Starting phenix.real_space_refine
on Fri Aug 22 18:12:33 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8pb1_17580/08_2025/8pb1_17580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pb1_17580/08_2025/8pb1_17580.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pb1_17580/08_2025/8pb1_17580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pb1_17580/08_2025/8pb1_17580.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pb1_17580/08_2025/8pb1_17580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pb1_17580/08_2025/8pb1_17580.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      56      5.16       5
     C    4160      2.51       5
     N    1137      2.21       5
     O    1299      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6652
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1247
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1247
          Classifications: {'peptide': 157}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 152}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2336
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 293, 2336
          Classifications: {'peptide': 293}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 278}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 1542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1542
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 15, 'TRANS': 174}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 1420
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1420
          Classifications: {'peptide': 189}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 176}
          Chain breaks: 3
    Chain: "E"
      Number of atoms: 50
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 50
          Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.44, per 1000 atoms: 0.22
  Number of scatterers: 6652
  At special positions: 0
  Unit cell: (88.335, 131.37, 129.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      56     16.00
     O    1299      8.00
     N    1137      7.00
     C    4160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=16, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A 106 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 192 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  81 " - pdb=" SG  CYS A 119 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  92 " - pdb=" SG  CYS B 197 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  50 " - pdb=" SG  CYS B  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 167 " - pdb=" SG  CYS B 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 305 " - pdb=" SG  CYS B 331 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 311 " - pdb=" SG  CYS B 328 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  53 " - pdb=" SG  CYS C  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  81 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 194 " - pdb=" SG  CYS C 216 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  28 " - pdb=" SG  CYS D 127 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  51 " - pdb=" SG  CYS D 111 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 145 " - pdb=" SG  CYS D 156 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 186 " - pdb=" SG  CYS D 194 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    ALPHA1-3
      " BMA E   3 " - " MAN E   4 "
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG C 601 " - " ASN C 169 "
      " NAG C 602 " - " ASN C 144 "
      " NAG D 801 " - " ASN D 224 "
      " NAG D 802 " - " ASN D  48 "
      " NAG E   1 " - " ASN B 220 "
  Time building additional restraints: 0.65
  Conformation dependent library (CDL) restraints added in 359.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 18 sheets defined
      13.9% alpha, 41.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 55
      removed outlier: 4.329A  pdb=" N   GLN A  36 " --> pdb=" O   ARG A  32 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   GLU A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 81
    Processing helix  chain 'A' and resid 114 through 143
      removed outlier: 4.153A  pdb=" N   LEU A 118 " --> pdb=" O   LEU A 114 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 167
      removed outlier: 4.230A  pdb=" N   LEU A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 214
      removed outlier: 3.777A  pdb=" N   MET A 189 " --> pdb=" O   TYR A 185 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   THR A 200 " --> pdb=" O   HIS A 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 81 through 85
      removed outlier: 3.586A  pdb=" N   ALA B  85 " --> pdb=" O   PHE B  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 92
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 27
      removed outlier: 7.025A  pdb=" N   VAL B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   CYS B  90 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   HIS B  99 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   TYR B  88 " --> pdb=" O   HIS B  99 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   HIS B 101 " --> pdb=" O   GLY B  86 " (cutoff:3.500A)
      removed outlier: 6.582A  pdb=" N   GLY B  86 " --> pdb=" O   HIS B 101 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLY B  70 " --> pdb=" O   TRP B  60 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 24 through 27
      removed outlier: 7.025A  pdb=" N   VAL B  30 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   TYR B  31 " --> pdb=" O   LEU B 103 " (cutoff:3.500A)
      removed outlier: 7.894A  pdb=" N   HIS B 105 " --> pdb=" O   TYR B  31 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL B  33 " --> pdb=" O   HIS B 105 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   LYS B 107 " --> pdb=" O   VAL B  33 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL B  35 " --> pdb=" O   LYS B 107 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 44 through 49
    Processing sheet with id=AA4, first strand: chain 'B' and resid 117 through 118
      removed outlier: 4.261A  pdb=" N   LEU B 142 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 118
      removed outlier: 4.261A  pdb=" N   LEU B 142 " --> pdb=" O   LYS B 118 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   GLU B 185 " --> pdb=" O   VAL B 143 " (cutoff:3.500A)
      removed outlier: 6.027A  pdb=" N   ARG B 182 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)
      removed outlier: 6.264A  pdb=" N   VAL B 177 " --> pdb=" O   ARG B 182 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TYR B 184 " --> pdb=" O   GLU B 175 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   GLU B 175 " --> pdb=" O   TYR B 184 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   LYS B 186 " --> pdb=" O   SER B 173 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 153 through 154
    Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 243
    Processing sheet with id=AA8, first strand: chain 'B' and resid 294 through 296
    Processing sheet with id=AA9, first strand: chain 'C' and resid 47 through 54
      removed outlier: 6.495A  pdb=" N   ASP C  68 " --> pdb=" O   PRO C  48 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   ASN C  50 " --> pdb=" O   GLN C  66 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLN C  66 " --> pdb=" O   ASN C  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 96 through 101
      removed outlier: 6.038A  pdb=" N   HIS C  76 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER C 126 " --> pdb=" O   MET C 133 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   MET C 133 " --> pdb=" O   SER C 126 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 96 through 101
      removed outlier: 6.038A  pdb=" N   HIS C  76 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 156 through 160
      removed outlier: 3.574A  pdb=" N   TRP C 168 " --> pdb=" O   GLU C 214 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU C 214 " --> pdb=" O   TRP C 168 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 190 through 193
      removed outlier: 3.529A  pdb=" N   GLN C 179 " --> pdb=" O   ARG C 230 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ARG C 230 " --> pdb=" O   GLN C 179 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 31 through 36
      removed outlier: 3.708A  pdb=" N   GLN D  36 " --> pdb=" O   ASN D  48 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ASN D  48 " --> pdb=" O   GLN D  36 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 40 through 42
      removed outlier: 6.194A  pdb=" N   ILE D  41 " --> pdb=" O   GLY D 134 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   CYS D 127 " --> pdb=" O   CYS D 111 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   LEU D  70 " --> pdb=" O   ASN D  81 " (cutoff:3.500A)
      removed outlier: 5.254A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  70 " (cutoff:3.500A)
      removed outlier: 7.044A  pdb=" N   LYS D  72 " --> pdb=" O   VAL D  79 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 196 through 198
      removed outlier: 4.445A  pdb=" N   THR D 153 " --> pdb=" O   GLU D 148 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU D 148 " --> pdb=" O   THR D 153 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ASN D 159 " --> pdb=" O   ASN D 142 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   ASN D 142 " --> pdb=" O   ASN D 159 " (cutoff:3.500A)
      removed outlier: 8.791A  pdb=" N   ILE D 239 " --> pdb=" O   CYS D 145 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   GLN D 147 " --> pdb=" O   ILE D 239 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 180 through 188
      removed outlier: 3.568A  pdb=" N   GLY D 223 " --> pdb=" O   ASN D 220 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 180 through 188

    282 hydrogen bonds defined for protein.
    738 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.97

  Time building geometry restraints manager: 0.86 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.21 -     1.34: 2013
        1.34 -     1.46: 1370
        1.46 -     1.58: 3328
        1.58 -     1.70: 1
        1.70 -     1.82: 75
  Bond restraints: 6787
  Sorted by residual:
  bond pdb=" N   VAL D 146 "
       pdb=" CA  VAL D 146 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.039 1.14e-02 7.69e+03 1.17e+01
  bond pdb=" N   SER D 144 "
       pdb=" CA  SER D 144 "
    ideal  model  delta    sigma   weight residual
    1.454  1.495 -0.040 1.23e-02 6.61e+03 1.08e+01
  bond pdb=" N   VAL B 249 "
       pdb=" CA  VAL B 249 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.05e+01
  bond pdb=" N   CYS B 311 "
       pdb=" CA  CYS B 311 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.25e-02 6.40e+03 8.83e+00
  bond pdb=" N   ILE D 237 "
       pdb=" CA  ILE D 237 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.19e-02 7.06e+03 8.63e+00
  ... (remaining 6782 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 8752
        1.84 -     3.67: 358
        3.67 -     5.51: 73
        5.51 -     7.35: 13
        7.35 -     9.19: 5
  Bond angle restraints: 9201
  Sorted by residual:
  angle pdb=" N   ALA B 327 "
        pdb=" CA  ALA B 327 "
        pdb=" C   ALA B 327 "
      ideal   model   delta    sigma   weight residual
     109.85  100.66    9.19 1.58e+00 4.01e-01 3.38e+01
  angle pdb=" CA  ALA B 327 "
        pdb=" C   ALA B 327 "
        pdb=" O   ALA B 327 "
      ideal   model   delta    sigma   weight residual
     121.46  116.48    4.98 1.17e+00 7.31e-01 1.81e+01
  angle pdb=" C   GLN B 248 "
        pdb=" CA  GLN B 248 "
        pdb=" CB  GLN B 248 "
      ideal   model   delta    sigma   weight residual
     109.37  117.13   -7.76 1.91e+00 2.74e-01 1.65e+01
  angle pdb=" C   ASN B 238 "
        pdb=" N   LEU B 239 "
        pdb=" CA  LEU B 239 "
      ideal   model   delta    sigma   weight residual
     120.95  115.48    5.47 1.40e+00 5.10e-01 1.53e+01
  angle pdb=" CA  ASN B 246 "
        pdb=" C   ASN B 246 "
        pdb=" O   ASN B 246 "
      ideal   model   delta    sigma   weight residual
     121.28  116.77    4.51 1.19e+00 7.06e-01 1.44e+01
  ... (remaining 9196 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.34: 3903
       21.34 -    42.69: 296
       42.69 -    64.03: 44
       64.03 -    85.38: 13
       85.38 -   106.72: 8
  Dihedral angle restraints: 4264
    sinusoidal: 1848
      harmonic: 2416
  Sorted by residual:
  dihedral pdb=" CB  CYS A  60 "
           pdb=" SG  CYS A  60 "
           pdb=" SG  CYS A 192 "
           pdb=" CB  CYS A 192 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.40  -66.40     1      1.00e+01 1.00e-02 5.76e+01
  dihedral pdb=" CB  CYS B 305 "
           pdb=" SG  CYS B 305 "
           pdb=" SG  CYS B 331 "
           pdb=" CB  CYS B 331 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -144.02   58.02     1      1.00e+01 1.00e-02 4.52e+01
  dihedral pdb=" CB  CYS C 194 "
           pdb=" SG  CYS C 194 "
           pdb=" SG  CYS C 216 "
           pdb=" CB  CYS C 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  146.74  -53.74     1      1.00e+01 1.00e-02 3.92e+01
  ... (remaining 4261 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.111: 1006
       0.111 -    0.221: 46
       0.221 -    0.332: 6
       0.332 -    0.442: 1
       0.442 -    0.553: 1
  Chirality restraints: 1060
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 220 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.85   -0.55 2.00e-01 2.50e+01 7.65e+00
  chirality pdb=" CA  GLN B 240 "
            pdb=" N   GLN B 240 "
            pdb=" C   GLN B 240 "
            pdb=" CB  GLN B 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  ILE D 237 "
            pdb=" N   ILE D 237 "
            pdb=" C   ILE D 237 "
            pdb=" CB  ILE D 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 1057 not shown)

  Planarity restraints: 1171
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 324 "   -0.025 2.00e-02 2.50e+03   4.95e-02 2.45e+01
        pdb=" C   SER B 324 "    0.086 2.00e-02 2.50e+03
        pdb=" O   SER B 324 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   LYS B 325 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 108 "    0.046 5.00e-02 4.00e+02   6.82e-02 7.44e+00
        pdb=" N   PRO A 109 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A 109 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 109 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 325 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   LYS B 325 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LYS B 325 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TRP B 326 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1168 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1325
        2.78 -     3.31: 5767
        3.31 -     3.84: 10280
        3.84 -     4.37: 11344
        4.37 -     4.90: 20260
  Nonbonded interactions: 48976
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D 171 "
            pdb=" OE1 GLN D 185 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OG1 THR B  61 "
            pdb=" OG1 THR B  89 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OD2 ASP B 234 "
            pdb=" OG  SER B 258 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OE2 GLU B 108 "
            pdb=" OH  TYR C 143 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   SER C 171 "
            pdb=" OG  SER C 171 "
     model   vdw
     2.300 3.040
  ... (remaining 48971 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.970
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088   6811  Z= 0.276
  Angle     :  0.890  16.631   9257  Z= 0.489
  Chirality :  0.059   0.553   1060
  Planarity :  0.006   0.068   1166
  Dihedral  : 15.489 106.722   2640
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  1.19 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.29), residues: 803
  helix:  0.91 (0.54), residues: 96
  sheet:  0.23 (0.32), residues: 275
  loop : -1.67 (0.27), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 127 
 TYR   0.009   0.001   TYR A 130 
 PHE   0.009   0.001   PHE C 108 
 TRP   0.034   0.002   TRP C 123 
 HIS   0.003   0.001   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 6787)
  covalent geometry    : angle       0.86222 ( 9201)
  SS BOND              : bond        0.00363 (   16)
  SS BOND              : angle       1.26372 (   32)
  hydrogen bonds       : bond        0.10976 (  249)
  hydrogen bonds       : angle       6.56107 (  738)
  link_ALPHA1-3        : bond        0.00700 (    1)
  link_ALPHA1-3        : angle       1.47999 (    3)
  link_BETA1-4         : bond        0.00481 (    2)
  link_BETA1-4         : angle       1.70666 (    6)
  link_NAG-ASN         : bond        0.00805 (    5)
  link_NAG-ASN         : angle       5.24993 (   15)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 126
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A   56 LYS cc_start: 0.7422 (ptmm) cc_final: 0.7108 (ptpp)
REVERT: A   66 ASP cc_start: 0.8261 (m-30) cc_final: 0.8024 (m-30)
REVERT: A  164 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7572 (tp-100)
REVERT: B   44 GLU cc_start: 0.6883 (tt0) cc_final: 0.6321 (mp0)
REVERT: B   45 THR cc_start: 0.8499 (m) cc_final: 0.8161 (m)
REVERT: B  264 SER cc_start: 0.8575 (p) cc_final: 0.8363 (p)
REVERT: C  181 ARG cc_start: 0.7242 (ptp-170) cc_final: 0.6651 (ptt-90)
REVERT: D  191 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7707 (mtt90)
  outliers start: 2
  outliers final: 1
  residues processed: 128
  average time/residue: 0.0970
  time to fit residues: 16.1867
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain D residue  191 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0770
   chunk 33 optimal weight:    0.2980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.3980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.4738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
C 179 GLN
D  36 GLN
D 185 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.114029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.085903 restraints weight = 17237.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.088714 restraints weight = 9354.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.090517 restraints weight = 6525.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.091647 restraints weight = 5257.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.092316 restraints weight = 4604.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   6811  Z= 0.131
  Angle     :  0.655  15.195   9257  Z= 0.326
  Chirality :  0.043   0.262   1060
  Planarity :  0.004   0.038   1166
  Dihedral  : 10.176  77.061   1047
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  :  9.11 %
    Favored  : 89.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.64 (0.29), residues: 803
  helix:  1.64 (0.55), residues: 96
  sheet:  0.34 (0.31), residues: 282
  loop : -1.51 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  72 
 TYR   0.014   0.001   TYR A 124 
 PHE   0.013   0.001   PHE D 109 
 TRP   0.036   0.001   TRP C 123 
 HIS   0.009   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6787)
  covalent geometry    : angle       0.61941 ( 9201)
  SS BOND              : bond        0.00281 (   16)
  SS BOND              : angle       1.34087 (   32)
  hydrogen bonds       : bond        0.03970 (  249)
  hydrogen bonds       : angle       5.35495 (  738)
  link_ALPHA1-3        : bond        0.01007 (    1)
  link_ALPHA1-3        : angle       1.58477 (    3)
  link_BETA1-4         : bond        0.00580 (    2)
  link_BETA1-4         : angle       1.99653 (    6)
  link_NAG-ASN         : bond        0.00623 (    5)
  link_NAG-ASN         : angle       4.87968 (   15)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8012 (mttt) cc_final: 0.7559 (tttt)
REVERT: A   66 ASP cc_start: 0.8223 (m-30) cc_final: 0.8012 (m-30)
REVERT: A  164 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7507 (tp-100)
REVERT: B   23 MET cc_start: 0.7360 (tpt) cc_final: 0.6998 (tpt)
REVERT: B   44 GLU cc_start: 0.6940 (tt0) cc_final: 0.6347 (mp0)
REVERT: B   45 THR cc_start: 0.8490 (m) cc_final: 0.8098 (m)
REVERT: B  264 SER cc_start: 0.8517 (p) cc_final: 0.8314 (p)
REVERT: C  181 ARG cc_start: 0.7106 (ptp-170) cc_final: 0.6590 (ptt-90)
REVERT: C  223 MET cc_start: 0.6533 (ptp) cc_final: 0.6073 (ptp)
REVERT: D  189 ASP cc_start: 0.8532 (p0) cc_final: 0.6858 (p0)
REVERT: D  191 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7666 (mtt90)
  outliers start: 10
  outliers final: 5
  residues processed: 110
  average time/residue: 0.0904
  time to fit residues: 13.2055
Evaluate side-chains
  104 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   81 ASN
Chi-restraints excluded: chain D residue  143 ILE
Chi-restraints excluded: chain D residue  145 CYS
Chi-restraints excluded: chain D residue  191 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.110849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.082327 restraints weight = 17177.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.084977 restraints weight = 9687.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.086681 restraints weight = 6916.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.087741 restraints weight = 5642.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088424 restraints weight = 4980.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   6811  Z= 0.191
  Angle     :  0.683  16.129   9257  Z= 0.332
  Chirality :  0.043   0.232   1060
  Planarity :  0.004   0.040   1166
  Dihedral  :  8.605  56.365   1047
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.55 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.30), residues: 803
  helix:  1.92 (0.53), residues: 96
  sheet:  0.39 (0.32), residues: 285
  loop : -1.50 (0.28), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 213 
 TYR   0.017   0.001   TYR C  61 
 PHE   0.015   0.002   PHE C 108 
 TRP   0.018   0.002   TRP C 109 
 HIS   0.006   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 6787)
  covalent geometry    : angle       0.64317 ( 9201)
  SS BOND              : bond        0.00292 (   16)
  SS BOND              : angle       1.31545 (   32)
  hydrogen bonds       : bond        0.04156 (  249)
  hydrogen bonds       : angle       5.18012 (  738)
  link_ALPHA1-3        : bond        0.01092 (    1)
  link_ALPHA1-3        : angle       2.33089 (    3)
  link_BETA1-4         : bond        0.00376 (    2)
  link_BETA1-4         : angle       1.74321 (    6)
  link_NAG-ASN         : bond        0.00398 (    5)
  link_NAG-ASN         : angle       5.32481 (   15)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LYS cc_start: 0.8970 (ttpp) cc_final: 0.8751 (tmmt)
REVERT: A   66 ASP cc_start: 0.8370 (m-30) cc_final: 0.8061 (m-30)
REVERT: A  160 ASP cc_start: 0.8425 (m-30) cc_final: 0.8164 (m-30)
REVERT: A  164 GLN cc_start: 0.7959 (tm-30) cc_final: 0.7581 (tp-100)
REVERT: B   23 MET cc_start: 0.7638 (tpt) cc_final: 0.7181 (tpt)
REVERT: B   44 GLU cc_start: 0.7059 (tt0) cc_final: 0.6655 (mp0)
REVERT: B   45 THR cc_start: 0.8552 (m) cc_final: 0.8214 (m)
REVERT: B   58 ILE cc_start: 0.8025 (mm) cc_final: 0.7484 (mm)
REVERT: B  264 SER cc_start: 0.8550 (p) cc_final: 0.8343 (p)
REVERT: C  137 LYS cc_start: 0.8842 (mmtt) cc_final: 0.8588 (ptpp)
REVERT: D  189 ASP cc_start: 0.8177 (p0) cc_final: 0.7858 (p0)
REVERT: D  207 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.5614 (mp)
  outliers start: 15
  outliers final: 6
  residues processed: 104
  average time/residue: 0.0736
  time to fit residues: 10.7662
Evaluate side-chains
  102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  213 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.111943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.083533 restraints weight = 17464.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.086278 restraints weight = 9664.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.087985 restraints weight = 6817.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.089124 restraints weight = 5538.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.089821 restraints weight = 4860.581|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6811  Z= 0.123
  Angle     :  0.612  14.776   9257  Z= 0.297
  Chirality :  0.042   0.224   1060
  Planarity :  0.004   0.038   1166
  Dihedral  :  7.528  55.804   1043
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.80 %
    Favored  : 84.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.36 (0.30), residues: 803
  helix:  2.06 (0.54), residues: 96
  sheet:  0.58 (0.32), residues: 281
  loop : -1.41 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 183 
 TYR   0.019   0.001   TYR A 124 
 PHE   0.010   0.001   PHE A 198 
 TRP   0.011   0.001   TRP C 109 
 HIS   0.005   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6787)
  covalent geometry    : angle       0.57649 ( 9201)
  SS BOND              : bond        0.00170 (   16)
  SS BOND              : angle       0.71362 (   32)
  hydrogen bonds       : bond        0.03770 (  249)
  hydrogen bonds       : angle       4.94323 (  738)
  link_ALPHA1-3        : bond        0.01112 (    1)
  link_ALPHA1-3        : angle       2.28039 (    3)
  link_BETA1-4         : bond        0.00508 (    2)
  link_BETA1-4         : angle       1.68654 (    6)
  link_NAG-ASN         : bond        0.00427 (    5)
  link_NAG-ASN         : angle       4.91088 (   15)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8334 (m-30) cc_final: 0.8020 (m-30)
REVERT: A  126 ASP cc_start: 0.8542 (t0) cc_final: 0.8210 (t0)
REVERT: A  160 ASP cc_start: 0.8339 (m-30) cc_final: 0.7895 (m-30)
REVERT: A  164 GLN cc_start: 0.7915 (tm-30) cc_final: 0.7537 (tp-100)
REVERT: B   23 MET cc_start: 0.7921 (tpt) cc_final: 0.7489 (tpt)
REVERT: B   44 GLU cc_start: 0.6998 (tt0) cc_final: 0.6655 (mp0)
REVERT: B   58 ILE cc_start: 0.8023 (mm) cc_final: 0.7499 (mm)
REVERT: B  264 SER cc_start: 0.8512 (p) cc_final: 0.8310 (p)
REVERT: C   67 TYR cc_start: 0.7278 (t80) cc_final: 0.6563 (t80)
REVERT: D  207 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5430 (mp)
  outliers start: 7
  outliers final: 5
  residues processed: 102
  average time/residue: 0.0714
  time to fit residues: 10.2175
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  207 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0970
   chunk 65 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0000
   chunk 2 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.111453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.082661 restraints weight = 17745.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.085411 restraints weight = 9810.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.087134 restraints weight = 6922.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.088211 restraints weight = 5627.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.088927 restraints weight = 4967.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6811  Z= 0.152
  Angle     :  0.631  14.992   9257  Z= 0.304
  Chirality :  0.042   0.223   1060
  Planarity :  0.004   0.040   1166
  Dihedral  :  6.831  55.451   1043
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.19 %
    Favored  : 82.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.30), residues: 803
  helix:  1.91 (0.53), residues: 96
  sheet:  0.55 (0.32), residues: 281
  loop : -1.42 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 182 
 TYR   0.013   0.001   TYR C  61 
 PHE   0.011   0.001   PHE C 108 
 TRP   0.011   0.001   TRP C 109 
 HIS   0.004   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 6787)
  covalent geometry    : angle       0.59506 ( 9201)
  SS BOND              : bond        0.00172 (   16)
  SS BOND              : angle       0.66868 (   32)
  hydrogen bonds       : bond        0.03793 (  249)
  hydrogen bonds       : angle       4.90379 (  738)
  link_ALPHA1-3        : bond        0.01064 (    1)
  link_ALPHA1-3        : angle       2.52375 (    3)
  link_BETA1-4         : bond        0.00457 (    2)
  link_BETA1-4         : angle       1.61395 (    6)
  link_NAG-ASN         : bond        0.00354 (    5)
  link_NAG-ASN         : angle       4.99186 (   15)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.7922 (tttt) cc_final: 0.7515 (tttt)
REVERT: A   66 ASP cc_start: 0.8373 (m-30) cc_final: 0.8036 (m-30)
REVERT: A   75 THR cc_start: 0.7776 (OUTLIER) cc_final: 0.7338 (p)
REVERT: A  126 ASP cc_start: 0.8542 (t0) cc_final: 0.8168 (t0)
REVERT: A  164 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7588 (tp-100)
REVERT: B   23 MET cc_start: 0.8135 (tpt) cc_final: 0.7843 (tpt)
REVERT: B   44 GLU cc_start: 0.7044 (tt0) cc_final: 0.6666 (mp0)
REVERT: B   58 ILE cc_start: 0.8042 (mm) cc_final: 0.7749 (mm)
REVERT: B  264 SER cc_start: 0.8526 (p) cc_final: 0.8315 (p)
REVERT: C   67 TYR cc_start: 0.7371 (t80) cc_final: 0.6581 (t80)
REVERT: D  192 GLN cc_start: 0.8305 (pm20) cc_final: 0.8105 (pm20)
REVERT: D  207 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.5495 (mp)
  outliers start: 20
  outliers final: 13
  residues processed: 111
  average time/residue: 0.0703
  time to fit residues: 11.0237
Evaluate side-chains
  111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue  155 MET
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   80 CYS
Chi-restraints excluded: chain C residue  123 TRP
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  144 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  213 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 62 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 77 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 240 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.111884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.083310 restraints weight = 17841.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.086050 restraints weight = 9833.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.087816 restraints weight = 6922.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.088931 restraints weight = 5621.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.089611 restraints weight = 4938.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6811  Z= 0.132
  Angle     :  0.609  14.264   9257  Z= 0.295
  Chirality :  0.042   0.221   1060
  Planarity :  0.004   0.044   1166
  Dihedral  :  6.552  55.565   1043
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 16.25 %
    Favored  : 81.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.35 (0.30), residues: 803
  helix:  1.87 (0.53), residues: 96
  sheet:  0.61 (0.33), residues: 281
  loop : -1.38 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 182 
 TYR   0.013   0.001   TYR C  61 
 PHE   0.010   0.001   PHE C 108 
 TRP   0.009   0.001   TRP C 109 
 HIS   0.004   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6787)
  covalent geometry    : angle       0.57607 ( 9201)
  SS BOND              : bond        0.00158 (   16)
  SS BOND              : angle       0.63972 (   32)
  hydrogen bonds       : bond        0.03665 (  249)
  hydrogen bonds       : angle       4.83692 (  738)
  link_ALPHA1-3        : bond        0.01023 (    1)
  link_ALPHA1-3        : angle       2.06623 (    3)
  link_BETA1-4         : bond        0.00462 (    2)
  link_BETA1-4         : angle       1.44810 (    6)
  link_NAG-ASN         : bond        0.00335 (    5)
  link_NAG-ASN         : angle       4.76795 (   15)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8329 (m-30) cc_final: 0.7944 (m-30)
REVERT: A  126 ASP cc_start: 0.8532 (t70) cc_final: 0.8153 (t0)
REVERT: A  164 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7586 (tp-100)
REVERT: B   44 GLU cc_start: 0.7059 (tt0) cc_final: 0.6706 (mp0)
REVERT: B  264 SER cc_start: 0.8506 (p) cc_final: 0.8302 (p)
REVERT: C   67 TYR cc_start: 0.7404 (t80) cc_final: 0.6576 (t80)
REVERT: C  181 ARG cc_start: 0.7356 (ptp-170) cc_final: 0.6437 (ptt-90)
REVERT: D  207 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.5483 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0712
  time to fit residues: 10.7829
Evaluate side-chains
  101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   80 CYS
Chi-restraints excluded: chain C residue  123 TRP
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  144 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  207 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 74 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 37 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 80 optimal weight:    8.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  87 GLN
B  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.110860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.082282 restraints weight = 17769.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.084975 restraints weight = 9925.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.086705 restraints weight = 7039.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.087806 restraints weight = 5714.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.088441 restraints weight = 5043.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6811  Z= 0.161
  Angle     :  0.633  14.561   9257  Z= 0.310
  Chirality :  0.042   0.220   1060
  Planarity :  0.004   0.043   1166
  Dihedral  :  6.433  55.548   1043
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 17.04 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.30), residues: 803
  helix:  1.77 (0.53), residues: 96
  sheet:  0.49 (0.32), residues: 289
  loop : -1.41 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 183 
 TYR   0.012   0.001   TYR C  61 
 PHE   0.011   0.001   PHE C 108 
 TRP   0.048   0.002   TRP B  60 
 HIS   0.004   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6787)
  covalent geometry    : angle       0.60080 ( 9201)
  SS BOND              : bond        0.00195 (   16)
  SS BOND              : angle       0.59933 (   32)
  hydrogen bonds       : bond        0.03823 (  249)
  hydrogen bonds       : angle       4.88511 (  738)
  link_ALPHA1-3        : bond        0.00881 (    1)
  link_ALPHA1-3        : angle       1.97402 (    3)
  link_BETA1-4         : bond        0.00400 (    2)
  link_BETA1-4         : angle       1.40204 (    6)
  link_NAG-ASN         : bond        0.00280 (    5)
  link_NAG-ASN         : angle       4.89074 (   15)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8379 (m-30) cc_final: 0.8026 (m-30)
REVERT: A   75 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7437 (p)
REVERT: A  126 ASP cc_start: 0.8550 (t70) cc_final: 0.8205 (t0)
REVERT: A  164 GLN cc_start: 0.8045 (tm-30) cc_final: 0.7615 (tp-100)
REVERT: B   44 GLU cc_start: 0.7056 (tt0) cc_final: 0.6742 (mp0)
REVERT: B  264 SER cc_start: 0.8513 (p) cc_final: 0.8299 (p)
REVERT: C   67 TYR cc_start: 0.7433 (t80) cc_final: 0.6527 (t80)
REVERT: C  181 ARG cc_start: 0.7360 (ptp-170) cc_final: 0.6399 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.8490 (mm)
  outliers start: 20
  outliers final: 14
  residues processed: 106
  average time/residue: 0.0709
  time to fit residues: 10.6783
Evaluate side-chains
  104 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   80 CYS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  144 SER
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  199 LEU
Chi-restraints excluded: chain D residue  207 LEU
Chi-restraints excluded: chain D residue  213 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 34 optimal weight:    0.3980
   chunk 54 optimal weight:    0.0370
   chunk 6 optimal weight:    0.0970
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.4256

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.112333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.084114 restraints weight = 17665.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.086851 restraints weight = 9744.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.088598 restraints weight = 6873.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.089736 restraints weight = 5559.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.090433 restraints weight = 4885.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6811  Z= 0.109
  Angle     :  0.603  13.256   9257  Z= 0.293
  Chirality :  0.041   0.223   1060
  Planarity :  0.004   0.044   1166
  Dihedral  :  6.228  55.678   1043
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 17.83 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.37 (0.30), residues: 803
  helix:  1.87 (0.53), residues: 96
  sheet:  0.54 (0.32), residues: 289
  loop : -1.38 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 183 
 TYR   0.014   0.001   TYR C  61 
 PHE   0.008   0.001   PHE B 266 
 TRP   0.024   0.001   TRP B  60 
 HIS   0.003   0.000   HIS A 144 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6787)
  covalent geometry    : angle       0.57550 ( 9201)
  SS BOND              : bond        0.00168 (   16)
  SS BOND              : angle       0.61968 (   32)
  hydrogen bonds       : bond        0.03506 (  249)
  hydrogen bonds       : angle       4.71970 (  738)
  link_ALPHA1-3        : bond        0.00860 (    1)
  link_ALPHA1-3        : angle       1.52977 (    3)
  link_BETA1-4         : bond        0.00542 (    2)
  link_BETA1-4         : angle       1.30283 (    6)
  link_NAG-ASN         : bond        0.00359 (    5)
  link_NAG-ASN         : angle       4.39197 (   15)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8338 (m-30) cc_final: 0.7983 (m-30)
REVERT: A   75 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7455 (p)
REVERT: A  126 ASP cc_start: 0.8496 (t70) cc_final: 0.8149 (t0)
REVERT: A  160 ASP cc_start: 0.8368 (m-30) cc_final: 0.7980 (m-30)
REVERT: A  164 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7746 (tp-100)
REVERT: B   23 MET cc_start: 0.7377 (tpp) cc_final: 0.6799 (tpt)
REVERT: B   44 GLU cc_start: 0.6962 (tt0) cc_final: 0.6649 (mp0)
REVERT: C   67 TYR cc_start: 0.7382 (t80) cc_final: 0.6477 (t80)
REVERT: C  181 ARG cc_start: 0.7349 (ptp-170) cc_final: 0.6483 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8522 (mm)
REVERT: D  207 LEU cc_start: 0.6328 (tp) cc_final: 0.5342 (mp)
  outliers start: 14
  outliers final: 11
  residues processed: 101
  average time/residue: 0.0703
  time to fit residues: 10.1709
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   80 CYS
Chi-restraints excluded: chain C residue  123 TRP
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  199 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:   20.0000
   chunk 37 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 48 optimal weight:    0.4980
   chunk 31 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 65 optimal weight:   30.0000
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.110964 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.082511 restraints weight = 17827.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.085228 restraints weight = 9927.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.086931 restraints weight = 7025.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.088042 restraints weight = 5722.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.088712 restraints weight = 5033.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6811  Z= 0.150
  Angle     :  0.627  13.892   9257  Z= 0.306
  Chirality :  0.042   0.222   1060
  Planarity :  0.004   0.043   1166
  Dihedral  :  6.212  55.475   1043
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.63 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.40 (0.30), residues: 803
  helix:  1.80 (0.53), residues: 96
  sheet:  0.53 (0.32), residues: 294
  loop : -1.41 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 183 
 TYR   0.011   0.001   TYR C  61 
 PHE   0.010   0.001   PHE C 108 
 TRP   0.021   0.001   TRP B  60 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6787)
  covalent geometry    : angle       0.59782 ( 9201)
  SS BOND              : bond        0.00177 (   16)
  SS BOND              : angle       0.62115 (   32)
  hydrogen bonds       : bond        0.03667 (  249)
  hydrogen bonds       : angle       4.72983 (  738)
  link_ALPHA1-3        : bond        0.00748 (    1)
  link_ALPHA1-3        : angle       1.65386 (    3)
  link_BETA1-4         : bond        0.00438 (    2)
  link_BETA1-4         : angle       1.28609 (    6)
  link_NAG-ASN         : bond        0.00297 (    5)
  link_NAG-ASN         : angle       4.65071 (   15)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8352 (m-30) cc_final: 0.8005 (m-30)
REVERT: A   75 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7540 (p)
REVERT: A  126 ASP cc_start: 0.8532 (t70) cc_final: 0.8162 (t0)
REVERT: B   23 MET cc_start: 0.7423 (tpp) cc_final: 0.6844 (tpt)
REVERT: B   44 GLU cc_start: 0.7032 (tt0) cc_final: 0.6705 (mp0)
REVERT: C   67 TYR cc_start: 0.7391 (t80) cc_final: 0.6433 (t80)
REVERT: C  181 ARG cc_start: 0.7393 (ptp-170) cc_final: 0.6401 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8542 (mm)
  outliers start: 15
  outliers final: 12
  residues processed: 97
  average time/residue: 0.0650
  time to fit residues: 9.1352
Evaluate side-chains
  99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   80 CYS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain C residue  186 THR
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  199 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 50 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 69 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    0.2980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B  91 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.111962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.083640 restraints weight = 17715.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.086367 restraints weight = 9824.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088143 restraints weight = 6934.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.089245 restraints weight = 5613.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.089918 restraints weight = 4935.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6811  Z= 0.116
  Angle     :  0.615  13.266   9257  Z= 0.300
  Chirality :  0.041   0.225   1060
  Planarity :  0.004   0.044   1166
  Dihedral  :  6.147  55.672   1043
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.76 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.30), residues: 803
  helix:  1.99 (0.54), residues: 96
  sheet:  0.58 (0.32), residues: 294
  loop : -1.37 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  72 
 TYR   0.013   0.001   TYR C  61 
 PHE   0.008   0.001   PHE B 266 
 TRP   0.020   0.001   TRP B  60 
 HIS   0.003   0.001   HIS A 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6787)
  covalent geometry    : angle       0.58763 ( 9201)
  SS BOND              : bond        0.00152 (   16)
  SS BOND              : angle       0.61020 (   32)
  hydrogen bonds       : bond        0.03516 (  249)
  hydrogen bonds       : angle       4.67607 (  738)
  link_ALPHA1-3        : bond        0.00718 (    1)
  link_ALPHA1-3        : angle       1.48800 (    3)
  link_BETA1-4         : bond        0.00528 (    2)
  link_BETA1-4         : angle       1.18732 (    6)
  link_NAG-ASN         : bond        0.00352 (    5)
  link_NAG-ASN         : angle       4.41804 (   15)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1606 Ramachandran restraints generated.
    803 Oldfield, 0 Emsley, 803 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8348 (m-30) cc_final: 0.7986 (m-30)
REVERT: A   75 THR cc_start: 0.7969 (OUTLIER) cc_final: 0.7574 (p)
REVERT: A  126 ASP cc_start: 0.8515 (t70) cc_final: 0.8150 (t0)
REVERT: A  160 ASP cc_start: 0.8343 (m-30) cc_final: 0.7974 (m-30)
REVERT: B   44 GLU cc_start: 0.6993 (tt0) cc_final: 0.6718 (mp0)
REVERT: C   67 TYR cc_start: 0.7385 (t80) cc_final: 0.6476 (t80)
REVERT: C  181 ARG cc_start: 0.7357 (ptp-170) cc_final: 0.6450 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8537 (mm)
  outliers start: 14
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0684
  time to fit residues: 9.8770
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain B residue  312 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain C residue   80 CYS
Chi-restraints excluded: chain C residue  148 THR
Chi-restraints excluded: chain C residue  157 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   40 VAL
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  199 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 72 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 27 optimal weight:    0.1980
   chunk 68 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0770
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.112419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.084447 restraints weight = 17424.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.087186 restraints weight = 9612.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.088941 restraints weight = 6770.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.090038 restraints weight = 5482.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.090598 restraints weight = 4817.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6811  Z= 0.110
  Angle     :  0.614  12.810   9257  Z= 0.297
  Chirality :  0.041   0.227   1060
  Planarity :  0.004   0.042   1166
  Dihedral  :  6.052  55.668   1043
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 18.89 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.30), residues: 803
  helix:  2.11 (0.53), residues: 96
  sheet:  0.66 (0.32), residues: 292
  loop : -1.34 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 183 
 TYR   0.012   0.001   TYR C  61 
 PHE   0.008   0.001   PHE B 266 
 TRP   0.020   0.001   TRP B  60 
 HIS   0.004   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6787)
  covalent geometry    : angle       0.58974 ( 9201)
  SS BOND              : bond        0.00154 (   16)
  SS BOND              : angle       0.59138 (   32)
  hydrogen bonds       : bond        0.03434 (  249)
  hydrogen bonds       : angle       4.58682 (  738)
  link_ALPHA1-3        : bond        0.00646 (    1)
  link_ALPHA1-3        : angle       1.42025 (    3)
  link_BETA1-4         : bond        0.00538 (    2)
  link_BETA1-4         : angle       1.17746 (    6)
  link_NAG-ASN         : bond        0.00397 (    5)
  link_NAG-ASN         : angle       4.22267 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1684.72 seconds
wall clock time: 29 minutes 45.01 seconds (1785.01 seconds total)