Starting phenix.real_space_refine
on Thu Jan 16 20:30:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zba_39899/01_2025/8zba_39899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zba_39899/01_2025/8zba_39899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zba_39899/01_2025/8zba_39899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zba_39899/01_2025/8zba_39899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zba_39899/01_2025/8zba_39899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zba_39899/01_2025/8zba_39899.cif"
  }
  resolution = 3.57
  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=   0.035
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      84      5.16       5
     C    6256      2.51       5
     N    1718      2.21       5
     O    1915      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-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9973
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2453
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 2453
          Classifications: {'peptide': 313}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 294}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 2493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2493
          Classifications: {'peptide': 317}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 298}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "a"
      Number of atoms: 2518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 319, 2518
          Classifications: {'peptide': 319}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 300}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "b"
      Number of atoms: 2509
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 318, 2509
          Classifications: {'peptide': 318}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 299}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 6.71, per 1000 atoms: 0.67
  Number of scatterers: 9973
  At special positions: 0
  Unit cell: (93.5, 106.25, 105.4, 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      84     16.00
     O    1915      8.00
     N    1718      7.00
     C    6256      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=24, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A  15 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 179 " - pdb=" SG  CYS A 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 280 " - pdb=" SG  CYS A 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B  15 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 179 " - pdb=" SG  CYS B 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 280 " - pdb=" SG  CYS B 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a   4 " - pdb=" SG  CYS a  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a  55 " - pdb=" SG  CYS a 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 179 " - pdb=" SG  CYS a 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 280 " - pdb=" SG  CYS a 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 291 " - pdb=" SG  CYS a 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS a 313 " - pdb=" SG  CYS a 316 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b   4 " - pdb=" SG  CYS b  15 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b  55 " - pdb=" SG  CYS b 143 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 179 " - pdb=" SG  CYS b 224 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 280 " - pdb=" SG  CYS b 329 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 291 " - pdb=" SG  CYS b 312 " distance=2.03
    Simple disulfide: pdb=" SG  CYS b 313 " - pdb=" SG  CYS b 316 " 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
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 940.0 milliseconds
  

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2306

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 24 sheets defined
      13.7% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 40 through 52
    Processing helix  chain 'A' and resid 63 through 83
      removed outlier: 5.158A  pdb=" N   ASP A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 5.131A  pdb=" N   GLU A  74 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 227 through 231
      removed outlier: 3.910A  pdb=" N   THR A 231 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 27
    Processing helix  chain 'B' and resid 38 through 52
      removed outlier: 3.660A  pdb=" N   ALA B  43 " --> pdb=" O   PRO B  39 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   GLU B  52 " --> pdb=" O   ALA B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 82
      removed outlier: 5.199A  pdb=" N   ASP B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 5.234A  pdb=" N   GLU B  74 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 144 through 146
      No H-bonds generated for 'chain 'B' and resid 144 through 146'
    Processing helix  chain 'B' and resid 227 through 231
      removed outlier: 3.952A  pdb=" N   THR B 231 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 249
      removed outlier: 3.988A  pdb=" N   GLY B 249 " --> pdb=" O   ARG B 245 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 38 through 52
      removed outlier: 3.613A  pdb=" N   SER a  44 " --> pdb=" O   VAL a  40 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 61 through 82
      removed outlier: 5.088A  pdb=" N   ASP a  73 " --> pdb=" O   ARG a  69 " (cutoff:3.500A)
      removed outlier: 4.926A  pdb=" N   GLU a  74 " --> pdb=" O   SER a  70 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 227 through 231
      removed outlier: 4.103A  pdb=" N   THR a 231 " --> pdb=" O   LEU a 228 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 38 through 53
      removed outlier: 3.568A  pdb=" N   LEU b  42 " --> pdb=" O   ASP b  38 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA b  43 " --> pdb=" O   PRO b  39 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   SER b  44 " --> pdb=" O   VAL b  40 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU b  51 " --> pdb=" O   LYS b  47 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   GLU b  52 " --> pdb=" O   ALA b  48 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLY b  53 " --> pdb=" O   SER b  49 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 61 through 76
      removed outlier: 4.718A  pdb=" N   ASP b  73 " --> pdb=" O   ARG b  69 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   GLU b  74 " --> pdb=" O   SER b  70 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 227 through 231
      removed outlier: 3.986A  pdb=" N   THR b 231 " --> pdb=" O   LEU b 228 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15
      removed outlier: 4.564A  pdb=" N   LYS A  14 " --> pdb=" O   ALA A   5 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ALA A   5 " --> pdb=" O   LYS A  14 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   GLN a   2 " --> pdb=" O   ILE A   6 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.201A  pdb=" N   ARG A 166 " --> pdb=" O   PHE A 158 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   PHE A 158 " --> pdb=" O   ARG A 166 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   TYR A 168 " --> pdb=" O   GLU A 156 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57
      removed outlier: 7.283A  pdb=" N   GLY A  56 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 88 through 89
      removed outlier: 3.563A  pdb=" N   VAL A  89 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 218
      removed outlier: 6.453A  pdb=" N   GLY A 203 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   LEU A 216 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   TRP A 201 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   PHE A 200 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS A 192 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLY a 185 " --> pdb=" O   GLY a 196 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277
    Processing sheet with id=AA7, first strand: chain 'A' and resid 285 through 287
    Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 15
      removed outlier: 3.576A  pdb=" N   GLU B  12 " --> pdb=" O   ASN B   7 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   LYS B  14 " --> pdb=" O   ALA B   5 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   ALA B   5 " --> pdb=" O   LYS B  14 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN b   2 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 35
      removed outlier: 3.783A  pdb=" N   SER B  33 " --> pdb=" O   THR B 165 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL B 167 " --> pdb=" O   SER B  33 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57
      removed outlier: 7.087A  pdb=" N   GLY B  56 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154
    Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 275
      removed outlier: 4.440A  pdb=" N   LEU B 216 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   ILE B 213 " --> pdb=" O   HIS B 205 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   HIS B 205 " --> pdb=" O   ILE B 213 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LYS B 192 " --> pdb=" O   ASN B 189 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 312 through 313
    Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 324
    Processing sheet with id=AB6, first strand: chain 'a' and resid 56 through 57
      removed outlier: 6.924A  pdb=" N   GLY a  56 " --> pdb=" O   VAL a 149 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'a' and resid 86 through 87
    Processing sheet with id=AB8, first strand: chain 'a' and resid 153 through 154
    Processing sheet with id=AB9, first strand: chain 'a' and resid 201 through 207
      removed outlier: 6.667A  pdb=" N   TRP a 201 " --> pdb=" O   LEU a 216 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LEU a 216 " --> pdb=" O   TRP a 201 " (cutoff:3.500A)
      removed outlier: 6.252A  pdb=" N   GLY a 203 " --> pdb=" O   HIS a 214 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   ALA a 218 " --> pdb=" O   LEU a 273 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'a' and resid 298 through 299
      removed outlier: 3.901A  pdb=" N   THR a 298 " --> pdb=" O   TYR a 331 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TRP a 330 " --> pdb=" O   PHE a 323 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'b' and resid 87 through 90
      removed outlier: 6.902A  pdb=" N   SER b  87 " --> pdb=" O   PHE b 133 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   ILE b 135 " --> pdb=" O   SER b  87 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   VAL b  89 " --> pdb=" O   ILE b 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'b' and resid 195 through 197
      removed outlier: 3.557A  pdb=" N   MET b 202 " --> pdb=" O   HIS b 195 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE b 200 " --> pdb=" O   SER b 197 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   TRP b 201 " --> pdb=" O   LEU b 216 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   LEU b 216 " --> pdb=" O   TRP b 201 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLY b 203 " --> pdb=" O   HIS b 214 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'b' and resid 275 through 276
    Processing sheet with id=AC5, first strand: chain 'b' and resid 286 through 287
      removed outlier: 3.706A  pdb=" N   CYS b 313 " --> pdb=" O   ILE b 286 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'b' and resid 298 through 299
      removed outlier: 3.690A  pdb=" N   THR b 298 " --> pdb=" O   TYR b 331 " (cutoff:3.500A)

    198 hydrogen bonds defined for protein.
    525 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: 2.61

  Time building geometry restraints manager: 2.53 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: 3285
        1.34 -     1.46: 2528
        1.46 -     1.59: 4303
        1.59 -     1.72: 0
        1.72 -     1.84: 120
  Bond restraints: 10236
  Sorted by residual:
  bond pdb=" CA  VAL a 167 "
       pdb=" C   VAL a 167 "
    ideal  model  delta    sigma   weight residual
    1.522  1.472  0.050 1.29e-02 6.01e+03 1.49e+01
  bond pdb=" CA  ARG A 166 "
       pdb=" C   ARG A 166 "
    ideal  model  delta    sigma   weight residual
    1.525  1.495  0.030 1.28e-02 6.10e+03 5.53e+00
  bond pdb=" C   VAL a 167 "
       pdb=" O   VAL a 167 "
    ideal  model  delta    sigma   weight residual
    1.237  1.213  0.024 1.09e-02 8.42e+03 5.04e+00
  bond pdb=" N   TYR a 168 "
       pdb=" CA  TYR a 168 "
    ideal  model  delta    sigma   weight residual
    1.456  1.431  0.025 1.14e-02 7.69e+03 4.78e+00
  bond pdb=" CA  VAL A 162 "
       pdb=" C   VAL A 162 "
    ideal  model  delta    sigma   weight residual
    1.523  1.495  0.028 1.27e-02 6.20e+03 4.76e+00
  ... (remaining 10231 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 13480
        1.59 -     3.19: 306
        3.19 -     4.78: 59
        4.78 -     6.37: 6
        6.37 -     7.96: 2
  Bond angle restraints: 13853
  Sorted by residual:
  angle pdb=" N   THR A 164 "
        pdb=" CA  THR A 164 "
        pdb=" C   THR A 164 "
      ideal   model   delta    sigma   weight residual
     113.89  105.93    7.96 1.58e+00 4.01e-01 2.54e+01
  angle pdb=" N   ILE a 177 "
        pdb=" CA  ILE a 177 "
        pdb=" C   ILE a 177 "
      ideal   model   delta    sigma   weight residual
     112.96  109.07    3.89 1.00e+00 1.00e+00 1.51e+01
  angle pdb=" CA  PRO a 103 "
        pdb=" C   PRO a 103 "
        pdb=" N   PHE a 104 "
      ideal   model   delta    sigma   weight residual
     114.74  118.06   -3.32 1.03e+00 9.43e-01 1.04e+01
  angle pdb=" C   VAL A 162 "
        pdb=" CA  VAL A 162 "
        pdb=" CB  VAL A 162 "
      ideal   model   delta    sigma   weight residual
     111.29  106.77    4.52 1.64e+00 3.72e-01 7.60e+00
  angle pdb=" C   ILE a  78 "
        pdb=" N   PHE a  79 "
        pdb=" CA  PHE a  79 "
      ideal   model   delta    sigma   weight residual
     122.38  117.52    4.86 1.81e+00 3.05e-01 7.22e+00
  ... (remaining 13848 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.47: 5466
       17.47 -    34.94: 528
       34.94 -    52.40: 87
       52.40 -    69.87: 20
       69.87 -    87.34: 14
  Dihedral angle restraints: 6115
    sinusoidal: 2519
      harmonic: 3596
  Sorted by residual:
  dihedral pdb=" CB  CYS b  55 "
           pdb=" SG  CYS b  55 "
           pdb=" SG  CYS b 143 "
           pdb=" CB  CYS b 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -173.34   87.34     1      1.00e+01 1.00e-02 9.15e+01
  dihedral pdb=" CB  CYS a  55 "
           pdb=" SG  CYS a  55 "
           pdb=" SG  CYS a 143 "
           pdb=" CB  CYS a 143 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  176.22  -83.22     1      1.00e+01 1.00e-02 8.47e+01
  dihedral pdb=" CB  CYS b 291 "
           pdb=" SG  CYS b 291 "
           pdb=" SG  CYS b 312 "
           pdb=" CB  CYS b 312 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  173.55  -80.55     1      1.00e+01 1.00e-02 8.02e+01
  ... (remaining 6112 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 887
       0.034 -    0.067: 345
       0.067 -    0.101: 133
       0.101 -    0.135: 58
       0.135 -    0.168: 8
  Chirality restraints: 1431
  Sorted by residual:
  chirality pdb=" CA  MET a 318 "
            pdb=" N   MET a 318 "
            pdb=" C   MET a 318 "
            pdb=" CB  MET a 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.08e-01
  chirality pdb=" CA  THR A 160 "
            pdb=" N   THR A 160 "
            pdb=" C   THR A 160 "
            pdb=" CB  THR A 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.93e-01
  chirality pdb=" CA  ILE A 257 "
            pdb=" N   ILE A 257 "
            pdb=" C   ILE A 257 "
            pdb=" CB  ILE A 257 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.01e-01
  ... (remaining 1428 not shown)

  Planarity restraints: 1813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 266 "    0.050 5.00e-02 4.00e+02   7.59e-02 9.22e+00
        pdb=" N   PRO A 267 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A 267 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 267 "    0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 314 "    0.012 2.00e-02 2.50e+03   2.30e-02 5.30e+00
        pdb=" C   ARG B 314 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   ARG B 314 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER B 315 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 314 "   -0.012 2.00e-02 2.50e+03   2.29e-02 5.25e+00
        pdb=" C   ARG A 314 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ARG A 314 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 315 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1810 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1750
        2.77 -     3.30: 8918
        3.30 -     3.83: 15167
        3.83 -     4.37: 17335
        4.37 -     4.90: 31228
  Nonbonded interactions: 74398
  Sorted by model distance:
  nonbonded pdb=" N   ASP B   1 "
            pdb=" O   ILE b   6 "
     model   vdw
     2.234 3.120
  nonbonded pdb=" OG1 THR B 165 "
            pdb=" OE2 GLU b  12 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG  SER B  87 "
            pdb=" O   GLY B 131 "
     model   vdw
     2.259 3.040
  nonbonded pdb=" OD1 ASP A  38 "
            pdb=" N   LYS A  41 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" OG  SER B 304 "
            pdb=" NZ  LYS B 306 "
     model   vdw
     2.271 3.120
  ... (remaining 74393 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 108 or resid 130 through 139 or (resid 140 throu \ 
gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ 
ough 160 or resid 166 through 337))
  selection = (chain 'B' and (resid 1 through 26 or resid 31 through 108 or resid 130 through  \ 
139 or (resid 140 through 141 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 142 through 160 or resid 166 through 337))
  selection = (chain 'a' and (resid 1 through 26 or resid 31 through 108 or resid 130 through  \ 
140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 142 through 337))
  selection = (chain 'b' and (resid 1 through 26 or resid 31 through 140 or (resid 141 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 142 through 337))
}

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:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.140
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
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      :  0.003   0.050  10236  Z= 0.206
  Angle     :  0.592   7.963  13853  Z= 0.321
  Chirality :  0.045   0.168   1431
  Planarity :  0.005   0.076   1813
  Dihedral  : 13.820  86.434   3737
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.72 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.46 (0.23), residues: 1241
  helix:  1.33 (0.45), residues: 136
  sheet: -3.00 (0.37), residues: 167
  loop : -1.97 (0.20), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 150 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.014   0.001   PHE a 104 
 TYR   0.013   0.001   TYR a  34 
 ARG   0.003   0.000   ARG a 245 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 GLU cc_start: 0.6850 (tp30) cc_final: 0.6589 (tm-30)
REVERT: A   71 ARG cc_start: 0.7897 (mmt90) cc_final: 0.6394 (mtt180)
REVERT: A   94 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7058 (pttt)
REVERT: A  169 MET cc_start: 0.7967 (mtt) cc_final: 0.7762 (mtt)
REVERT: A  235 SER cc_start: 0.6761 (m) cc_final: 0.6341 (p)
REVERT: B   71 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.4885 (tpt170)
REVERT: B   92 ASP cc_start: 0.5949 (t70) cc_final: 0.5688 (t70)
REVERT: B  168 TYR cc_start: 0.7694 (m-80) cc_final: 0.6868 (m-10)
REVERT: B  176 THR cc_start: 0.8371 (m) cc_final: 0.8085 (p)
REVERT: a   34 TYR cc_start: 0.6625 (m-80) cc_final: 0.6400 (m-80)
REVERT: a   67 MET cc_start: 0.8186 (tmm) cc_final: 0.7745 (ttp)
REVERT: a   79 PHE cc_start: 0.3626 (p90) cc_final: 0.3346 (p90)
REVERT: b   12 GLU cc_start: 0.7190 (mm-30) cc_final: 0.5844 (mm-30)
REVERT: b  158 PHE cc_start: 0.6881 (m-10) cc_final: 0.6384 (t80)
REVERT: b  167 VAL cc_start: 0.5593 (m) cc_final: 0.5138 (t)
REVERT: b  169 MET cc_start: 0.7066 (mmm) cc_final: 0.6522 (mmm)
REVERT: b  177 ILE cc_start: 0.8503 (mp) cc_final: 0.8222 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.2630
  time to fit residues: 91.2947
Evaluate side-chains
  170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 93 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 97 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0870
   chunk 72 optimal weight:    0.9980
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
B 189 ASN
B 265 ASN
B 324 HIS
a  76 ASN
a  82 ASN
a 290 ASN
b 102 HIS
b 290 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4562 r_free = 0.4562 target = 0.225139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.182777 restraints weight = 10588.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.176730 restraints weight = 15852.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.174744 restraints weight = 11362.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  10236  Z= 0.205
  Angle     :  0.612   9.284  13853  Z= 0.317
  Chirality :  0.046   0.157   1431
  Planarity :  0.005   0.052   1813
  Dihedral  :  4.349  18.683   1356
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.99 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 10.33 %
    Favored  : 88.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.57 (0.23), residues: 1241
  helix:  1.09 (0.44), residues: 138
  sheet: -2.97 (0.35), residues: 183
  loop : -2.03 (0.20), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP a 311 
 HIS   0.004   0.001   HIS A 205 
 PHE   0.029   0.001   PHE a  79 
 TYR   0.012   0.001   TYR a  32 
 ARG   0.004   0.000   ARG a  69 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 185
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.8155 (mmt90) cc_final: 0.6650 (mtt180)
REVERT: A   94 LYS cc_start: 0.7682 (mmtt) cc_final: 0.6931 (pttm)
REVERT: A  136 ASP cc_start: 0.8283 (p0) cc_final: 0.8026 (p0)
REVERT: A  235 SER cc_start: 0.6476 (m) cc_final: 0.6125 (p)
REVERT: B   10 LYS cc_start: 0.7834 (tttp) cc_final: 0.7581 (tmtt)
REVERT: B   71 ARG cc_start: 0.7349 (mmt-90) cc_final: 0.4750 (tpt170)
REVERT: B   92 ASP cc_start: 0.5865 (t70) cc_final: 0.5578 (t70)
REVERT: a   76 ASN cc_start: 0.6762 (m110) cc_final: 0.6551 (m110)
REVERT: a   79 PHE cc_start: 0.3773 (p90) cc_final: 0.3280 (p90)
REVERT: a  168 TYR cc_start: 0.7430 (m-80) cc_final: 0.7106 (m-80)
REVERT: b   10 LYS cc_start: 0.6600 (tttm) cc_final: 0.5828 (tmtt)
REVERT: b   12 GLU cc_start: 0.7230 (mm-30) cc_final: 0.5866 (mm-30)
REVERT: b  158 PHE cc_start: 0.7024 (m-10) cc_final: 0.6375 (t80)
  outliers start: 17
  outliers final: 9
  residues processed: 194
  average time/residue: 0.2222
  time to fit residues: 60.2088
Evaluate side-chains
  168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 159
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain B residue   42 LEU
Chi-restraints excluded: chain a residue    2 GLN
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue   89 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 85 optimal weight:    0.8980
   chunk 10 optimal weight:    6.9990
   chunk 22 optimal weight:    0.2980
   chunk 86 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 102 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 109 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
a  82 ASN
** a 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4554 r_free = 0.4554 target = 0.224412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.178496 restraints weight = 10636.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.176072 restraints weight = 14579.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.169954 restraints weight = 10419.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10236  Z= 0.192
  Angle     :  0.582   9.467  13853  Z= 0.299
  Chirality :  0.045   0.183   1431
  Planarity :  0.005   0.052   1813
  Dihedral  :  4.252  17.810   1356
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.19 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.86 %
    Favored  : 85.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.50 (0.23), residues: 1241
  helix:  1.21 (0.45), residues: 139
  sheet: -2.78 (0.37), residues: 173
  loop : -2.04 (0.20), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP a  68 
 HIS   0.011   0.001   HIS B 214 
 PHE   0.027   0.001   PHE a  79 
 TYR   0.009   0.001   TYR B 260 
 ARG   0.007   0.000   ARG B  11 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 171
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   71 ARG cc_start: 0.8134 (mmt90) cc_final: 0.6642 (mtt180)
REVERT: A   94 LYS cc_start: 0.7763 (mmtt) cc_final: 0.6922 (pttm)
REVERT: A  136 ASP cc_start: 0.8211 (p0) cc_final: 0.7960 (p0)
REVERT: A  235 SER cc_start: 0.6892 (m) cc_final: 0.6454 (p)
REVERT: B   10 LYS cc_start: 0.7551 (tttp) cc_final: 0.7345 (tmtt)
REVERT: B   92 ASP cc_start: 0.5698 (t70) cc_final: 0.5409 (t70)
REVERT: a  274 GLU cc_start: 0.6945 (tt0) cc_final: 0.6739 (mt-10)
REVERT: a  286 ILE cc_start: 0.7585 (OUTLIER) cc_final: 0.7219 (pt)
REVERT: b   10 LYS cc_start: 0.6505 (tttm) cc_final: 0.5719 (tttt)
REVERT: b   12 GLU cc_start: 0.7151 (mm-30) cc_final: 0.5858 (mm-30)
REVERT: b  158 PHE cc_start: 0.6999 (m-10) cc_final: 0.6436 (t80)
  outliers start: 22
  outliers final: 13
  residues processed: 182
  average time/residue: 0.2069
  time to fit residues: 53.8501
Evaluate side-chains
  168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue    2 GLN
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain b residue   89 VAL
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  298 THR
Chi-restraints excluded: chain b residue  318 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 92 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 44 optimal weight:    9.9990
   chunk 29 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 80 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
a  82 ASN
a 102 HIS
b 263 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4540 r_free = 0.4540 target = 0.222989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.176377 restraints weight = 10554.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.175782 restraints weight = 14149.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.168916 restraints weight = 9772.472|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10236  Z= 0.199
  Angle     :  0.572   7.767  13853  Z= 0.294
  Chirality :  0.044   0.169   1431
  Planarity :  0.005   0.050   1813
  Dihedral  :  4.219  18.450   1356
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.35 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 13.86 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.50 (0.23), residues: 1241
  helix:  1.12 (0.45), residues: 141
  sheet: -2.65 (0.37), residues: 175
  loop : -2.06 (0.19), residues: 925

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP b 150 
 HIS   0.010   0.001   HIS B 214 
 PHE   0.028   0.001   PHE a  79 
 TYR   0.008   0.001   TYR a  97 
 ARG   0.010   0.000   ARG B  11 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7804 (mmtt) cc_final: 0.6927 (pttm)
REVERT: A  136 ASP cc_start: 0.8236 (p0) cc_final: 0.7968 (p0)
REVERT: B   67 MET cc_start: 0.6080 (tpt) cc_final: 0.5773 (tpp)
REVERT: B   92 ASP cc_start: 0.5718 (t70) cc_final: 0.5418 (t70)
REVERT: a  274 GLU cc_start: 0.6888 (tt0) cc_final: 0.6637 (mt-10)
REVERT: a  286 ILE cc_start: 0.7565 (OUTLIER) cc_final: 0.7198 (pt)
REVERT: b   10 LYS cc_start: 0.6535 (tttm) cc_final: 0.5807 (tttt)
REVERT: b   12 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6034 (mm-30)
REVERT: b   35 TYR cc_start: 0.7043 (m-80) cc_final: 0.6688 (m-10)
REVERT: b  158 PHE cc_start: 0.6927 (m-10) cc_final: 0.6460 (t80)
REVERT: b  169 MET cc_start: 0.6882 (mmm) cc_final: 0.6529 (mmm)
  outliers start: 29
  outliers final: 19
  residues processed: 179
  average time/residue: 0.2042
  time to fit residues: 52.1693
Evaluate side-chains
  169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  212 MET
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue   44 SER
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue    2 GLN
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain a residue  329 CYS
Chi-restraints excluded: chain b residue   42 LEU
Chi-restraints excluded: chain b residue   89 VAL
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  298 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 101 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 28 optimal weight:    0.0670
   chunk 98 optimal weight:    3.9990
   chunk 92 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    2.0126

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  82 ASN
** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  91 GLN
b 102 HIS
b 195 HIS
b 265 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4608 r_free = 0.4608 target = 0.224900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.174836 restraints weight = 11069.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.174882 restraints weight = 16338.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.173038 restraints weight = 11536.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.068  10236  Z= 0.348
  Angle     :  0.668   7.200  13853  Z= 0.349
  Chirality :  0.047   0.174   1431
  Planarity :  0.005   0.061   1813
  Dihedral  :  4.854  18.163   1356
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 12.33 %
    Favored  : 87.59 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 17.03 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.68 (0.23), residues: 1241
  helix:  0.79 (0.45), residues: 149
  sheet: -2.50 (0.37), residues: 180
  loop : -2.24 (0.19), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 330 
 HIS   0.011   0.002   HIS B 214 
 PHE   0.042   0.002   PHE a  79 
 TYR   0.016   0.002   TYR a  97 
 ARG   0.010   0.001   ARG b  69 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 156
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8084 (mmtt) cc_final: 0.7061 (pttm)
REVERT: B   67 MET cc_start: 0.6322 (tpt) cc_final: 0.6038 (tpp)
REVERT: B   71 ARG cc_start: 0.7992 (mmp80) cc_final: 0.7594 (mmp80)
REVERT: B   92 ASP cc_start: 0.5562 (t70) cc_final: 0.5214 (t70)
REVERT: a   66 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7889 (tm-30)
REVERT: b   10 LYS cc_start: 0.6761 (tttm) cc_final: 0.6134 (tttt)
REVERT: b   12 GLU cc_start: 0.7135 (mm-30) cc_final: 0.5882 (mm-30)
REVERT: b  158 PHE cc_start: 0.7077 (m-10) cc_final: 0.6517 (t80)
  outliers start: 33
  outliers final: 21
  residues processed: 176
  average time/residue: 0.2026
  time to fit residues: 52.1120
Evaluate side-chains
  166 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 145
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 SER
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  146 SER
Chi-restraints excluded: chain a residue  156 GLU
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  180 ASP
Chi-restraints excluded: chain b residue  298 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   chunk 41 optimal weight:   20.0000
   chunk 93 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 58 optimal weight:    6.9990
   chunk 45 optimal weight:    0.0370
   chunk 46 optimal weight:    6.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.3862

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
a  82 ASN
** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  91 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.225816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.171159 restraints weight = 11103.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.164410 restraints weight = 13766.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.160598 restraints weight = 11058.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.3368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  10236  Z= 0.262
  Angle     :  0.629   7.185  13853  Z= 0.326
  Chirality :  0.045   0.152   1431
  Planarity :  0.005   0.056   1813
  Dihedral  :  4.680  18.857   1356
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 10.23 %
    Favored  : 89.69 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 17.84 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.62 (0.23), residues: 1241
  helix:  1.12 (0.46), residues: 141
  sheet: -2.46 (0.37), residues: 180
  loop : -2.22 (0.19), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 330 
 HIS   0.011   0.001   HIS B 214 
 PHE   0.054   0.002   PHE B  79 
 TYR   0.011   0.001   TYR a  97 
 ARG   0.009   0.000   ARG b  69 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 143
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.8048 (mmtt) cc_final: 0.7000 (pttm)
REVERT: B   67 MET cc_start: 0.6261 (tpt) cc_final: 0.5928 (tpp)
REVERT: B   71 ARG cc_start: 0.7633 (mmp80) cc_final: 0.7256 (mmp80)
REVERT: B   92 ASP cc_start: 0.5889 (t70) cc_final: 0.5507 (t70)
REVERT: a   11 ARG cc_start: 0.7175 (mmm-85) cc_final: 0.6956 (mmm-85)
REVERT: a   13 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8271 (tt)
REVERT: a   66 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7909 (tm-30)
REVERT: b   10 LYS cc_start: 0.6611 (tttm) cc_final: 0.5797 (tttt)
REVERT: b   12 GLU cc_start: 0.7363 (mm-30) cc_final: 0.5858 (mm-30)
REVERT: b   35 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.6642 (m-10)
REVERT: b  102 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6942 (m90)
REVERT: b  158 PHE cc_start: 0.7126 (m-10) cc_final: 0.6331 (t80)
  outliers start: 36
  outliers final: 26
  residues processed: 165
  average time/residue: 0.1867
  time to fit residues: 45.9951
Evaluate side-chains
  168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 139
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  132 SER
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain a residue   13 LEU
Chi-restraints excluded: chain a residue   29 LEU
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  146 SER
Chi-restraints excluded: chain a residue  156 GLU
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain b residue   35 TYR
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue  102 HIS
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  205 HIS
Chi-restraints excluded: chain b residue  231 THR
Chi-restraints excluded: chain b residue  298 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 101 optimal weight:    6.9990
   chunk 59 optimal weight:    7.9990
   chunk 118 optimal weight:    0.9980
   chunk 73 optimal weight:    7.9990
   chunk 94 optimal weight:    0.0870
   chunk 106 optimal weight:    0.0870
   chunk 14 optimal weight:    6.9990
   chunk 57 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.5936

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
a  82 ASN
b  91 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.218326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.180607 restraints weight = 10744.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.173261 restraints weight = 13535.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.170116 restraints weight = 13771.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.4096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  10236  Z= 0.187
  Angle     :  0.579   8.050  13853  Z= 0.300
  Chirality :  0.044   0.146   1431
  Planarity :  0.005   0.054   1813
  Dihedral  :  4.314  18.661   1356
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.11 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.02 %
    Favored  : 78.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.51 (0.23), residues: 1241
  helix:  1.41 (0.47), residues: 142
  sheet: -2.68 (0.37), residues: 180
  loop : -2.12 (0.19), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP b 150 
 HIS   0.011   0.001   HIS B 214 
 PHE   0.050   0.001   PHE B  79 
 TYR   0.008   0.001   TYR B  35 
 ARG   0.004   0.000   ARG a  11 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 153
  time to evaluate  : 1.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7439 (mmtt) cc_final: 0.6647 (pttm)
REVERT: B   67 MET cc_start: 0.6178 (tpt) cc_final: 0.5920 (tpp)
REVERT: B   71 ARG cc_start: 0.7815 (mmp80) cc_final: 0.7532 (mmp80)
REVERT: B   92 ASP cc_start: 0.5406 (t70) cc_final: 0.5037 (t70)
REVERT: a   13 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8358 (tt)
REVERT: a   66 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7647 (tm-30)
REVERT: b   10 LYS cc_start: 0.6725 (tttm) cc_final: 0.6243 (tttt)
REVERT: b   12 GLU cc_start: 0.6971 (mm-30) cc_final: 0.5726 (mm-30)
REVERT: b  158 PHE cc_start: 0.6905 (m-10) cc_final: 0.6390 (t80)
REVERT: b  255 ASN cc_start: 0.7374 (t0) cc_final: 0.6508 (t0)
  outliers start: 32
  outliers final: 25
  residues processed: 174
  average time/residue: 0.1799
  time to fit residues: 47.0807
Evaluate side-chains
  162 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 1.061 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue   13 LEU
Chi-restraints excluded: chain a residue   29 LEU
Chi-restraints excluded: chain a residue   82 ASN
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  146 SER
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain a residue  333 MET
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  205 HIS
Chi-restraints excluded: chain b residue  231 THR
Chi-restraints excluded: chain b residue  298 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 62 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 117 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 121 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0770
   overall best weight:    0.8740

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  82 ASN
b  91 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4523 r_free = 0.4523 target = 0.220997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.183503 restraints weight = 10750.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.174107 restraints weight = 14628.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.171315 restraints weight = 14296.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.4072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7378
moved from start:          0.3596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  10236  Z= 0.213
  Angle     :  0.594   9.284  13853  Z= 0.309
  Chirality :  0.045   0.146   1431
  Planarity :  0.005   0.051   1813
  Dihedral  :  4.332  18.835   1356
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.91 %
    Favored  : 90.01 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.38 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.53 (0.23), residues: 1241
  helix:  1.40 (0.46), residues: 143
  sheet: -2.72 (0.34), residues: 206
  loop : -2.08 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP b 150 
 HIS   0.011   0.001   HIS B 214 
 PHE   0.052   0.002   PHE B  79 
 TYR   0.009   0.001   TYR a  97 
 ARG   0.004   0.000   ARG b  69 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 145
  time to evaluate  : 1.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7508 (mmtt) cc_final: 0.6663 (pttm)
REVERT: B   67 MET cc_start: 0.6258 (tpt) cc_final: 0.5953 (tpp)
REVERT: B   71 ARG cc_start: 0.7790 (mmp80) cc_final: 0.7514 (mmp80)
REVERT: B   92 ASP cc_start: 0.5460 (t70) cc_final: 0.5088 (t70)
REVERT: a   13 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8441 (tt)
REVERT: a   66 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7668 (tm-30)
REVERT: b   10 LYS cc_start: 0.6817 (tttm) cc_final: 0.6304 (tttt)
REVERT: b   12 GLU cc_start: 0.6976 (mm-30) cc_final: 0.5721 (mm-30)
REVERT: b  158 PHE cc_start: 0.6942 (m-10) cc_final: 0.6416 (t80)
  outliers start: 34
  outliers final: 27
  residues processed: 167
  average time/residue: 0.1808
  time to fit residues: 45.1711
Evaluate side-chains
  165 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 137
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 SER
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue   13 LEU
Chi-restraints excluded: chain a residue   29 LEU
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  102 HIS
Chi-restraints excluded: chain a residue  146 SER
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain b residue   42 LEU
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  205 HIS
Chi-restraints excluded: chain b residue  231 THR
Chi-restraints excluded: chain b residue  298 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   chunk 114 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 63 optimal weight:    7.9990
   chunk 68 optimal weight:    0.6980
   overall best weight:    1.4984

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  82 ASN
** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.209597 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 97)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140910 restraints weight = 10850.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.143055 restraints weight = 8693.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.143621 restraints weight = 7351.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  10236  Z= 0.280
  Angle     :  0.650  11.561  13853  Z= 0.339
  Chirality :  0.046   0.154   1431
  Planarity :  0.005   0.050   1813
  Dihedral  :  4.622  18.604   1356
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 11.36 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 19.75 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.60 (0.23), residues: 1241
  helix:  1.11 (0.46), residues: 147
  sheet: -2.57 (0.35), residues: 202
  loop : -2.17 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 330 
 HIS   0.011   0.002   HIS B 214 
 PHE   0.051   0.002   PHE B  79 
 TYR   0.012   0.001   TYR a  97 
 ARG   0.005   0.000   ARG b  69 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 138
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LYS cc_start: 0.7883 (mmtt) cc_final: 0.6746 (pttm)
REVERT: B   67 MET cc_start: 0.6166 (tpt) cc_final: 0.5895 (tpp)
REVERT: B   92 ASP cc_start: 0.5857 (t70) cc_final: 0.5487 (t70)
REVERT: a   13 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8302 (tt)
REVERT: a   66 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7844 (tm-30)
REVERT: a   82 ASN cc_start: 0.7648 (OUTLIER) cc_final: 0.7367 (t0)
REVERT: b   10 LYS cc_start: 0.6542 (tttm) cc_final: 0.5708 (tmtt)
REVERT: b   12 GLU cc_start: 0.7299 (mm-30) cc_final: 0.5702 (mm-30)
REVERT: b  102 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6802 (m-70)
REVERT: b  158 PHE cc_start: 0.7035 (m-10) cc_final: 0.6223 (t80)
  outliers start: 32
  outliers final: 26
  residues processed: 161
  average time/residue: 0.1769
  time to fit residues: 43.1473
Evaluate side-chains
  163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 134
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 SER
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue   13 LEU
Chi-restraints excluded: chain a residue   29 LEU
Chi-restraints excluded: chain a residue   82 ASN
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  102 HIS
Chi-restraints excluded: chain a residue  146 SER
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain b residue   42 LEU
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue  102 HIS
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  176 THR
Chi-restraints excluded: chain b residue  177 ILE
Chi-restraints excluded: chain b residue  205 HIS
Chi-restraints excluded: chain b residue  231 THR
Chi-restraints excluded: chain b residue  298 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 117 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 121 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 86 optimal weight:    0.5980
   chunk 7 optimal weight:    5.9990
   chunk 105 optimal weight:    7.9990
   chunk 102 optimal weight:    0.8980
   chunk 77 optimal weight:    0.8980
   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 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  82 ASN
b  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.214571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.143170 restraints weight = 10906.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.146317 restraints weight = 8673.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.147435 restraints weight = 7071.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.3833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10236  Z= 0.208
  Angle     :  0.607  10.877  13853  Z= 0.315
  Chirality :  0.045   0.141   1431
  Planarity :  0.005   0.049   1813
  Dihedral  :  4.425  19.872   1356
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.70 %
    Favored  : 91.22 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.93 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.48 (0.23), residues: 1241
  helix:  1.35 (0.47), residues: 141
  sheet: -2.42 (0.36), residues: 197
  loop : -2.11 (0.20), residues: 903

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP b 150 
 HIS   0.011   0.001   HIS B 214 
 PHE   0.053   0.002   PHE B  79 
 TYR   0.008   0.001   TYR a  97 
 ARG   0.003   0.000   ARG A 140 

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

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

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2482 Ramachandran restraints generated.
    1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 141
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLU cc_start: 0.8310 (tp30) cc_final: 0.8091 (tp30)
REVERT: B   67 MET cc_start: 0.6249 (tpt) cc_final: 0.5981 (tpp)
REVERT: B   71 ARG cc_start: 0.7501 (mmp80) cc_final: 0.7291 (mmp80)
REVERT: B   92 ASP cc_start: 0.5894 (t70) cc_final: 0.5534 (t70)
REVERT: a   66 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7793 (tm-30)
REVERT: b   10 LYS cc_start: 0.6556 (tttm) cc_final: 0.5903 (tttt)
REVERT: b   12 GLU cc_start: 0.7440 (mm-30) cc_final: 0.5968 (mm-30)
REVERT: b  102 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.6899 (m-70)
REVERT: b  158 PHE cc_start: 0.7049 (m-10) cc_final: 0.6232 (t80)
REVERT: b  255 ASN cc_start: 0.7230 (t0) cc_final: 0.6598 (t0)
  outliers start: 29
  outliers final: 26
  residues processed: 162
  average time/residue: 0.1809
  time to fit residues: 44.3192
Evaluate side-chains
  163 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    4 CYS
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  264 THR
Chi-restraints excluded: chain A residue  307 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  316 CYS
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue   44 SER
Chi-restraints excluded: chain B residue  214 HIS
Chi-restraints excluded: chain a residue   29 LEU
Chi-restraints excluded: chain a residue   82 ASN
Chi-restraints excluded: chain a residue   88 VAL
Chi-restraints excluded: chain a residue  102 HIS
Chi-restraints excluded: chain a residue  146 SER
Chi-restraints excluded: chain a residue  188 VAL
Chi-restraints excluded: chain a residue  286 ILE
Chi-restraints excluded: chain a residue  321 VAL
Chi-restraints excluded: chain b residue   42 LEU
Chi-restraints excluded: chain b residue   57 LEU
Chi-restraints excluded: chain b residue  102 HIS
Chi-restraints excluded: chain b residue  167 VAL
Chi-restraints excluded: chain b residue  205 HIS
Chi-restraints excluded: chain b residue  231 THR
Chi-restraints excluded: chain b residue  298 THR
Chi-restraints excluded: chain b residue  318 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 44 optimal weight:    8.9990
   chunk 117 optimal weight:    0.9980
   chunk 109 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 53 optimal weight:    0.3980
   chunk 87 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 119 optimal weight:   30.0000
   chunk 110 optimal weight:    0.8980
   chunk 6 optimal weight:    4.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  82 ASN
** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
b  91 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4421 r_free = 0.4421 target = 0.208898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.140068 restraints weight = 10859.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.142007 restraints weight = 8689.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.143454 restraints weight = 7428.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  10236  Z= 0.298
  Angle     :  0.657  11.714  13853  Z= 0.342
  Chirality :  0.046   0.153   1431
  Planarity :  0.005   0.048   1813
  Dihedral  :  4.637  18.948   1356
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  : 12.09 %
    Favored  : 87.83 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.29 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.59 (0.23), residues: 1241
  helix:  1.02 (0.46), residues: 148
  sheet: -2.44 (0.35), residues: 201
  loop : -2.19 (0.20), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 330 
 HIS   0.010   0.002   HIS B 214 
 PHE   0.054   0.002   PHE B  79 
 TYR   0.012   0.001   TYR a  97 
 ARG   0.005   0.000   ARG b  69 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3245.75 seconds
wall clock time: 59 minutes 14.91 seconds (3554.91 seconds total)