Starting phenix.real_space_refine
on Sat May 10 18:46:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pb1_17580/05_2025/8pb1_17580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pb1_17580/05_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_17580/05_2025/8pb1_17580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pb1_17580/05_2025/8pb1_17580.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pb1_17580/05_2025/8pb1_17580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pb1_17580/05_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-5687/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: 5.42, per 1000 atoms: 0.81
  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: 1.67
  Conformation dependent library (CDL) restraints added in 872.0 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: 0.82
  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: 1.88

  Time building geometry restraints manager: 1.92 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:             4.470
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     19.540
  Find NCS groups from input model:        0.060
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.390
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.718 
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: 0.1937
  time to fit residues: 32.2092
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  : 0.717 
-------------------------------------------------------------------------------
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:    0.9990
   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:    0.9584

-------------------------------------------------------------------------------
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 = 0.112695 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.084428 restraints weight = 17010.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.087190 restraints weight = 9397.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.088908 restraints weight = 6609.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   6811  Z= 0.160
  Angle     :  0.671  15.788   9257  Z= 0.334
  Chirality :  0.043   0.271   1060
  Planarity :  0.004   0.039   1166
  Dihedral  : 10.222  76.816   1047
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.01
  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   0.038   0.002   TRP C 123 
 HIS   0.009   0.001   HIS A 196 
 PHE   0.013   0.001   PHE C 108 
 TYR   0.014   0.001   TYR A 124 
 ARG   0.004   0.001   ARG A  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00574 (    5)
  link_NAG-ASN         : angle       5.08418 (   15)
  link_BETA1-4         : bond        0.00710 (    2)
  link_BETA1-4         : angle       1.83622 (    6)
  link_ALPHA1-3        : bond        0.01163 (    1)
  link_ALPHA1-3        : angle       1.65899 (    3)
  hydrogen bonds       : bond        0.04123 (  249)
  hydrogen bonds       : angle       5.39373 (  738)
  SS BOND              : bond        0.00388 (   16)
  SS BOND              : angle       1.55023 (   32)
  covalent geometry    : bond        0.00379 ( 6787)
  covalent geometry    : angle       0.63169 ( 9201)

*********************** 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  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.8070 (mttt) cc_final: 0.7602 (tttt)
REVERT: A   66 ASP cc_start: 0.8324 (m-30) cc_final: 0.8099 (m-30)
REVERT: A   72 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8236 (mmt90)
REVERT: A  164 GLN cc_start: 0.7851 (tm-30) cc_final: 0.7481 (tp-100)
REVERT: B   44 GLU cc_start: 0.6965 (tt0) cc_final: 0.6380 (mp0)
REVERT: B   45 THR cc_start: 0.8513 (m) cc_final: 0.8109 (m)
REVERT: B  264 SER cc_start: 0.8516 (p) cc_final: 0.8313 (p)
REVERT: C  181 ARG cc_start: 0.7248 (ptp-170) cc_final: 0.6592 (ptt-90)
REVERT: D  189 ASP cc_start: 0.8547 (p0) cc_final: 0.6843 (p0)
REVERT: D  191 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7653 (mtt90)
  outliers start: 11
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1869
  time to fit residues: 28.0588
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  : 0.812 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 44 optimal weight:    0.5980
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.111857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.083286 restraints weight = 17470.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.086035 restraints weight = 9698.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.087804 restraints weight = 6853.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   6811  Z= 0.156
  Angle     :  0.646  15.498   9257  Z= 0.316
  Chirality :  0.042   0.232   1060
  Planarity :  0.004   0.040   1166
  Dihedral  :  8.908  59.428   1047
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.29 %
    Favored  : 86.13 %
  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: -0.54 (0.29), residues: 803
  helix:  1.86 (0.54), residues: 96
  sheet:  0.39 (0.32), residues: 282
  loop : -1.47 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 109 
 HIS   0.006   0.001   HIS A 196 
 PHE   0.012   0.001   PHE C 108 
 TYR   0.016   0.001   TYR C  61 
 ARG   0.004   0.000   ARG A  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00455 (    5)
  link_NAG-ASN         : angle       5.08067 (   15)
  link_BETA1-4         : bond        0.00590 (    2)
  link_BETA1-4         : angle       1.75014 (    6)
  link_ALPHA1-3        : bond        0.01125 (    1)
  link_ALPHA1-3        : angle       2.04250 (    3)
  hydrogen bonds       : bond        0.04002 (  249)
  hydrogen bonds       : angle       5.17008 (  738)
  SS BOND              : bond        0.00268 (   16)
  SS BOND              : angle       1.30808 (   32)
  covalent geometry    : bond        0.00365 ( 6787)
  covalent geometry    : angle       0.60654 ( 9201)

*********************** 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: 12
    poor density    : 101
  time to evaluate  : 0.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LYS cc_start: 0.8961 (ttpp) cc_final: 0.8751 (tmmt)
REVERT: A   66 ASP cc_start: 0.8354 (m-30) cc_final: 0.8059 (m-30)
REVERT: A  164 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7466 (tp-100)
REVERT: B   44 GLU cc_start: 0.7054 (tt0) cc_final: 0.6421 (mp0)
REVERT: B  264 SER cc_start: 0.8510 (p) cc_final: 0.8302 (p)
REVERT: C  137 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8575 (ptpp)
REVERT: C  181 ARG cc_start: 0.7274 (ptp-170) cc_final: 0.6676 (ptt-90)
  outliers start: 12
  outliers final: 7
  residues processed: 108
  average time/residue: 0.1624
  time to fit residues: 24.3349
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  : 0.802 
-------------------------------------------------------------------------------
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  249 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue  145 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 70 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 22 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 20 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** D  36 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.110464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.081702 restraints weight = 17632.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084431 restraints weight = 9863.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.086159 restraints weight = 7005.225|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   6811  Z= 0.185
  Angle     :  0.656  15.755   9257  Z= 0.322
  Chirality :  0.043   0.219   1060
  Planarity :  0.004   0.041   1166
  Dihedral  :  7.704  56.303   1043
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.40 %
    Favored  : 83.88 %
  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: -0.50 (0.30), residues: 803
  helix:  1.94 (0.53), residues: 96
  sheet:  0.42 (0.32), residues: 283
  loop : -1.46 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 109 
 HIS   0.005   0.001   HIS A 196 
 PHE   0.013   0.002   PHE C 180 
 TYR   0.019   0.001   TYR A 124 
 ARG   0.004   0.001   ARG A  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00350 (    5)
  link_NAG-ASN         : angle       5.20810 (   15)
  link_BETA1-4         : bond        0.00425 (    2)
  link_BETA1-4         : angle       1.59140 (    6)
  link_ALPHA1-3        : bond        0.01065 (    1)
  link_ALPHA1-3        : angle       2.48438 (    3)
  hydrogen bonds       : bond        0.04094 (  249)
  hydrogen bonds       : angle       5.07691 (  738)
  SS BOND              : bond        0.00273 (   16)
  SS BOND              : angle       1.27357 (   32)
  covalent geometry    : bond        0.00437 ( 6787)
  covalent geometry    : angle       0.61576 ( 9201)

*********************** 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
  114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8429 (m-30) cc_final: 0.8098 (m-30)
REVERT: A  160 ASP cc_start: 0.8395 (m-30) cc_final: 0.8193 (m-30)
REVERT: A  164 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7547 (tp-100)
REVERT: B   23 MET cc_start: 0.8080 (tpt) cc_final: 0.7722 (tpt)
REVERT: B   44 GLU cc_start: 0.7071 (tt0) cc_final: 0.6678 (mp0)
REVERT: B  264 SER cc_start: 0.8531 (p) cc_final: 0.8322 (p)
  outliers start: 13
  outliers final: 8
  residues processed: 106
  average time/residue: 0.1571
  time to fit residues: 23.3911
Evaluate side-chains
  105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain D residue  145 CYS
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:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0980
   chunk 8 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0970
   chunk 25 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 31 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.4378

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

Flipped N/Q/H residues before XYZ refinement:
B 240 GLN
D  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.112209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.083743 restraints weight = 17403.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.086529 restraints weight = 9625.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.088269 restraints weight = 6757.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6811  Z= 0.111
  Angle     :  0.620  14.175   9257  Z= 0.299
  Chirality :  0.042   0.223   1060
  Planarity :  0.004   0.037   1166
  Dihedral  :  6.928  55.658   1043
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 16.25 %
    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: -0.38 (0.30), residues: 803
  helix:  2.05 (0.53), residues: 96
  sheet:  0.52 (0.32), residues: 281
  loop : -1.38 (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 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00454 (    5)
  link_NAG-ASN         : angle       4.66476 (   15)
  link_BETA1-4         : bond        0.00533 (    2)
  link_BETA1-4         : angle       1.68292 (    6)
  link_ALPHA1-3        : bond        0.01198 (    1)
  link_ALPHA1-3        : angle       2.30810 (    3)
  hydrogen bonds       : bond        0.03648 (  249)
  hydrogen bonds       : angle       4.85363 (  738)
  SS BOND              : bond        0.00253 (   16)
  SS BOND              : angle       1.17225 (   32)
  covalent geometry    : bond        0.00254 ( 6787)
  covalent geometry    : angle       0.58593 ( 9201)

*********************** 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
  111 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 LYS cc_start: 0.8965 (tmmt) cc_final: 0.8726 (ttpp)
REVERT: A   54 LYS cc_start: 0.7908 (tttt) cc_final: 0.7383 (tttt)
REVERT: A   66 ASP cc_start: 0.8363 (m-30) cc_final: 0.8011 (m-30)
REVERT: A  164 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7542 (tp-100)
REVERT: B   23 MET cc_start: 0.8130 (tpt) cc_final: 0.7921 (tpt)
REVERT: B   44 GLU cc_start: 0.7017 (tt0) cc_final: 0.6655 (mp0)
REVERT: C   67 TYR cc_start: 0.7355 (t80) cc_final: 0.6523 (t80)
REVERT: D  147 GLN cc_start: 0.4804 (tm-30) cc_final: 0.4415 (tm-30)
REVERT: D  189 ASP cc_start: 0.8314 (p0) cc_final: 0.7757 (p0)
  outliers start: 11
  outliers final: 7
  residues processed: 107
  average time/residue: 0.1621
  time to fit residues: 24.3427
Evaluate side-chains
  100 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 VAL
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  145 CYS
Chi-restraints excluded: chain D residue  163 VAL
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:    0.0870
   chunk 70 optimal weight:    8.9990
   chunk 2 optimal weight:    0.9990
   chunk 69 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 78 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7158

-------------------------------------------------------------------------------
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 = 0.3931 r_free = 0.3931 target = 0.111924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.083564 restraints weight = 17537.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.086281 restraints weight = 9688.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.088039 restraints weight = 6851.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6811  Z= 0.129
  Angle     :  0.626  14.235   9257  Z= 0.304
  Chirality :  0.042   0.225   1060
  Planarity :  0.004   0.037   1166
  Dihedral  :  6.669  55.568   1043
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.64 %
    Favored  : 80.85 %
  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: -0.39 (0.30), residues: 803
  helix:  2.13 (0.53), residues: 96
  sheet:  0.52 (0.32), residues: 281
  loop : -1.43 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP B  60 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.009   0.001   PHE C 108 
 TYR   0.021   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00398 (    5)
  link_NAG-ASN         : angle       4.71752 (   15)
  link_BETA1-4         : bond        0.00509 (    2)
  link_BETA1-4         : angle       1.58566 (    6)
  link_ALPHA1-3        : bond        0.01011 (    1)
  link_ALPHA1-3        : angle       2.09293 (    3)
  hydrogen bonds       : bond        0.03611 (  249)
  hydrogen bonds       : angle       4.86566 (  738)
  SS BOND              : bond        0.00224 (   16)
  SS BOND              : angle       1.13662 (   32)
  covalent geometry    : bond        0.00301 ( 6787)
  covalent geometry    : angle       0.59229 ( 9201)

*********************** 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
  114 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8356 (m-30) cc_final: 0.7991 (m-30)
REVERT: A   75 THR cc_start: 0.7772 (OUTLIER) cc_final: 0.7328 (p)
REVERT: A  160 ASP cc_start: 0.8340 (m-30) cc_final: 0.8016 (m-30)
REVERT: A  164 GLN cc_start: 0.7982 (tm-30) cc_final: 0.7560 (tp-100)
REVERT: B   23 MET cc_start: 0.8229 (tpt) cc_final: 0.8001 (tpt)
REVERT: B   44 GLU cc_start: 0.7027 (tt0) cc_final: 0.6673 (mp0)
REVERT: C   67 TYR cc_start: 0.7357 (t80) cc_final: 0.6535 (t80)
REVERT: D  207 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.5701 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 109
  average time/residue: 0.1629
  time to fit residues: 25.3535
Evaluate side-chains
  105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
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  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  145 CYS
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 68 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 47 optimal weight:    0.8980
   chunk 35 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 196 HIS
B  91 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.111849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.083511 restraints weight = 17414.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.086210 restraints weight = 9690.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.087951 restraints weight = 6873.248|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6811  Z= 0.133
  Angle     :  0.640  14.037   9257  Z= 0.309
  Chirality :  0.042   0.223   1060
  Planarity :  0.004   0.044   1166
  Dihedral  :  6.451  55.553   1043
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  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: -0.43 (0.30), residues: 803
  helix:  2.11 (0.54), residues: 96
  sheet:  0.49 (0.32), residues: 283
  loop : -1.46 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  60 
 HIS   0.004   0.001   HIS A 196 
 PHE   0.020   0.001   PHE D 212 
 TYR   0.024   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00352 (    5)
  link_NAG-ASN         : angle       4.67487 (   15)
  link_BETA1-4         : bond        0.00461 (    2)
  link_BETA1-4         : angle       1.45834 (    6)
  link_ALPHA1-3        : bond        0.00906 (    1)
  link_ALPHA1-3        : angle       1.90153 (    3)
  hydrogen bonds       : bond        0.03580 (  249)
  hydrogen bonds       : angle       4.84030 (  738)
  SS BOND              : bond        0.00239 (   16)
  SS BOND              : angle       1.18272 (   32)
  covalent geometry    : bond        0.00312 ( 6787)
  covalent geometry    : angle       0.60787 ( 9201)

*********************** 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
  112 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8362 (m-30) cc_final: 0.7978 (m-30)
REVERT: A   75 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7450 (p)
REVERT: A  164 GLN cc_start: 0.8030 (tm-30) cc_final: 0.7593 (tp-100)
REVERT: B   23 MET cc_start: 0.8233 (tpt) cc_final: 0.7850 (tpp)
REVERT: B   44 GLU cc_start: 0.7048 (tt0) cc_final: 0.6656 (mp0)
REVERT: C   67 TYR cc_start: 0.7358 (t80) cc_final: 0.6505 (t80)
REVERT: D  207 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.5815 (mp)
  outliers start: 15
  outliers final: 12
  residues processed: 108
  average time/residue: 0.1569
  time to fit residues: 23.9843
Evaluate side-chains
  105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
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  157 VAL
Chi-restraints excluded: chain C residue  184 MET
Chi-restraints excluded: chain D residue   50 SER
Chi-restraints excluded: chain D residue   81 ASN
Chi-restraints excluded: chain D residue  124 VAL
Chi-restraints excluded: chain D residue  145 CYS
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  207 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 12 optimal weight:    0.3980
   chunk 19 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 68 optimal weight:    9.9990
   chunk 71 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.111341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082869 restraints weight = 17638.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.085595 restraints weight = 9820.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.087329 restraints weight = 6955.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6811  Z= 0.139
  Angle     :  0.642  13.998   9257  Z= 0.311
  Chirality :  0.042   0.224   1060
  Planarity :  0.004   0.042   1166
  Dihedral  :  6.340  55.505   1043
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.10 %
    Favored  : 79.66 %
  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: -0.45 (0.30), residues: 803
  helix:  2.06 (0.53), residues: 96
  sheet:  0.41 (0.32), residues: 289
  loop : -1.44 (0.29), residues: 418

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   0.010   0.001   PHE C 108 
 TYR   0.028   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    5)
  link_NAG-ASN         : angle       4.67936 (   15)
  link_BETA1-4         : bond        0.00456 (    2)
  link_BETA1-4         : angle       1.35875 (    6)
  link_ALPHA1-3        : bond        0.00878 (    1)
  link_ALPHA1-3        : angle       1.78323 (    3)
  hydrogen bonds       : bond        0.03603 (  249)
  hydrogen bonds       : angle       4.83067 (  738)
  SS BOND              : bond        0.00234 (   16)
  SS BOND              : angle       1.16867 (   32)
  covalent geometry    : bond        0.00328 ( 6787)
  covalent geometry    : angle       0.60989 ( 9201)

*********************** 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
  109 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8374 (m-30) cc_final: 0.7993 (m-30)
REVERT: A   75 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7535 (p)
REVERT: A  164 GLN cc_start: 0.7993 (tm-30) cc_final: 0.7741 (tp-100)
REVERT: A  186 ARG cc_start: 0.6454 (ptt-90) cc_final: 0.6077 (ptt-90)
REVERT: B   44 GLU cc_start: 0.7060 (tt0) cc_final: 0.6691 (mp0)
REVERT: C   67 TYR cc_start: 0.7352 (t80) cc_final: 0.6531 (t80)
  outliers start: 17
  outliers final: 13
  residues processed: 105
  average time/residue: 0.1579
  time to fit residues: 23.7271
Evaluate side-chains
  105 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 91
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
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  145 CYS
Chi-restraints excluded: chain D residue  163 VAL
Chi-restraints excluded: chain D residue  207 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:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0000
   chunk 28 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    0.4984

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.112131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.083955 restraints weight = 17591.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.086682 restraints weight = 9767.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.088425 restraints weight = 6875.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6811  Z= 0.115
  Angle     :  0.633  13.295   9257  Z= 0.308
  Chirality :  0.042   0.227   1060
  Planarity :  0.004   0.042   1166
  Dihedral  :  6.228  55.685   1043
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 18.76 %
    Favored  : 79.66 %
  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: -0.40 (0.30), residues: 803
  helix:  2.07 (0.54), residues: 96
  sheet:  0.48 (0.32), residues: 289
  loop : -1.43 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  60 
 HIS   0.003   0.000   HIS A 144 
 PHE   0.012   0.001   PHE D 212 
 TYR   0.026   0.001   TYR A 124 
 ARG   0.003   0.000   ARG A  72 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00383 (    5)
  link_NAG-ASN         : angle       4.40269 (   15)
  link_BETA1-4         : bond        0.00515 (    2)
  link_BETA1-4         : angle       1.26613 (    6)
  link_ALPHA1-3        : bond        0.00827 (    1)
  link_ALPHA1-3        : angle       1.53437 (    3)
  hydrogen bonds       : bond        0.03456 (  249)
  hydrogen bonds       : angle       4.80400 (  738)
  SS BOND              : bond        0.00230 (   16)
  SS BOND              : angle       1.14926 (   32)
  covalent geometry    : bond        0.00265 ( 6787)
  covalent geometry    : angle       0.60460 ( 9201)

*********************** 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
  99 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.751 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8361 (m-30) cc_final: 0.7984 (m-30)
REVERT: A   75 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7534 (p)
REVERT: A  164 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7730 (tp-100)
REVERT: B   44 GLU cc_start: 0.6987 (tt0) cc_final: 0.6694 (mp0)
REVERT: C   67 TYR cc_start: 0.7456 (t80) cc_final: 0.6486 (t80)
  outliers start: 12
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1497
  time to fit residues: 20.4747
Evaluate side-chains
  96 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
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  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  145 CYS
Chi-restraints excluded: chain D residue  163 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 81
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0770
   chunk 48 optimal weight:    0.0980
   chunk 56 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8342

-------------------------------------------------------------------------------
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 = 0.3925 r_free = 0.3925 target = 0.111438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.083048 restraints weight = 17897.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.085717 restraints weight = 9894.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.087514 restraints weight = 7017.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6811  Z= 0.138
  Angle     :  0.633  13.658   9257  Z= 0.311
  Chirality :  0.042   0.225   1060
  Planarity :  0.004   0.041   1166
  Dihedral  :  6.221  55.579   1043
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 18.89 %
    Favored  : 79.52 %
  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:  2.00 (0.54), residues: 96
  sheet:  0.56 (0.32), residues: 292
  loop : -1.41 (0.29), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  60 
 HIS   0.003   0.000   HIS A 144 
 PHE   0.011   0.001   PHE D 212 
 TYR   0.027   0.001   TYR A 124 
 ARG   0.003   0.000   ARG C 183 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00324 (    5)
  link_NAG-ASN         : angle       4.54720 (   15)
  link_BETA1-4         : bond        0.00486 (    2)
  link_BETA1-4         : angle       1.23679 (    6)
  link_ALPHA1-3        : bond        0.00716 (    1)
  link_ALPHA1-3        : angle       1.55682 (    3)
  hydrogen bonds       : bond        0.03545 (  249)
  hydrogen bonds       : angle       4.83498 (  738)
  SS BOND              : bond        0.00242 (   16)
  SS BOND              : angle       1.16481 (   32)
  covalent geometry    : bond        0.00325 ( 6787)
  covalent geometry    : angle       0.60287 ( 9201)

********************** 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
  98 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.8384 (m-30) cc_final: 0.8009 (m-30)
REVERT: A   75 THR cc_start: 0.8009 (OUTLIER) cc_final: 0.7589 (p)
REVERT: B   44 GLU cc_start: 0.7036 (tt0) cc_final: 0.6703 (mp0)
REVERT: C   67 TYR cc_start: 0.7379 (t80) cc_final: 0.6499 (t80)
REVERT: C  166 MET cc_start: 0.8260 (mtt) cc_final: 0.7867 (mtt)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1585
  time to fit residues: 21.6122
Evaluate side-chains
  94 residues out of total 759 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.780 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain B residue  310 VAL
Chi-restraints excluded: chain C residue   74 VAL
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  145 CYS
Chi-restraints excluded: chain D residue  163 VAL
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:    0.5980
   chunk 68 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 = 0.3900 r_free = 0.3900 target = 0.109815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.081230 restraints weight = 17875.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.083896 restraints weight = 9991.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.085593 restraints weight = 7111.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   6811  Z= 0.200
  Angle     :  0.689  14.850   9257  Z= 0.338
  Chirality :  0.043   0.220   1060
  Planarity :  0.004   0.043   1166
  Dihedral  :  6.356  55.928   1043
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.42 %
    Favored  : 79.00 %
  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: -0.43 (0.30), residues: 803
  helix:  1.93 (0.54), residues: 96
  sheet:  0.50 (0.32), residues: 290
  loop : -1.46 (0.29), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 109 
 HIS   0.004   0.001   HIS A 168 
 PHE   0.013   0.002   PHE C 180 
 TYR   0.026   0.001   TYR A 124 
 ARG   0.004   0.000   ARG C 183 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00221 (    5)
  link_NAG-ASN         : angle       5.05094 (   15)
  link_BETA1-4         : bond        0.00302 (    2)
  link_BETA1-4         : angle       1.20468 (    6)
  link_ALPHA1-3        : bond        0.00708 (    1)
  link_ALPHA1-3        : angle       1.80440 (    3)
  hydrogen bonds       : bond        0.03937 (  249)
  hydrogen bonds       : angle       4.95679 (  738)
  SS BOND              : bond        0.00249 (   16)
  SS BOND              : angle       1.23864 (   32)
  covalent geometry    : bond        0.00475 ( 6787)
  covalent geometry    : angle       0.65446 ( 9201)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2802.96 seconds
wall clock time: 49 minutes 41.19 seconds (2981.19 seconds total)