Starting phenix.real_space_refine
on Thu Mar  6 03:00:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xpd_22285/03_2025/6xpd_22285.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xpd_22285/03_2025/6xpd_22285.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2025/6xpd_22285.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2025/6xpd_22285.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2025/6xpd_22285.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xpd_22285/03_2025/6xpd_22285.cif"
  }
  resolution = 3.8
  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=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 144 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     S      32      5.16       5
     C    3010      2.51       5
     N     754      2.21       5
     O     822      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4622
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2309
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 2309
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2309
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 9, 'TRANS': 293}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2325  SG  CYS A  53      42.422  21.767  23.908  1.00 88.16           S
  ATOM   2246  SG  CYS B 361      39.757  15.017  23.922  1.00 99.56           S
  ATOM   2271  SG  CYS B 364      39.570  17.025  26.950  1.00 81.28           S
  ATOM     16  SG  CYS B  53      33.976  39.660  23.918  1.00 89.15           S
  ATOM   4555  SG  CYS A 361      36.712  46.426  23.890  1.00100.58           S
  ATOM   4580  SG  CYS A 364      36.887  44.419  26.919  1.00 82.53           S

  Time building chain proxies: 3.53, per 1000 atoms: 0.76
  Number of scatterers: 4622
  At special positions: 0
  Unit cell: (77.19, 62.25, 102.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      4     29.99
     S      32     16.00
     O     822      8.00
     N     754      7.00
     C    3010      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.82
  Conformation dependent library (CDL) restraints added in 579.0 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" ND1 HIS A 318 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A 301 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B  53 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 364 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS B  54 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS A 361 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS B  52 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 301 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 318 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  53 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 364 "
        pdb="ZN    ZN B 402 " - pdb=" ND1 HIS A  54 "
        pdb="ZN    ZN B 402 " - pdb=" SG  CYS B 361 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS A  52 "
      Number of angles added : 4


  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1164

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 2 sheets defined
      69.0% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'B' and resid 63 through 94
      removed outlier: 3.844A  pdb=" N   TYR B  67 " --> pdb=" O   GLY B  63 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA B  68 " --> pdb=" O   ALA B  64 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   GLY B  92 " --> pdb=" O   GLU B  88 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS B  93 " --> pdb=" O   VAL B  89 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B  94 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 126
      removed outlier: 4.078A  pdb=" N   HIS B 106 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU B 107 " --> pdb=" O   ASP B 103 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   LEU B 108 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS B 126 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 168
    Processing helix  chain 'B' and resid 176 through 196
      removed outlier: 3.637A  pdb=" N   ILE B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 241
      removed outlier: 3.688A  pdb=" N   ASN B 224 " --> pdb=" O   HIS B 220 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL B 231 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU B 232 " --> pdb=" O   SER B 228 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   SER B 234 " --> pdb=" O   SER B 230 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 275
      removed outlier: 4.478A  pdb=" N   ILE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 293
    Processing helix  chain 'B' and resid 326 through 342
      removed outlier: 3.983A  pdb=" N   VAL B 330 " --> pdb=" O   ASP B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 365
      removed outlier: 4.655A  pdb=" N   LEU B 362 " --> pdb=" O   PRO B 359 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   PHE B 363 " --> pdb=" O   ASP B 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 94
      removed outlier: 3.843A  pdb=" N   TYR A  67 " --> pdb=" O   GLY A  63 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   ALA A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   GLY A  92 " --> pdb=" O   GLU A  88 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 126
      removed outlier: 4.036A  pdb=" N   HIS A 106 " --> pdb=" O   THR A 102 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A 107 " --> pdb=" O   ASP A 103 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LEU A 108 " --> pdb=" O   ALA A 104 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LYS A 126 " --> pdb=" O   TRP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 168
    Processing helix  chain 'A' and resid 176 through 196
      removed outlier: 3.637A  pdb=" N   ILE A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER A 182 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ALA A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 241
      removed outlier: 3.688A  pdb=" N   ASN A 224 " --> pdb=" O   HIS A 220 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   VAL A 231 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 232 " --> pdb=" O   SER A 228 " (cutoff:3.500A)
      removed outlier: 4.226A  pdb=" N   SER A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 275
      removed outlier: 4.478A  pdb=" N   ILE A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 293
    Processing helix  chain 'A' and resid 326 through 342
      removed outlier: 3.983A  pdb=" N   VAL A 330 " --> pdb=" O   ASP A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 365
      removed outlier: 4.655A  pdb=" N   LEU A 362 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   PHE A 363 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 297 through 304
      removed outlier: 5.680A  pdb=" N   VAL B 300 " --> pdb=" O   ALA B 320 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   ALA B 320 " --> pdb=" O   VAL B 300 " (cutoff:3.500A)
      removed outlier: 5.163A  pdb=" N   SER B 302 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   HIS B 318 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   LEU B 315 " --> pdb=" O   THR B 348 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 297 through 304
      removed outlier: 5.679A  pdb=" N   VAL A 300 " --> pdb=" O   ALA A 320 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ALA A 320 " --> pdb=" O   VAL A 300 " (cutoff:3.500A)
      removed outlier: 5.162A  pdb=" N   SER A 302 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   HIS A 318 " --> pdb=" O   SER A 302 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   LEU A 315 " --> pdb=" O   THR A 348 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    894 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.20

  Time building geometry restraints manager: 1.47 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1432
        1.34 -     1.46: 1103
        1.46 -     1.58: 2135
        1.58 -     1.70: 0
        1.70 -     1.82: 44
  Bond restraints: 4714
  Sorted by residual:
  bond pdb=" CA  THR A 348 "
       pdb=" CB  THR A 348 "
    ideal  model  delta    sigma   weight residual
    1.527  1.498  0.029 2.48e-02 1.63e+03 1.38e+00
  bond pdb=" C   SER B 262 "
       pdb=" O   SER B 262 "
    ideal  model  delta    sigma   weight residual
    1.237  1.250 -0.014 1.17e-02 7.31e+03 1.36e+00
  bond pdb=" CA  THR B 348 "
       pdb=" CB  THR B 348 "
    ideal  model  delta    sigma   weight residual
    1.527  1.499  0.029 2.48e-02 1.63e+03 1.33e+00
  bond pdb=" CG  LEU B 308 "
       pdb=" CD1 LEU B 308 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.20e+00
  bond pdb=" CG  LEU A 308 "
       pdb=" CD1 LEU A 308 "
    ideal  model  delta    sigma   weight residual
    1.521  1.485  0.036 3.30e-02 9.18e+02 1.16e+00
  ... (remaining 4709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.28: 5932
        1.28 -     2.56: 369
        2.56 -     3.85: 91
        3.85 -     5.13: 22
        5.13 -     6.41: 8
  Bond angle restraints: 6422
  Sorted by residual:
  angle pdb=" C   SER B 353 "
        pdb=" N   PRO B 354 "
        pdb=" CA  PRO B 354 "
      ideal   model   delta    sigma   weight residual
     119.05  122.88   -3.83 1.11e+00 8.12e-01 1.19e+01
  angle pdb=" C   SER A 353 "
        pdb=" N   PRO A 354 "
        pdb=" CA  PRO A 354 "
      ideal   model   delta    sigma   weight residual
     119.05  122.56   -3.51 1.11e+00 8.12e-01 9.98e+00
  angle pdb=" C   ASP B 356 "
        pdb=" N   GLN B 357 "
        pdb=" CA  GLN B 357 "
      ideal   model   delta    sigma   weight residual
     122.41  117.98    4.43 1.41e+00 5.03e-01 9.86e+00
  angle pdb=" C   ASP A 356 "
        pdb=" N   GLN A 357 "
        pdb=" CA  GLN A 357 "
      ideal   model   delta    sigma   weight residual
     122.16  118.05    4.11 1.50e+00 4.44e-01 7.51e+00
  angle pdb=" N   PRO B 354 "
        pdb=" CA  PRO B 354 "
        pdb=" C   PRO B 354 "
      ideal   model   delta    sigma   weight residual
     113.53  110.13    3.40 1.39e+00 5.18e-01 6.00e+00
  ... (remaining 6417 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.92: 2330
       12.92 -    25.83: 325
       25.83 -    38.75: 94
       38.75 -    51.67: 28
       51.67 -    64.58: 11
  Dihedral angle restraints: 2788
    sinusoidal: 1008
      harmonic: 1780
  Sorted by residual:
  dihedral pdb=" CA  LEU B 308 "
           pdb=" C   LEU B 308 "
           pdb=" N   THR B 309 "
           pdb=" CA  THR B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.52  -22.48     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  LEU A 308 "
           pdb=" C   LEU A 308 "
           pdb=" N   THR A 309 "
           pdb=" CA  THR A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  dihedral pdb=" CA  GLU A  88 "
           pdb=" C   GLU A  88 "
           pdb=" N   VAL A  89 "
           pdb=" CA  VAL A  89 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.64   19.36     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 2785 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 520
       0.039 -    0.078: 232
       0.078 -    0.118: 41
       0.118 -    0.157: 5
       0.157 -    0.196: 2
  Chirality restraints: 800
  Sorted by residual:
  chirality pdb=" CA  ASP A 356 "
            pdb=" N   ASP A 356 "
            pdb=" C   ASP A 356 "
            pdb=" CB  ASP A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.61e-01
  chirality pdb=" CA  ASP B 356 "
            pdb=" N   ASP B 356 "
            pdb=" C   ASP B 356 "
            pdb=" CB  ASP B 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.38e-01
  chirality pdb=" CB  ILE A 305 "
            pdb=" CA  ILE A 305 "
            pdb=" CG1 ILE A 305 "
            pdb=" CG2 ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.52    0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 797 not shown)

  Planarity restraints: 776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 220 "   -0.010 2.00e-02 2.50e+03   1.21e-02 2.18e+00
        pdb=" CG  HIS B 220 "    0.026 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 220 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 220 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 220 "    0.002 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 220 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 220 "    0.011 2.00e-02 2.50e+03   1.20e-02 2.16e+00
        pdb=" CG  HIS A 220 "   -0.026 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 220 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 220 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 220 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 220 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 365 "    0.006 2.00e-02 2.50e+03   1.22e-02 1.49e+00
        pdb=" C   GLU B 365 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   GLU B 365 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ASP B 366 "    0.007 2.00e-02 2.50e+03
  ... (remaining 773 not shown)

  Histogram of nonbonded interaction distances:
        1.46 -     2.15: 3
        2.15 -     2.84: 1695
        2.84 -     3.52: 7055
        3.52 -     4.21: 10088
        4.21 -     4.90: 17725
  Nonbonded interactions: 36566
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 352 "
            pdb="ZN    ZN A 401 "
     model   vdw
     1.461 2.230
  nonbonded pdb=" OE2 GLU B 352 "
            pdb="ZN    ZN B 401 "
     model   vdw
     1.781 2.230
  nonbonded pdb=" OG1 THR B 348 "
            pdb=" OG1 THR A 348 "
     model   vdw
     2.140 3.040
  nonbonded pdb=" O   GLN B 227 "
            pdb=" OG  SER B 230 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   GLN A 227 "
            pdb=" OG  SER A 230 "
     model   vdw
     2.185 3.040
  ... (remaining 36561 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     16.380
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
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      :  0.007   0.036   4714  Z= 0.456
  Angle     :  0.770   6.410   6422  Z= 0.430
  Chirality :  0.043   0.196    800
  Planarity :  0.003   0.022    776
  Dihedral  : 14.372  64.582   1624
  Min Nonbonded Distance : 1.461

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  : 12.50 %
    Favored  : 87.30 %
  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: -3.83 (0.30), residues: 594
  helix: -1.82 (0.22), residues: 384
  sheet: -3.84 (0.69), residues: 46
  loop : -3.48 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 122 
 HIS   0.014   0.002   HIS B 220 
 PHE   0.020   0.002   PHE A  82 
 TYR   0.011   0.002   TYR B 160 
 ARG   0.001   0.000   ARG A 331 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 134
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: B   71 LYS cc_start: 0.8578 (ttmt) cc_final: 0.8312 (ttpp)
REVERT: B  288 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8783 (ttmm)
REVERT: B  295 ASP cc_start: 0.7659 (p0) cc_final: 0.7168 (p0)
REVERT: A   71 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8300 (ttpp)
REVERT: A   85 MET cc_start: 0.6314 (tmm) cc_final: 0.5953 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 134
  average time/residue: 0.2065
  time to fit residues: 33.4396
Evaluate side-chains
  88 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 47 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
B 172 GLN
B 211 ASN
A 106 HIS
A 172 GLN
A 211 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.118236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.097419 restraints weight = 8688.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.099891 restraints weight = 5132.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.101560 restraints weight = 3674.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4714  Z= 0.178
  Angle     :  0.566   5.306   6422  Z= 0.295
  Chirality :  0.038   0.111    800
  Planarity :  0.004   0.032    776
  Dihedral  :  4.616  21.033    630
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.45 %
    Favored  : 83.01 %
  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: -0.31 (0.36), residues: 594
  helix:  0.97 (0.26), residues: 390
  sheet: -3.75 (0.73), residues: 40
  loop : -2.06 (0.53), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.006   0.001   HIS A 197 
 PHE   0.016   0.001   PHE A  82 
 TYR   0.006   0.001   TYR A 160 
 ARG   0.002   0.000   ARG B 325 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 122
  time to evaluate  : 0.481 
Fit side-chains
REVERT: B   72 TRP cc_start: 0.7179 (m100) cc_final: 0.6563 (t-100)
REVERT: A   72 TRP cc_start: 0.7053 (m100) cc_final: 0.6656 (t-100)
REVERT: A   85 MET cc_start: 0.6305 (tmm) cc_final: 0.5904 (tmm)
  outliers start: 13
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1056
  time to fit residues: 18.8785
Evaluate side-chains
  98 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 12 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0040
   chunk 4 optimal weight:    0.9980
   overall best weight:    1.3596

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

Flipped N/Q/H residues before XYZ refinement:
B 211 ASN
A 211 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.098222 restraints weight = 8767.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.100730 restraints weight = 5164.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.102380 restraints weight = 3690.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.2995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   4714  Z= 0.170
  Angle     :  0.567   8.060   6422  Z= 0.285
  Chirality :  0.038   0.134    800
  Planarity :  0.004   0.032    776
  Dihedral  :  4.278  20.805    630
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 20.70 %
    Favored  : 75.59 %
  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:  0.77 (0.37), residues: 594
  helix:  1.92 (0.26), residues: 384
  sheet: -3.81 (0.67), residues: 40
  loop : -1.70 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 122 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.012   0.001   PHE A  82 
 TYR   0.019   0.001   TYR B  67 
 ARG   0.000   0.000   ARG B 331 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.500 
Fit side-chains
REVERT: B   72 TRP cc_start: 0.7201 (m100) cc_final: 0.6504 (t-100)
REVERT: A   72 TRP cc_start: 0.7205 (m100) cc_final: 0.6628 (t-100)
REVERT: A   85 MET cc_start: 0.6328 (tmm) cc_final: 0.5916 (tmm)
  outliers start: 19
  outliers final: 19
  residues processed: 105
  average time/residue: 0.1047
  time to fit residues: 15.5132
Evaluate side-chains
  106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain B residue  353 SER
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0970
   chunk 17 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    7.9990
   chunk 25 optimal weight:    8.9990
   chunk 2 optimal weight:    9.9990
   chunk 37 optimal weight:    6.9990
   chunk 54 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.1382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.120724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100205 restraints weight = 8798.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.102738 restraints weight = 5184.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104378 restraints weight = 3704.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4714  Z= 0.159
  Angle     :  0.546   6.304   6422  Z= 0.273
  Chirality :  0.037   0.109    800
  Planarity :  0.003   0.033    776
  Dihedral  :  4.072  19.082    630
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 21.29 %
    Favored  : 74.22 %
  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:  1.11 (0.37), residues: 594
  helix:  2.04 (0.26), residues: 392
  sheet: -3.37 (0.72), residues: 40
  loop : -1.47 (0.55), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 122 
 HIS   0.007   0.001   HIS A 220 
 PHE   0.027   0.001   PHE B 240 
 TYR   0.019   0.001   TYR B  67 
 ARG   0.001   0.000   ARG B 215 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.503 
Fit side-chains
REVERT: B   72 TRP cc_start: 0.7288 (OUTLIER) cc_final: 0.6535 (t-100)
REVERT: B  110 ASN cc_start: 0.7962 (m-40) cc_final: 0.7660 (m-40)
REVERT: A   72 TRP cc_start: 0.7217 (m100) cc_final: 0.6525 (t-100)
REVERT: A  315 LEU cc_start: 0.9077 (tt) cc_final: 0.8868 (tt)
  outliers start: 23
  outliers final: 18
  residues processed: 110
  average time/residue: 0.1052
  time to fit residues: 16.5553
Evaluate side-chains
  102 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    0.0040
   chunk 41 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    2.1998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.118680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.098219 restraints weight = 8969.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.100697 restraints weight = 5288.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102299 restraints weight = 3792.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4714  Z= 0.209
  Angle     :  0.591   9.325   6422  Z= 0.294
  Chirality :  0.040   0.151    800
  Planarity :  0.004   0.034    776
  Dihedral  :  4.118  19.449    630
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 24.41 %
    Favored  : 70.70 %
  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:  1.05 (0.37), residues: 594
  helix:  2.02 (0.26), residues: 392
  sheet: -3.47 (0.63), residues: 46
  loop : -1.41 (0.56), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 122 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.020   0.001   PHE B 240 
 TYR   0.019   0.001   TYR B  67 
 ARG   0.001   0.000   ARG B 215 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.475 
Fit side-chains
REVERT: B  348 THR cc_start: 0.8121 (p) cc_final: 0.7697 (p)
REVERT: A   72 TRP cc_start: 0.7228 (OUTLIER) cc_final: 0.6469 (t-100)
REVERT: A  348 THR cc_start: 0.7994 (p) cc_final: 0.7595 (p)
  outliers start: 25
  outliers final: 22
  residues processed: 107
  average time/residue: 0.0998
  time to fit residues: 15.4394
Evaluate side-chains
  107 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 84
  time to evaluate  : 0.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  151 ILE
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 24 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 57 optimal weight:    9.9990
   chunk 17 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 59 optimal weight:    0.4980
   overall best weight:    3.0988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.095965 restraints weight = 8896.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.098414 restraints weight = 5269.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.100003 restraints weight = 3780.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4714  Z= 0.258
  Angle     :  0.650   9.906   6422  Z= 0.318
  Chirality :  0.040   0.135    800
  Planarity :  0.004   0.036    776
  Dihedral  :  4.285  20.108    630
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 26.37 %
    Favored  : 68.95 %
  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:  1.01 (0.36), residues: 594
  helix:  1.89 (0.26), residues: 390
  sheet: -3.14 (0.83), residues: 34
  loop : -1.40 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 122 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.017   0.001   PHE B 240 
 TYR   0.019   0.001   TYR B  67 
 ARG   0.002   0.000   ARG B 215 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 99
  time to evaluate  : 0.507 
Fit side-chains
REVERT: B  215 ARG cc_start: 0.8055 (ttt-90) cc_final: 0.7811 (ttp80)
REVERT: A  151 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8770 (mm)
REVERT: A  215 ARG cc_start: 0.8025 (ttt-90) cc_final: 0.7689 (ttp-170)
  outliers start: 24
  outliers final: 21
  residues processed: 113
  average time/residue: 0.1163
  time to fit residues: 18.0237
Evaluate side-chains
  116 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 35 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 174 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.115082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.094730 restraints weight = 8869.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.097012 restraints weight = 5375.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.098646 restraints weight = 3936.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4714  Z= 0.305
  Angle     :  0.654   8.253   6422  Z= 0.332
  Chirality :  0.041   0.116    800
  Planarity :  0.004   0.037    776
  Dihedral  :  4.486  20.855    630
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 26.37 %
    Favored  : 68.36 %
  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:  0.82 (0.36), residues: 594
  helix:  1.76 (0.26), residues: 390
  sheet: -3.14 (0.85), residues: 34
  loop : -1.54 (0.52), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 122 
 HIS   0.011   0.001   HIS B 220 
 PHE   0.031   0.002   PHE A 240 
 TYR   0.019   0.002   TYR B  67 
 ARG   0.002   0.000   ARG B 215 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.519 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6162 (tp-100) cc_final: 0.5820 (pm20)
REVERT: A  151 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8792 (mm)
  outliers start: 27
  outliers final: 24
  residues processed: 114
  average time/residue: 0.1164
  time to fit residues: 18.2471
Evaluate side-chains
  114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  305 ILE
Chi-restraints excluded: chain B residue  309 THR
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  167 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:   10.0000
   chunk 11 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 53 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 16 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0270
   overall best weight:    1.3442

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.120399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.100464 restraints weight = 8885.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.102922 restraints weight = 5298.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.104386 restraints weight = 3812.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4714  Z= 0.182
  Angle     :  0.618  11.829   6422  Z= 0.305
  Chirality :  0.039   0.148    800
  Planarity :  0.004   0.037    776
  Dihedral  :  4.107  19.792    630
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 29.49 %
    Favored  : 66.80 %
  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:  1.05 (0.36), residues: 594
  helix:  2.01 (0.26), residues: 384
  sheet: -3.03 (0.88), residues: 34
  loop : -1.53 (0.51), residues: 176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.010   0.001   HIS B 220 
 PHE   0.028   0.001   PHE A 240 
 TYR   0.020   0.001   TYR B  67 
 ARG   0.001   0.000   ARG A 215 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.514 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6292 (tp-100) cc_final: 0.5211 (mt0)
  outliers start: 19
  outliers final: 14
  residues processed: 106
  average time/residue: 0.1011
  time to fit residues: 15.4560
Evaluate side-chains
  103 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 30 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 56 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.118395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.098136 restraints weight = 9069.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100582 restraints weight = 5376.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.102185 restraints weight = 3863.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
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   0.031   4714  Z= 0.220
  Angle     :  0.644  11.902   6422  Z= 0.316
  Chirality :  0.039   0.123    800
  Planarity :  0.004   0.038    776
  Dihedral  :  4.169  17.954    630
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 29.10 %
    Favored  : 67.58 %
  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:  1.02 (0.36), residues: 594
  helix:  1.85 (0.26), residues: 390
  sheet: -3.05 (0.86), residues: 34
  loop : -1.28 (0.53), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 122 
 HIS   0.018   0.001   HIS B 220 
 PHE   0.027   0.002   PHE A 240 
 TYR   0.019   0.001   TYR B  67 
 ARG   0.001   0.000   ARG A 165 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.535 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6262 (tp-100) cc_final: 0.5127 (mt0)
  outliers start: 17
  outliers final: 16
  residues processed: 104
  average time/residue: 0.1029
  time to fit residues: 15.3883
Evaluate side-chains
  102 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0970
   chunk 0 optimal weight:   30.0000
   chunk 38 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 5 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   overall best weight:    1.6982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.119825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.099710 restraints weight = 8881.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.102153 restraints weight = 5285.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.103732 restraints weight = 3791.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4714  Z= 0.195
  Angle     :  0.644  12.601   6422  Z= 0.311
  Chirality :  0.039   0.120    800
  Planarity :  0.004   0.039    776
  Dihedral  :  4.108  18.729    630
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 29.69 %
    Favored  : 66.99 %
  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:  1.02 (0.36), residues: 594
  helix:  1.87 (0.25), residues: 392
  sheet: -2.96 (0.89), residues: 34
  loop : -1.43 (0.53), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.016   0.001   HIS B 220 
 PHE   0.025   0.001   PHE A 240 
 TYR   0.021   0.001   TYR B  67 
 ARG   0.001   0.000   ARG B 215 

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.504 
Fit side-chains
REVERT: B  174 GLN cc_start: 0.6296 (tp-100) cc_final: 0.5203 (mt0)
  outliers start: 17
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1084
  time to fit residues: 16.2182
Evaluate side-chains
  106 residues out of total 518 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   72 TRP
Chi-restraints excluded: chain B residue  163 CYS
Chi-restraints excluded: chain B residue  180 ILE
Chi-restraints excluded: chain B residue  250 ILE
Chi-restraints excluded: chain B residue  264 ILE
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  295 ASP
Chi-restraints excluded: chain B residue  319 VAL
Chi-restraints excluded: chain A residue   72 TRP
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  250 ILE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  295 ASP
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  353 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 2 optimal weight:    9.9990
   chunk 44 optimal weight:    0.0670
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 55 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.1524

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

Flipped N/Q/H residues before XYZ refinement:
** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.121794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.101746 restraints weight = 8858.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.104168 restraints weight = 5268.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.105797 restraints weight = 3802.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.4220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4714  Z= 0.173
  Angle     :  0.639  12.419   6422  Z= 0.305
  Chirality :  0.038   0.125    800
  Planarity :  0.004   0.039    776
  Dihedral  :  3.927  16.263    630
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 30.08 %
    Favored  : 66.60 %
  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:  1.21 (0.36), residues: 594
  helix:  1.97 (0.25), residues: 392
  sheet: -2.47 (1.04), residues: 28
  loop : -1.38 (0.51), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 122 
 HIS   0.015   0.001   HIS B 220 
 PHE   0.023   0.001   PHE A 240 
 TYR   0.021   0.001   TYR B  67 
 ARG   0.000   0.000   ARG B 325 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1475.37 seconds
wall clock time: 26 minutes 41.77 seconds (1601.77 seconds total)