   1250  CE1 HIS A 163      -4.297   0.419 -12.926  1.00  0.00          C   
+ATOM   1251  NE2 HIS A 163      -5.148   1.162 -13.613  1.00  0.00          N   
+ATOM   1252  N   SER A 164      -0.416  -1.652 -17.433  1.00  0.00          N   
+ATOM   1253  CA  SER A 164       0.122  -2.646 -18.356  1.00  0.00          C   
+ATOM   1254  C   SER A 164      -0.175  -4.063 -17.877  1.00  0.00          C   
+ATOM   1255  CB  SER A 164       1.630  -2.462 -18.523  1.00  0.00          C   
+ATOM   1256  O   SER A 164      -0.055  -4.360 -16.687  1.00  0.00          O   
+ATOM   1257  OG  SER A 164       2.304  -2.686 -17.297  1.00  0.00          O   
+ATOM   1258  N   TYR A 165      -0.841  -4.799 -18.656  1.00  0.00          N   
+ATOM   1259  CA  TYR A 165      -1.123  -6.182 -18.287  1.00  0.00          C   
+ATOM   1260  C   TYR A 165      -0.783  -7.132 -19.429  1.00  0.00          C   
+ATOM   1261  CB  TYR A 165      -2.594  -6.345 -17.894  1.00  0.00          C   
+ATOM   1262  O   TYR A 165      -0.643  -6.705 -20.578  1.00  0.00          O   
+ATOM   1263  CG  TYR A 165      -3.559  -6.039 -19.013  1.00  0.00          C   
+ATOM   1264  CD1 TYR A 165      -3.953  -4.730 -19.282  1.00  0.00          C   
+ATOM   1265  CD2 TYR A 165      -4.080  -7.058 -19.804  1.00  0.00          C   
+ATOM   1266  CE1 TYR A 165      -4.843  -4.444 -20.312  1.00  0.00          C   
+ATOM   1267  CE2 TYR A 165      -4.971  -6.783 -20.836  1.00  0.00          C   
+ATOM   1268  OH  TYR A 165      -6.228  -5.197 -22.103  1.00  0.00          O   
+ATOM   1269  CZ  TYR A 165      -5.346  -5.475 -21.082  1.00  0.00          C   
+ATOM   1270  N   GLU A 166      -0.437  -8.271 -19.075  1.00  0.00          N   
+ATOM   1271  CA  GLU A 166      -0.092  -9.311 -20.039  1.00  0.00          C   
+ATOM   1272  C   GLU A 166      -1.292 -10.203 -20.342  1.00  0.00          C   
+ATOM   1273  CB  GLU A 166       1.075 -10.158 -19.523  1.00  0.00          C   
+ATOM   1274  O   GLU A 166      -1.951 -10.699 -19.426  1.00  0.00          O   
+ATOM   1275  CG  GLU A 166       1.667 -11.091 -20.569  1.00  0.00          C   
+ATOM   1276  CD  GLU A 166       2.944 -11.776 -20.108  1.00  0.00          C   
+ATOM   1277  OE1 GLU A 166       3.581 -11.289 -19.146  1.00  0.00          O   
+ATOM   1278  OE2 GLU A 166       3.310 -12.808 -20.713  1.00  0.00          O   
+ATOM   1279  N   GLU A 167      -1.701 -10.268 -21.599  1.00  0.00          N   
+ATOM   1280  CA  GLU A 167      -2.770 -11.135 -22.087  1.00  0.00          C   
+ATOM   1281  C   GLU A 167      -2.310 -11.956 -23.288  1.00  0.00          C   
+ATOM   1282  CB  GLU A 167      -4.006 -10.310 -22.455  1.00  0.00          C   
+ATOM   1283  O   GLU A 167      -1.837 -11.400 -24.282  1.00  0.00          O   
+ATOM   1284  CG  GLU A 167      -5.232 -11.150 -22.780  1.00  0.00          C   
+ATOM   1285  CD  GLU A 167      -6.476 -10.318 -23.048  1.00  0.00          C   
+ATOM   1286  OE1 GLU A 167      -6.367  -9.075 -23.139  1.00  0.00          O   
+ATOM   1287  OE2 GLU A 167      -7.570 -10.915 -23.165  1.00  0.00          O   
+ATOM   1288  N   ASP A 168      -2.308 -13.235 -23.226  1.00  0.00          N   
+ATOM   1289  CA  ASP A 168      -1.919 -14.168 -24.278  1.00  0.00          C   
+ATOM   1290  C   ASP A 168      -0.472 -13.938 -24.708  1.00  0.00          C   
+ATOM   1291  CB  ASP A 168      -2.852 -14.039 -25.483  1.00  0.00          C   
+ATOM   1292  O   ASP A 168      -0.162 -13.963 -25.901  1.00  0.00          O   
+ATOM   1293  CG  ASP A 168      -4.284 -14.437 -25.170  1.00  0.00          C   
+ATOM   1294  OD1 ASP A 168      -5.222 -13.831 -25.730  1.00  0.00          O   
+ATOM   1295  OD2 ASP A 168      -4.475 -15.363 -24.352  1.00  0.00          O   
+ATOM   1296  N   GLY A 169       0.378 -13.615 -23.661  1.00  0.00          N   
+ATOM   1297  CA  GLY A 169       1.802 -13.483 -23.928  1.00  0.00          C   
+ATOM   1298  C   GLY A 169       2.181 -12.123 -24.482  1.00  0.00          C   
+ATOM   1299  O   GLY A 169       3.340 -11.889 -24.830  1.00  0.00          O   
+ATOM   1300  N   VAL A 170       1.173 -11.220 -24.645  1.00  0.00          N   
+ATOM   1301  CA  VAL A 170       1.451  -9.891 -25.180  1.00  0.00          C   
+ATOM   1302  C   VAL A 170       1.131  -8.832 -24.128  1.00  0.00          C   
+ATOM   1303  CB  VAL A 170       0.648  -9.620 -26.472  1.00  0.00          C   
+ATOM   1304  O   VAL A 170       0.124  -8.932 -23.423  1.00  0.00          O   
+ATOM   1305  CG1 VAL A 170       0.954  -8.226 -27.016  1.00  0.00          C   
+ATOM   1306  CG2 VAL A 170       0.952 -10.686 -27.523  1.00  0.00          C   
+ATOM   1307  N   THR A 171       2.053  -7.976 -23.977  1.00  0.00          N   
+ATOM   1308  CA  THR A 171       1.846  -6.867 -23.053  1.00  0.00          C   
+ATOM   1309  C   THR A 171       0.857  -5.859 -23.631  1.00  0.00          C   
+ATOM   1310  CB  THR A 171       3.173  -6.158 -22.725  1.00  0.00          C   
+ATOM   1311  O   THR A 171       1.042  -5.370 -24.747  1.00  0.00          O   
+ATOM   1312  CG2 THR A 171       2.958  -5.020 -21.732  1.00  0.00          C   
+ATOM   1313  OG1 THR A 171       4.087  -7.105 -22.158  1.00  0.00          O   
+ATOM   1314  N   LYS A 172      -0.220  -5.669 -22.883  1.00  0.00          N   
+ATOM   1315  CA  LYS A 172      -1.215  -4.669 -23.260  1.00  0.00          C   
+ATOM   1316  C   LYS A 172      -1.232  -3.510 -22.267  1.00  0.00          C   
+ATOM   1317  CB  LYS A 172      -2.604  -5.301 -23.351  1.00  0.00          C   
+ATOM   1318  O   LYS A 172      -0.846  -3.673 -21.107  1.00  0.00          O   
+ATOM   1319  CG  LYS A 172      -2.720  -6.393 -24.405  1.00  0.00          C   
+ATOM   1320  CD  LYS A 172      -4.154  -6.886 -24.543  1.00  0.00          C   
+ATOM   1321  CE  LYS A 172      -4.280  -7.941 -25.634  1.00  0.00          C   
+ATOM   1322  NZ  LYS A 172      -5.700  -8.358 -25.841  1.00  0.00          N   
+ATOM   1323  N   SER A 173      -1.325  -2.368 -22.806  1.00  0.00          N   
+ATOM   1324  CA  SER A 173      -1.442  -1.178 -21.969  1.00  0.00          C   
+ATOM   1325  C   SER A 173      -2.815  -0.530 -22.119  1.00  0.00          C   
+ATOM   1326  CB  SER A 173      -0.350  -0.167 -22.320  1.00  0.00          C   
+ATOM   1327  O   SER A 173      -3.418  -0.584 -23.193  1.00  0.00          O   
+ATOM   1328  OG  SER A 173      -0.430   0.207 -23.684  1.00  0.00          O   
+ATOM   1329  N   ASP A 174      -3.338  -0.380 -21.075  1.00  0.00          N   
+ATOM   1330  CA  ASP A 174      -4.630   0.300 -21.062  1.00  0.00          C   
+ATOM   1331  C   ASP A 174      -4.627   1.467 -20.077  1.00  0.00          C   
+ATOM   1332  CB  ASP A 174      -5.749  -0.682 -20.712  1.00  0.00          C   
+ATOM   1333  O   ASP A 174      -3.834   1.488 -19.134  1.00  0.00          O   
+ATOM   1334  CG  ASP A 174      -7.118  -0.209 -21.168  1.00  0.00          C   
+ATOM   1335  OD1 ASP A 174      -8.137  -0.811 -20.767  1.00  0.00          O   
+ATOM   1336  OD2 ASP A 174      -7.178   0.774 -21.938  1.00  0.00          O   
+ATOM   1337  N   CYS A 175      -5.254   2.474 -20.569  1.00  0.00          N   
+ATOM   1338  CA  CYS A 175      -5.511   3.614 -19.696  1.00  0.00          C   
+ATOM   1339  C   CYS A 175      -6.886   3.506 -19.049  1.00  0.00          C   
+ATOM   1340  CB  CYS A 175      -5.407   4.922 -20.479  1.00  0.00          C   
+ATOM   1341  O   CYS A 175      -7.906   3.530 -19.740  1.00  0.00          O   
+ATOM   1342  SG  CYS A 175      -5.469   6.399 -19.441  1.00  0.00          S   
+ATOM   1343  N   ASP A 176      -6.926   3.117 -17.897  1.00  0.00          N   
+ATOM   1344  CA  ASP A 176      -8.216   2.947 -17.236  1.00  0.00          C   
+ATOM   1345  C   ASP A 176      -8.579   4.181 -16.413  1.00  0.00          C   
+ATOM   1346  CB  ASP A 176      -8.202   1.705 -16.343  1.00  0.00          C   
+ATOM   1347  O   ASP A 176      -8.390   4.199 -15.195  1.00  0.00          O   
+ATOM   1348  CG  ASP A 176      -9.574   1.352 -15.795  1.00  0.00          C   
+ATOM   1349  OD1 ASP A 176      -9.681   0.413 -14.978  1.00  0.00          O   
+ATOM   1350  OD2 ASP A 176     -10.557   2.018 -16.187  1.00  0.00          O   
+ATOM   1351  N   CYS A 177      -8.999   5.207 -17.129  1.00  0.00          N   
+ATOM   1352  CA  CYS A 177      -9.425   6.426 -16.450  1.00  0.00          C   
+ATOM   1353  C   CYS A 177     -10.930   6.422 -16.214  1.00  0.00          C   
+ATOM   1354  CB  CYS A 177      -9.030   7.658 -17.264  1.00  0.00          C   
+ATOM   1355  O   CYS A 177     -11.489   7.406 -15.726  1.00  0.00          O   
+ATOM   1356  SG  CYS A 177      -7.251   7.814 -17.535  1.00  0.00          S   
+ATOM   1357  N   GLU A 178     -11.529   5.450 -16.815  1.00  0.00          N   
+ATOM   1358  CA  GLU A 178     -12.986   5.385 -16.754  1.00  0.00          C   
+ATOM   1359  C   GLU A 178     -13.473   5.263 -15.313  1.00  0.00          C   
+ATOM   1360  CB  GLU A 178     -13.508   4.211 -17.586  1.00  0.00          C   
+ATOM   1361  O   GLU A 178     -14.584   5.686 -14.990  1.00  0.00          O   
+ATOM   1362  CG  GLU A 178     -13.379   4.417 -19.089  1.00  0.00          C   
+ATOM   1363  CD  GLU A 178     -13.985   3.285 -19.903  1.00  0.00          C   
+ATOM   1364  OE1 GLU A 178     -14.377   2.254 -19.312  1.00  0.00          O   
+ATOM   1365  OE2 GLU A 178     -14.069   3.431 -21.143  1.00  0.00          O   
+ATOM   1366  N   HIS A 179     -12.602   4.539 -14.596  1.00  0.00          N   
+ATOM   1367  CA  HIS A 179     -13.083   4.370 -13.230  1.00  0.00          C   
+ATOM   1368  C   HIS A 179     -12.913   5.654 -12.423  1.00  0.00          C   
+ATOM   1369  CB  HIS A 179     -12.350   3.217 -12.542  1.00  0.00          C   
+ATOM   1370  O   HIS A 179     -13.259   5.699 -11.241  1.00  0.00          O   
+ATOM   1371  CG  HIS A 179     -12.672   1.874 -13.117  1.00  0.00          C   
+ATOM   1372  CD2 HIS A 179     -11.913   1.007 -13.828  1.00  0.00          C   
+ATOM   1373  ND1 HIS A 179     -13.911   1.286 -12.986  1.00  0.00          N   
+ATOM   1374  CE1 HIS A 179     -13.900   0.111 -13.593  1.00  0.00          C   
+ATOM   1375  NE2 HIS A 179     -12.700  -0.082 -14.113  1.00  0.00          N   
+ATOM   1376  N   SER A 180     -12.761   6.762 -13.153  1.00  0.00          N   
+ATOM   1377  CA  SER A 180     -12.625   8.074 -12.529  1.00  0.00          C   
+ATOM   1378  C   SER A 180     -13.967   8.797 -12.465  1.00  0.00          C   
+ATOM   1379  CB  SER A 180     -11.612   8.928 -13.291  1.00  0.00          C   
+ATOM   1380  O   SER A 180     -14.740   8.767 -13.424  1.00  0.00          O   
+ATOM   1381  OG  SER A 180     -12.114   9.284 -14.568  1.00  0.00          O   
+ATOM   1382  N   PRO A 181     -14.719   8.802 -11.393  1.00  0.00          N   
+ATOM   1383  CA  PRO A 181     -15.790   9.799 -11.316  1.00  0.00          C   
+ATOM   1384  C   PRO A 181     -15.334  11.190 -11.748  1.00  0.00          C   
+ATOM   1385  CB  PRO A 181     -16.178   9.786  -9.836  1.00  0.00          C   
+ATOM   1386  O   PRO A 181     -14.337  11.704 -11.233  1.00  0.00          O   
+ATOM   1387  CG  PRO A 181     -14.965   9.275  -9.127  1.00  0.00          C   
+ATOM   1388  CD  PRO A 181     -14.184   8.416 -10.079  1.00  0.00          C   
+ATOM   1389  N   GLY A 182     -15.240  11.453 -13.029  1.00  0.00          N   
+ATOM   1390  CA  GLY A 182     -15.037  12.822 -13.476  1.00  0.00          C   
+ATOM   1391  C   GLY A 182     -15.937  13.820 -12.770  1.00  0.00          C   
+ATOM   1392  O   GLY A 182     -16.871  13.431 -12.066  1.00  0.00          O   
+ATOM   1393  N   PRO A 183     -15.396  14.822 -12.165  1.00  0.00          N   
+ATOM   1394  CA  PRO A 183     -16.219  15.888 -11.589  1.00  0.00          C   
+ATOM   1395  C   PRO A 183     -17.636  15.913 -12.158  1.00  0.00          C   
+ATOM   1396  CB  PRO A 183     -15.458  17.162 -11.964  1.00  0.00          C   
+ATOM   1397  O   PRO A 183     -17.838  15.604 -13.335  1.00  0.00          O   
+ATOM   1398  CG  PRO A 183     -14.695  16.803 -13.198  1.00  0.00          C   
+ATOM   1399  CD  PRO A 183     -14.401  15.330 -13.164  1.00  0.00          C   
+ATOM   1400  N   SER A 184     -18.521  15.085 -11.531  1.00  0.00          N   
+ATOM   1401  CA  SER A 184     -19.918  15.360 -11.852  1.00  0.00          C   
+ATOM   1402  C   SER A 184     -20.093  16.779 -12.385  1.00  0.00          C   
+ATOM   1403  CB  SER A 184     -20.801  15.157 -10.620  1.00  0.00          C   
+ATOM   1404  O   SER A 184     -19.543  17.730 -11.826  1.00  0.00          O   
+ATOM   1405  OG  SER A 184     -20.375  15.985  -9.553  1.00  0.00          O   
+ATOM   1406  N   GLU A 185     -19.658  16.958 -13.662  1.00  0.00          N   
+ATOM   1407  CA  GLU A 185     -20.167  18.200 -14.237  1.00  0.00          C   
+ATOM   1408  C   GLU A 185     -21.492  18.603 -13.597  1.00  0.00          C   
+ATOM   1409  CB  GLU A 185     -20.336  18.061 -15.752  1.00  0.00          C   
+ATOM   1410  O   GLU A 185     -22.450  17.827 -13.598  1.00  0.00          O   
+ATOM   1411  CG  GLU A 185     -19.029  17.836 -16.499  1.00  0.00          C   
+ATOM   1412  CD  GLU A 185     -18.110  19.046 -16.478  1.00  0.00          C   
+ATOM   1413  OE1 GLU A 185     -18.546  20.132 -16.032  1.00  0.00          O   
+ATOM   1414  OE2 GLU A 185     -16.944  18.908 -16.911  1.00  0.00          O   
+ATOM   1415  N   HIS A 186     -21.419  18.961 -12.324  1.00  0.00          N   
+ATOM   1416  CA  HIS A 186     -22.672  19.612 -11.958  1.00  0.00          C   
+ATOM   1417  C   HIS A 186     -23.102  20.617 -13.022  1.00  0.00          C   
+ATOM   1418  CB  HIS A 186     -22.539  20.307 -10.602  1.00  0.00          C   
+ATOM   1419  O   HIS A 186     -22.311  21.471 -13.430  1.00  0.00          O   
+ATOM   1420  CG  HIS A 186     -22.402  19.359  -9.453  1.00  0.00          C   
+ATOM   1421  CD2 HIS A 186     -21.354  19.097  -8.637  1.00  0.00          C   
+ATOM   1422  ND1 HIS A 186     -23.431  18.543  -9.034  1.00  0.00          N   
+ATOM   1423  CE1 HIS A 186     -23.020  17.819  -8.007  1.00  0.00          C   
+ATOM   1424  NE2 HIS A 186     -21.763  18.136  -7.746  1.00  0.00          N   
+ATOM   1425  N   HIS A 187     -23.592  20.072 -14.139  1.00  0.00          N   
+ATOM   1426  CA  HIS A 187     -24.308  20.983 -15.025  1.00  0.00          C   
+ATOM   1427  C   HIS A 187     -24.996  22.092 -14.235  1.00  0.00          C   
+ATOM   1428  CB  HIS A 187     -25.335  20.219 -15.862  1.00  0.00          C   
+ATOM   1429  O   HIS A 187     -25.860  21.819 -13.399  1.00  0.00          O   
+ATOM   1430  CG  HIS A 187     -24.723  19.267 -16.840  1.00  0.00          C   
+ATOM   1431  CD2 HIS A 187     -24.703  17.913 -16.868  1.00  0.00          C   
+ATOM   1432  ND1 HIS A 187     -24.026  19.687 -17.952  1.00  0.00          N   
+ATOM   1433  CE1 HIS A 187     -23.603  18.630 -18.624  1.00  0.00          C   
+ATOM   1434  NE2 HIS A 187     -24.000  17.541 -17.988  1.00  0.00          N   
+ATOM   1435  N   HIS A 188     -24.187  22.915 -13.610  1.00  0.00          N   
+ATOM   1436  CA  HIS A 188     -24.905  24.094 -13.140  1.00  0.00          C   
+ATOM   1437  C   HIS A 188     -25.814  24.656 -14.228  1.00  0.00          C   
+ATOM   1438  CB  HIS A 188     -23.923  25.168 -12.669  1.00  0.00          C   
+ATOM   1439  O   HIS A 188     -25.380  24.849 -15.366  1.00  0.00          O   
+ATOM   1440  CG  HIS A 188     -23.207  24.814 -11.404  1.00  0.00          C   
+ATOM   1441  CD2 HIS A 188     -21.913  24.489 -11.176  1.00  0.00          C   
+ATOM   1442  ND1 HIS A 188     -23.839  24.765 -10.181  1.00  0.00          N   
+ATOM   1443  CE1 HIS A 188     -22.961  24.425  -9.252  1.00  0.00          C   
+ATOM   1444  NE2 HIS A 188     -21.785  24.251  -9.830  1.00  0.00          N   
+ATOM   1445  N   HIS A 189     -26.993  24.045 -14.412  1.00  0.00          N   
+ATOM   1446  CA  HIS A 189     -28.031  24.708 -15.193  1.00  0.00          C   
+ATOM   1447  C   HIS A 189     -28.031  26.213 -14.944  1.00  0.00          C   
+ATOM   1448  CB  HIS A 189     -29.406  24.122 -14.865  1.00  0.00          C   
+ATOM   1449  O   HIS A 189     -27.980  26.656 -13.795  1.00  0.00          O   
+ATOM   1450  CG  HIS A 189     -29.586  22.714 -15.335  1.00  0.00          C   
+ATOM   1451  CD2 HIS A 189     -29.619  21.546 -14.652  1.00  0.00          C   
+ATOM   1452  ND1 HIS A 189     -29.755  22.390 -16.664  1.00  0.00          N   
+ATOM   1453  CE1 HIS A 189     -29.887  21.079 -16.778  1.00  0.00          C   
+ATOM   1454  NE2 HIS A 189     -29.808  20.543 -15.572  1.00  0.00          N   
+ATOM   1455  N   HIS A 190     -27.150  26.911 -15.639  1.00  0.00          N   
+ATOM   1456  CA  HIS A 190     -27.271  28.363 -15.688  1.00  0.00          C   
+ATOM   1457  C   HIS A 190     -28.733  28.796 -15.667  1.00  0.00          C   
+ATOM   1458  CB  HIS A 190     -26.577  28.917 -16.934  1.00  0.00          C   
+ATOM   1459  O   HIS A 190     -29.546  28.288 -16.443  1.00  0.00          O   
+ATOM   1460  CG  HIS A 190     -25.087  28.794 -16.896  1.00  0.00          C   
+ATOM   1461  CD2 HIS A 190     -24.243  27.997 -17.592  1.00  0.00          C   
+ATOM   1462  ND1 HIS A 190     -24.299  29.553 -16.058  1.00  0.00          N   
+ATOM   1463  CE1 HIS A 190     -23.030  29.227 -16.242  1.00  0.00          C   
+ATOM   1464  NE2 HIS A 190     -22.969  28.285 -17.168  1.00  0.00          N   
+ATOM   1465  N   HIS A 191     -29.301  28.820 -14.496  1.00  0.00          N   
+ATOM   1466  CA  HIS A 191     -30.497  29.651 -14.423  1.00  0.00          C   
+ATOM   1467  C   HIS A 191     -30.240  31.039 -15.001  1.00  0.00          C   
+ATOM   1468  CB  HIS A 191     -30.981  29.766 -12.976  1.00  0.00          C   
+ATOM   1469  O   HIS A 191     -29.144  31.584 -14.855  1.00  0.00          O   
+ATOM   1470  CG  HIS A 191     -31.644  28.528 -12.465  1.00  0.00          C   
+ATOM   1471  CD2 HIS A 191     -31.230  27.603 -11.566  1.00  0.00          C   
+ATOM   1472  ND1 HIS A 191     -32.892  28.123 -12.888  1.00  0.00          N   
+ATOM   1473  CE1 HIS A 191     -33.217  27.000 -12.270  1.00  0.00          C   
+ATOM   1474  NE2 HIS A 191     -32.226  26.664 -11.462  1.00  0.00          N   
+TER    1475      HIS A 191
+ENDMDL
+END