Starting phenix.real_space_refine
on Tue Mar 11 21:44:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pb1_17580/03_2025/8pb1_17580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pb1_17580/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pb1_17580/03_2025/8pb1_17580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pb1_17580/03_2025/8pb1_17580.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pb1_17580/03_2025/8pb1_17580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pb1_17580/03_2025/8pb1_17580.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.04, per 1000 atoms: 0.91
  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: 1.73
  Conformation dependent library (CDL) restraints added in 938.2 milliseconds
  

  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: 0.90
  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: 1.94

  Time building geometry restraints manager: 2.03 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:             4.700
  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:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     21.160
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.290
-------------------------------------------------------------------------------
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   6787  Z= 0.305
  Angle     :  0.862   9.187   9201  Z= 0.484
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.034   0.002   TRP C 123 
 HIS   0.003   0.001   HIS A 144 
 PHE   0.009   0.001   PHE C 108 
 TYR   0.009   0.001   TYR A 130 
 ARG   0.010   0.001   ARG C 127 

*********************** 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  : 0.816 
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: 0.2020
  time to fit residues: 33.7159
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  : 0.731 
-------------------------------------------------------------------------------
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 68 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 63 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
D 185 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.112680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.084415 restraints weight = 17010.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.087102 restraints weight = 9398.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.088877 restraints weight = 6656.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.1230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080   6787  Z= 0.241
  Angle     :  0.631   9.340   9201  Z= 0.324
  Chirality :  0.043   0.269   1060
  Planarity :  0.004   0.039   1166
  Dihedral  : 10.233  77.112   1047
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  :  9.25 %
    Favored  : 89.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.29), residues: 803
  helix:  1.62 (0.55), residues: 96
  sheet:  0.36 (0.32), residues: 273
  loop : -1.58 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP C 123 
 HIS   0.009   0.001   HIS A 196 
 PHE   0.013   0.001   PHE C 108 
 TYR   0.015   0.001   TYR A 124 
 ARG   0.004   0.001   ARG A  72 

*********************** 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
  115 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8073 (mttt) cc_final: 0.7608 (tttt)
REVERT: A   66 ASP cc_start: 0.8325 (m-30) cc_final: 0.8101 (m-30)
REVERT: A   72 ARG cc_start: 0.8462 (mmt90) cc_final: 0.8236 (mmt90)
REVERT: A  164 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7480 (tp-100)
REVERT: B   44 GLU cc_start: 0.6966 (tt0) cc_final: 0.6374 (mp0)
REVERT: B   45 THR cc_start: 0.8514 (m) cc_final: 0.8110 (m)
REVERT: B  264 SER cc_start: 0.8517 (p) cc_final: 0.8315 (p)
REVERT: C  181 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.6593 (ptt-90)
REVERT: D  189 ASP cc_start: 0.8548 (p0) cc_final: 0.6841 (p0)
REVERT: D  191 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7653 (mtt90)
  outliers start: 11
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1897
  time to fit residues: 28.2744
Evaluate side-chains
  106 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   81 ASN
Chi-restraints excluded: chain D residue  144 SER
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 38 optimal weight:    0.9980
   chunk 77 optimal weight:    4.9990
   chunk 22 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.2980
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 68 optimal weight:    7.9990
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
C 199 ASN
D  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.111233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.082644 restraints weight = 17492.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.085367 restraints weight = 9753.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.087073 restraints weight = 6904.745|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6787  Z= 0.264
  Angle     :  0.619   9.275   9201  Z= 0.313
  Chirality :  0.043   0.228   1060
  Planarity :  0.004   0.041   1166
  Dihedral  :  8.801  57.247   1047
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 12.95 %
    Favored  : 85.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.29), residues: 803
  helix:  1.87 (0.53), residues: 96
  sheet:  0.36 (0.32), residues: 284
  loop : -1.50 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 109 
 HIS   0.006   0.001   HIS A 196 
 PHE   0.013   0.001   PHE C 108 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.004   0.000   ARG A  72 

*********************** 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
  114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8762 (tmmt)
REVERT: A   66 ASP cc_start: 0.8391 (m-30) cc_final: 0.8103 (m-30)
REVERT: A  160 ASP cc_start: 0.8380 (m-30) cc_final: 0.8133 (m-30)
REVERT: A  164 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7521 (tp-100)
REVERT: B   23 MET cc_start: 0.7717 (tpt) cc_final: 0.7329 (tpt)
REVERT: B   44 GLU cc_start: 0.7058 (tt0) cc_final: 0.6524 (mp0)
REVERT: B   45 THR cc_start: 0.8568 (m) cc_final: 0.8208 (m)
REVERT: B  264 SER cc_start: 0.8495 (p) cc_final: 0.8282 (p)
REVERT: C  137 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8597 (ptpp)
  outliers start: 13
  outliers final: 6
  residues processed: 108
  average time/residue: 0.1636
  time to fit residues: 24.5257
Evaluate side-chains
  103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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 C residue  190 THR
Chi-restraints excluded: chain D residue   50 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 37 optimal weight:    0.3980
   chunk 20 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
B 240 GLN
C 199 ASN
** D  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.111888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.083352 restraints weight = 17632.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.086096 restraints weight = 9757.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.087832 restraints weight = 6884.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6787  Z= 0.187
  Angle     :  0.581   9.365   9201  Z= 0.290
  Chirality :  0.042   0.224   1060
  Planarity :  0.004   0.039   1166
  Dihedral  :  7.635  55.741   1043
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 14.93 %
    Favored  : 84.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.30), residues: 803
  helix:  2.06 (0.54), residues: 96
  sheet:  0.53 (0.32), residues: 281
  loop : -1.40 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 109 
 HIS   0.005   0.001   HIS A 196 
 PHE   0.009   0.001   PHE C 108 
 TYR   0.019   0.001   TYR A 124 
 ARG   0.003   0.000   ARG A  72 

*********************** 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
  109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.692 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8377 (m-30) cc_final: 0.8056 (m-30)
REVERT: A  126 ASP cc_start: 0.8502 (t0) cc_final: 0.8158 (t0)
REVERT: A  160 ASP cc_start: 0.8341 (m-30) cc_final: 0.7933 (m-30)
REVERT: A  164 GLN cc_start: 0.7893 (tm-30) cc_final: 0.7503 (tp-100)
REVERT: B   23 MET cc_start: 0.8003 (tpt) cc_final: 0.7614 (tpt)
REVERT: B   44 GLU cc_start: 0.7061 (tt0) cc_final: 0.6649 (mp0)
REVERT: B  264 SER cc_start: 0.8536 (p) cc_final: 0.8334 (p)
REVERT: C   67 TYR cc_start: 0.7320 (t80) cc_final: 0.6591 (t80)
REVERT: D  189 ASP cc_start: 0.8326 (p0) cc_final: 0.7734 (p0)
  outliers start: 8
  outliers final: 6
  residues processed: 107
  average time/residue: 0.1566
  time to fit residues: 23.4518
Evaluate side-chains
  103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
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  144 SER
Chi-restraints excluded: chain D residue  163 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 66 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    0.3980
   chunk 32 optimal weight:    0.4980
   chunk 25 optimal weight:    0.4980
   chunk 60 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0570
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
D  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.112933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.084637 restraints weight = 17343.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.087421 restraints weight = 9544.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.089145 restraints weight = 6690.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6787  Z= 0.153
  Angle     :  0.582   9.508   9201  Z= 0.287
  Chirality :  0.042   0.228   1060
  Planarity :  0.004   0.038   1166
  Dihedral  :  6.833  55.636   1043
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 15.98 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.30), residues: 803
  helix:  2.07 (0.54), residues: 96
  sheet:  0.63 (0.32), residues: 281
  loop : -1.41 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 109 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.008   0.001   PHE B 294 
 TYR   0.021   0.001   TYR A 124 
 ARG   0.003   0.000   ARG A  72 

*********************** 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
  113 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.7824 (tttt) cc_final: 0.7427 (tttt)
REVERT: A   66 ASP cc_start: 0.8357 (m-30) cc_final: 0.8038 (m-30)
REVERT: A  126 ASP cc_start: 0.8496 (t0) cc_final: 0.8140 (t0)
REVERT: A  164 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7582 (tp-100)
REVERT: B   44 GLU cc_start: 0.6988 (tt0) cc_final: 0.6603 (mp0)
REVERT: C   67 TYR cc_start: 0.7339 (t80) cc_final: 0.6509 (t80)
REVERT: C  223 MET cc_start: 0.6508 (ptp) cc_final: 0.6044 (ptp)
REVERT: D  207 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.5531 (mp)
  outliers start: 13
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1529
  time to fit residues: 23.7949
Evaluate side-chains
  102 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  123 TRP
Chi-restraints excluded: chain C residue  148 THR
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  207 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   chunk 57 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.112027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.083655 restraints weight = 17581.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.086382 restraints weight = 9735.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088105 restraints weight = 6882.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.2037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6787  Z= 0.204
  Angle     :  0.583   9.383   9201  Z= 0.292
  Chirality :  0.042   0.223   1060
  Planarity :  0.004   0.038   1166
  Dihedral  :  6.594  55.553   1043
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.78 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.30), residues: 803
  helix:  2.16 (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
 TRP   0.046   0.002   TRP B  60 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.012   0.001   PHE D 212 
 TYR   0.023   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

*********************** 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
  111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8371 (m-30) cc_final: 0.8020 (m-30)
REVERT: A   75 THR cc_start: 0.7788 (OUTLIER) cc_final: 0.7370 (p)
REVERT: A  126 ASP cc_start: 0.8539 (t70) cc_final: 0.8158 (t0)
REVERT: A  153 LYS cc_start: 0.8762 (mppt) cc_final: 0.8467 (mmmt)
REVERT: A  164 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7597 (tp-100)
REVERT: B   23 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7473 (tpt)
REVERT: B   44 GLU cc_start: 0.7062 (tt0) cc_final: 0.6716 (mp0)
REVERT: C   67 TYR cc_start: 0.7361 (t80) cc_final: 0.6512 (t80)
REVERT: D  207 LEU cc_start: 0.6555 (tp) cc_final: 0.5579 (mp)
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1482
  time to fit residues: 22.3791
Evaluate side-chains
  103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue   23 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 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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 76 optimal weight:    4.9990
   chunk 41 optimal weight:    8.9990
   chunk 55 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0670
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.112301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.083912 restraints weight = 17419.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.086653 restraints weight = 9651.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.088410 restraints weight = 6805.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6787  Z= 0.188
  Angle     :  0.586   9.382   9201  Z= 0.290
  Chirality :  0.042   0.223   1060
  Planarity :  0.004   0.045   1166
  Dihedral  :  6.357  55.537   1043
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.44 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.30), residues: 803
  helix:  2.12 (0.54), residues: 96
  sheet:  0.53 (0.32), residues: 289
  loop : -1.44 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  60 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.009   0.001   PHE C 180 
 TYR   0.026   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

*********************** 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
  107 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.799 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8376 (m-30) cc_final: 0.7985 (m-30)
REVERT: A   75 THR cc_start: 0.7960 (OUTLIER) cc_final: 0.7546 (p)
REVERT: A  126 ASP cc_start: 0.8520 (t70) cc_final: 0.8178 (t0)
REVERT: A  153 LYS cc_start: 0.8804 (mppt) cc_final: 0.8475 (mmmt)
REVERT: A  160 ASP cc_start: 0.8357 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  164 GLN cc_start: 0.8027 (tm-30) cc_final: 0.7799 (tp-100)
REVERT: B   44 GLU cc_start: 0.7060 (tt0) cc_final: 0.6704 (mp0)
REVERT: C   67 TYR cc_start: 0.7323 (t80) cc_final: 0.6433 (t80)
REVERT: C  181 ARG cc_start: 0.7323 (ptp-170) cc_final: 0.6432 (ptt-90)
REVERT: D  207 LEU cc_start: 0.6437 (tp) cc_final: 0.5525 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 104
  average time/residue: 0.1608
  time to fit residues: 23.6580
Evaluate side-chains
  103 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 68 optimal weight:    6.9990
   chunk 71 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0370
   chunk 38 optimal weight:    2.9990
   overall best weight:    1.5864

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.109822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.081009 restraints weight = 17814.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.083678 restraints weight = 10031.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.085372 restraints weight = 7166.704|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   6787  Z= 0.334
  Angle     :  0.653   9.266   9201  Z= 0.328
  Chirality :  0.043   0.217   1060
  Planarity :  0.004   0.043   1166
  Dihedral  :  6.447  56.156   1043
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.30), residues: 803
  helix:  1.77 (0.52), residues: 96
  sheet:  0.48 (0.32), residues: 291
  loop : -1.47 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  60 
 HIS   0.004   0.001   HIS B 105 
 PHE   0.016   0.002   PHE C 180 
 TYR   0.026   0.002   TYR A 124 
 ARG   0.004   0.001   ARG B 213 

*********************** 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
  111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.732 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.7717 (tttt) cc_final: 0.7514 (tttm)
REVERT: A   66 ASP cc_start: 0.8447 (m-30) cc_final: 0.8081 (m-30)
REVERT: A   75 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7715 (p)
REVERT: A  164 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7800 (tp-100)
REVERT: B   23 MET cc_start: 0.7746 (tpt) cc_final: 0.7365 (tpt)
REVERT: B   44 GLU cc_start: 0.7139 (tt0) cc_final: 0.6740 (mp0)
REVERT: C   67 TYR cc_start: 0.7410 (t80) cc_final: 0.6464 (t80)
REVERT: C  181 ARG cc_start: 0.7375 (ptp-170) cc_final: 0.6265 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8545 (mm)
REVERT: D  207 LEU cc_start: 0.6473 (tp) cc_final: 0.5398 (mp)
  outliers start: 16
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1531
  time to fit residues: 23.3945
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.742 
-------------------------------------------------------------------------------
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0370
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    0.0570
   chunk 30 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.3176

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.112130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.083866 restraints weight = 17551.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.086595 restraints weight = 9724.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.088359 restraints weight = 6862.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.2321

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6787  Z= 0.162
  Angle     :  0.627  10.247   9201  Z= 0.306
  Chirality :  0.042   0.223   1060
  Planarity :  0.004   0.045   1166
  Dihedral  :  6.276  55.698   1043
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.55 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.30), residues: 803
  helix:  1.83 (0.53), residues: 96
  sheet:  0.63 (0.32), residues: 290
  loop : -1.42 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  60 
 HIS   0.003   0.000   HIS A 144 
 PHE   0.008   0.001   PHE B 266 
 TYR   0.024   0.001   TYR A 124 
 ARG   0.003   0.000   ARG A  72 

*********************** 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: 13
    poor density    : 87
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.7850 (ttp) cc_final: 0.7318 (ttt)
REVERT: A   66 ASP cc_start: 0.8375 (m-30) cc_final: 0.7997 (m-30)
REVERT: A   75 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7674 (p)
REVERT: A  164 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7786 (tp-100)
REVERT: B   23 MET cc_start: 0.7750 (tpt) cc_final: 0.7386 (tpt)
REVERT: B   44 GLU cc_start: 0.7023 (tt0) cc_final: 0.6709 (mp0)
REVERT: C   67 TYR cc_start: 0.7359 (t80) cc_final: 0.6542 (t80)
REVERT: C  181 ARG cc_start: 0.7253 (ptp-170) cc_final: 0.6349 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8525 (mm)
REVERT: D  207 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5404 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1493
  time to fit residues: 21.1206
Evaluate side-chains
  98 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain D residue  207 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 78 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 51 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6582

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.111432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.083046 restraints weight = 17996.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.085828 restraints weight = 9729.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.087621 restraints weight = 6797.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6787  Z= 0.191
  Angle     :  0.609  10.958   9201  Z= 0.302
  Chirality :  0.043   0.369   1060
  Planarity :  0.004   0.044   1166
  Dihedral  :  6.191  55.624   1043
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 19.15 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.30), residues: 803
  helix:  1.82 (0.52), residues: 96
  sheet:  0.61 (0.32), residues: 292
  loop : -1.40 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  60 
 HIS   0.003   0.000   HIS A 144 
 PHE   0.009   0.001   PHE C 108 
 TYR   0.026   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

********************** 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
  101 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.836 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8409 (m-30) cc_final: 0.8030 (m-30)
REVERT: A   75 THR cc_start: 0.8111 (OUTLIER) cc_final: 0.7725 (p)
REVERT: A  164 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7806 (tp-100)
REVERT: B   23 MET cc_start: 0.7783 (tpt) cc_final: 0.7397 (tpt)
REVERT: B   44 GLU cc_start: 0.7040 (tt0) cc_final: 0.6681 (mp0)
REVERT: B  180 ASP cc_start: 0.7076 (t0) cc_final: 0.6049 (t0)
REVERT: B  181 GLN cc_start: 0.8677 (mp10) cc_final: 0.8217 (pp30)
REVERT: C   67 TYR cc_start: 0.7506 (t80) cc_final: 0.6523 (t80)
REVERT: C  181 ARG cc_start: 0.7323 (ptp-170) cc_final: 0.6427 (ptt-90)
REVERT: D  199 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8534 (mm)
REVERT: D  207 LEU cc_start: 0.6523 (OUTLIER) cc_final: 0.5507 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1554
  time to fit residues: 21.8812
Evaluate side-chains
  98 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain D residue  207 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 68 optimal weight:    6.9990
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    1.1122

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.110548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.082165 restraints weight = 17870.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.084836 restraints weight = 9939.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.086543 restraints weight = 7045.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6787  Z= 0.251
  Angle     :  0.631  10.060   9201  Z= 0.312
  Chirality :  0.043   0.302   1060
  Planarity :  0.004   0.046   1166
  Dihedral  :  6.234  55.469   1043
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 19.55 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.42 (0.30), residues: 803
  helix:  1.79 (0.52), residues: 96
  sheet:  0.52 (0.32), residues: 294
  loop : -1.44 (0.29), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  60 
 HIS   0.003   0.001   HIS A 168 
 PHE   0.011   0.001   PHE C 108 
 TYR   0.027   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2762.63 seconds
wall clock time: 48 minutes 35.59 seconds (2915.59 seconds total)