Starting phenix.real_space_refine
on Tue Feb 11 15:30:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7u9p_26404/02_2025/7u9p_26404.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7u9p_26404/02_2025/7u9p_26404.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7u9p_26404/02_2025/7u9p_26404.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7u9p_26404/02_2025/7u9p_26404.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7u9p_26404/02_2025/7u9p_26404.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7u9p_26404/02_2025/7u9p_26404.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      23      5.16       5
     C    3920      2.51       5
     N    1005      2.21       5
     O    1178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6126
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2116
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 268, 2116
          Classifications: {'peptide': 268}
          Link IDs: {'PTRANS': 16, 'TRANS': 251}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1507
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 10, 'TRANS': 173}
          Chain breaks: 9
    Chain: "H"
      Number of atoms: 1274
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 1274
          Classifications: {'peptide': 168}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 159}
          Chain breaks: 3
    Chain: "L"
      Number of atoms: 1173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 1173
          Classifications: {'peptide': 153}
          Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 142}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 4.52, per 1000 atoms: 0.74
  Number of scatterers: 6126
  At special positions: 0
  Unit cell: (78.57, 89.046, 123.093, 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      23     16.00
     O    1178      8.00
     N    1005      7.00
     C    3920      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 538 " - pdb=" SG  CYS A 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.05
    Simple disulfide: pdb=" SG  CYS H 102 " - pdb=" SG  CYS H 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG B1301 " - " ASN B  61 "
      " NAG B1302 " - " ASN B 234 "
      " NAG B1303 " - " ASN B 282 "
  Time building additional restraints: 1.42
  Conformation dependent library (CDL) restraints added in 895.2 milliseconds
  

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1440

  Finding SS restraints...
    Secondary structure from input PDB file:
      6 helices and 16 sheets defined
      4.1% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.635A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 4.052A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 384 through 388'
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.973A  pdb=" N   SER H  31 " --> pdb=" O   SER H  28 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   TYR H  32 " --> pdb=" O   PHE H  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 28 through 32'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 327 through 328
    Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358
      removed outlier: 4.236A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   VAL A 395 " --> pdb=" O   SER A 514 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   SER A 514 " --> pdb=" O   VAL A 395 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   ALA A 397 " --> pdb=" O   VAL A 512 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL A 512 " --> pdb=" O   ALA A 397 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   SER A 399 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   VAL A 510 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   VAL A 401 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   TYR A 508 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR A 376 " --> pdb=" O   ALA A 435 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358
      removed outlier: 4.236A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   VAL A 524 " --> pdb=" O   PHE A 392 " (cutoff:3.500A)
      removed outlier: 8.604A  pdb=" N   ASN A 394 " --> pdb=" O   ALA A 522 " (cutoff:3.500A)
      removed outlier: 10.742A  pdb=" N   ALA A 522 " --> pdb=" O   ASN A 394 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 540
      removed outlier: 3.624A  pdb=" N   THR A 588 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 565 through 566
      removed outlier: 7.263A  pdb=" N   PHE A 565 " --> pdb=" O   PHE B  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'B' and resid 28 through 30
    Processing sheet with id=AA7, first strand: chain 'B' and resid 48 through 55
      removed outlier: 3.521A  pdb=" N   LYS B 278 " --> pdb=" O   ASP B 287 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 84 through 85
      removed outlier: 3.575A  pdb=" N   LYS B 129 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 224 through 229
      removed outlier: 5.995A  pdb=" N   SER B 205 " --> pdb=" O   PRO B 225 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL B 227 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE B 203 " --> pdb=" O   VAL B 227 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASN B 188 " --> pdb=" O   GLU B  96 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA B  93 " --> pdb=" O   TYR B 266 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.565A  pdb=" N   LEU H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   SER H  25 " --> pdb=" O   LEU H   3 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLU H   5 " --> pdb=" O   GLU H  23 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 6.846A  pdb=" N   MET H  34 " --> pdb=" O   ALA H  50 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   ALA H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 18 through 20
      removed outlier: 3.866A  pdb=" N   LEU H  81 " --> pdb=" O   LEU H  20 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 149 through 150
      removed outlier: 3.635A  pdb=" N   SER H 190 " --> pdb=" O   CYS H 150 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 5 through 7
      removed outlier: 3.931A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   ILE L  75 " --> pdb=" O   VAL L  19 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.576A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 103 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ALA L  13 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
      removed outlier: 5.636A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 114 through 115

    129 hydrogen bonds defined for protein.
    309 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.88

  Time building geometry restraints manager: 1.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1790
        1.33 -     1.46: 1646
        1.46 -     1.58: 2808
        1.58 -     1.71: 0
        1.71 -     1.84: 27
  Bond restraints: 6271
  Sorted by residual:
  bond pdb=" CB  ARG A 509 "
       pdb=" CG  ARG A 509 "
    ideal  model  delta    sigma   weight residual
    1.520  1.423  0.097 3.00e-02 1.11e+03 1.04e+01
  bond pdb=" C   VAL A 433 "
       pdb=" N   ILE A 434 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.42e-02 4.96e+03 7.18e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.73e+00
  bond pdb=" CG  MET L   4 "
       pdb=" SD  MET L   4 "
    ideal  model  delta    sigma   weight residual
    1.803  1.743  0.060 2.50e-02 1.60e+03 5.73e+00
  bond pdb=" CA  SER A 494 "
       pdb=" CB  SER A 494 "
    ideal  model  delta    sigma   weight residual
    1.532  1.492  0.040 1.74e-02 3.30e+03 5.22e+00
  ... (remaining 6266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 8104
        2.45 -     4.90: 348
        4.90 -     7.35: 46
        7.35 -     9.80: 11
        9.80 -    12.25: 1
  Bond angle restraints: 8510
  Sorted by residual:
  angle pdb=" N   LYS L 169 "
        pdb=" CA  LYS L 169 "
        pdb=" C   LYS L 169 "
      ideal   model   delta    sigma   weight residual
     114.04  106.50    7.54 1.24e+00 6.50e-01 3.69e+01
  angle pdb=" CA  CYS A 525 "
        pdb=" CB  CYS A 525 "
        pdb=" SG  CYS A 525 "
      ideal   model   delta    sigma   weight residual
     114.40  126.65  -12.25 2.30e+00 1.89e-01 2.84e+01
  angle pdb=" C   CYS H 107 "
        pdb=" N   ASP H 108 "
        pdb=" CA  ASP H 108 "
      ideal   model   delta    sigma   weight residual
     121.54  131.22   -9.68 1.91e+00 2.74e-01 2.57e+01
  angle pdb=" C   SER B  31 "
        pdb=" N   PHE B  32 "
        pdb=" CA  PHE B  32 "
      ideal   model   delta    sigma   weight residual
     121.54  130.88   -9.34 1.91e+00 2.74e-01 2.39e+01
  angle pdb=" N   ALA H 109 "
        pdb=" CA  ALA H 109 "
        pdb=" C   ALA H 109 "
      ideal   model   delta    sigma   weight residual
     108.02   99.93    8.09 1.78e+00 3.16e-01 2.06e+01
  ... (remaining 8505 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.49: 3540
       16.49 -    32.98: 171
       32.98 -    49.47: 38
       49.47 -    65.96: 1
       65.96 -    82.45: 4
  Dihedral angle restraints: 3754
    sinusoidal: 1516
      harmonic: 2238
  Sorted by residual:
  dihedral pdb=" CB  CYS H 102 "
           pdb=" SG  CYS H 102 "
           pdb=" SG  CYS H 107 "
           pdb=" CB  CYS H 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.76  -68.76     1      1.00e+01 1.00e-02 6.12e+01
  dihedral pdb=" CA  CYS A 525 "
           pdb=" C   CYS A 525 "
           pdb=" N   GLY A 526 "
           pdb=" CA  GLY A 526 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.48  -25.52     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  GLU L 143 "
           pdb=" C   GLU L 143 "
           pdb=" N   ALA L 144 "
           pdb=" CA  ALA L 144 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.66  -23.34     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 3751 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 643
       0.062 -    0.124: 260
       0.124 -    0.185: 38
       0.185 -    0.247: 10
       0.247 -    0.309: 2
  Chirality restraints: 953
  Sorted by residual:
  chirality pdb=" CG  LEU L  33 "
            pdb=" CB  LEU L  33 "
            pdb=" CD1 LEU L  33 "
            pdb=" CD2 LEU L  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.28   -0.31 2.00e-01 2.50e+01 2.38e+00
  chirality pdb=" CA  ASP H 108 "
            pdb=" N   ASP H 108 "
            pdb=" C   ASP H 108 "
            pdb=" CB  ASP H 108 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CB  VAL A 350 "
            pdb=" CA  VAL A 350 "
            pdb=" CG1 VAL A 350 "
            pdb=" CG2 VAL A 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 950 not shown)

  Planarity restraints: 1087
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 462 "   -0.049 5.00e-02 4.00e+02   7.42e-02 8.81e+00
        pdb=" N   PRO A 463 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 113 "    0.027 2.00e-02 2.50e+03   1.73e-02 7.49e+00
        pdb=" CG  TRP H 113 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 113 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 113 "   -0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 113 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 113 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 113 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 113 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 113 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 113 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA L  43 "   -0.043 5.00e-02 4.00e+02   6.49e-02 6.74e+00
        pdb=" N   PRO L  44 "    0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO L  44 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO L  44 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1084 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1907
        2.82 -     3.34: 4660
        3.34 -     3.86: 9200
        3.86 -     4.38: 9990
        4.38 -     4.90: 18434
  Nonbonded interactions: 44191
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 394 "
            pdb=" OH  TYR B 200 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OH  TYR B  37 "
            pdb=" O   LEU B  54 "
     model   vdw
     2.342 3.040
  nonbonded pdb=" OH  TYR A 351 "
            pdb=" NE2 HIS H 101 "
     model   vdw
     2.347 3.120
  nonbonded pdb=" OG1 THR B 108 "
            pdb=" O   ASN B 234 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" NH2 ARG A 454 "
            pdb=" O   ASP A 467 "
     model   vdw
     2.352 3.120
  ... (remaining 44186 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.580
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.220
  Find NCS groups from input model:        0.080
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
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      :  0.013   0.102   6271  Z= 0.826
  Angle     :  1.181  12.250   8510  Z= 0.645
  Chirality :  0.067   0.309    953
  Planarity :  0.009   0.074   1083
  Dihedral  : 10.398  82.447   2290
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  : 11.56 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  3.54 %
    Favored  : 96.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -4.34 (0.25), residues: 735
  helix: -4.63 (0.62), residues: 18
  sheet: -2.25 (0.31), residues: 238
  loop : -3.34 (0.22), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.006   TRP H 113 
 HIS   0.008   0.002   HIS H  35 
 PHE   0.041   0.005   PHE A 347 
 TYR   0.042   0.005   TYR H  94 
 ARG   0.016   0.002   ARG A 509 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.717 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8216 (mm-40) cc_final: 0.7967 (mm-40)
REVERT: A  564 GLN cc_start: 0.7891 (mt0) cc_final: 0.7689 (mt0)
REVERT: B  281 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8388 (tm-30)
REVERT: L  108 ARG cc_start: 0.7466 (ptm-80) cc_final: 0.7153 (ptm160)
  outliers start: 1
  outliers final: 1
  residues processed: 122
  average time/residue: 0.2405
  time to fit residues: 36.5434
Evaluate side-chains
  100 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  524 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 56 optimal weight:   30.0000
   chunk 31 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
A 460 ASN
H  39 GLN
H 181 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.151953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.121833 restraints weight = 7935.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.123154 restraints weight = 4942.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.124630 restraints weight = 3883.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6271  Z= 0.172
  Angle     :  0.599   9.045   8510  Z= 0.312
  Chirality :  0.044   0.226    953
  Planarity :  0.005   0.054   1083
  Dihedral  :  5.487  22.921    915
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  :  7.37 %
    Favored  : 90.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -3.51 (0.27), residues: 735
  helix: -4.56 (0.52), residues: 20
  sheet: -1.46 (0.33), residues: 240
  loop : -2.87 (0.23), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 436 
 HIS   0.003   0.001   HIS B 207 
 PHE   0.015   0.001   PHE A 486 
 TYR   0.018   0.002   TYR L 140 
 ARG   0.003   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: A  414 GLN cc_start: 0.8151 (mm-40) cc_final: 0.7924 (mm110)
REVERT: A  515 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.8222 (p90)
REVERT: B   32 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5825 (m-10)
REVERT: H  110 PHE cc_start: 0.8479 (OUTLIER) cc_final: 0.8187 (p90)
REVERT: L  108 ARG cc_start: 0.7353 (ptm-80) cc_final: 0.7043 (ptm160)
  outliers start: 13
  outliers final: 7
  residues processed: 112
  average time/residue: 0.2125
  time to fit residues: 30.2536
Evaluate side-chains
  105 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  486 PHE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   32 PHE
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 43 optimal weight:    0.3980
   chunk 12 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 506 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.148603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.118182 restraints weight = 8071.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.119258 restraints weight = 5592.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.121514 restraints weight = 4366.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6271  Z= 0.199
  Angle     :  0.577   7.241   8510  Z= 0.297
  Chirality :  0.043   0.151    953
  Planarity :  0.005   0.043   1083
  Dihedral  :  4.972  20.244    914
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  :  8.55 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -3.08 (0.28), residues: 735
  helix: -3.82 (0.87), residues: 14
  sheet: -1.18 (0.33), residues: 246
  loop : -2.61 (0.24), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.013   0.002   PHE A 486 
 TYR   0.017   0.002   TYR L 140 
 ARG   0.003   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7978 (mm-40)
REVERT: A  515 PHE cc_start: 0.8689 (OUTLIER) cc_final: 0.8195 (p90)
REVERT: H  110 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8153 (p90)
  outliers start: 21
  outliers final: 11
  residues processed: 116
  average time/residue: 0.2124
  time to fit residues: 31.5190
Evaluate side-chains
  108 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  110 PHE
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 7 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0970
   chunk 74 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
B  81 ASN
B 239 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.150172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.119589 restraints weight = 8195.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.120751 restraints weight = 5776.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.123042 restraints weight = 4398.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6271  Z= 0.163
  Angle     :  0.548   6.732   8510  Z= 0.279
  Chirality :  0.043   0.143    953
  Planarity :  0.004   0.041   1083
  Dihedral  :  4.634  18.597    914
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 10.18 %
    Favored  : 87.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -2.64 (0.29), residues: 735
  helix: -3.74 (0.84), residues: 14
  sheet: -0.72 (0.35), residues: 235
  loop : -2.38 (0.25), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.013   0.001   PHE A 486 
 TYR   0.018   0.001   TYR L 140 
 ARG   0.003   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.646 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8037 (mm-40)
REVERT: A  515 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.8251 (p90)
REVERT: A  538 CYS cc_start: 0.4881 (t) cc_final: 0.4541 (t)
REVERT: B  139 PRO cc_start: 0.8299 (Cg_exo) cc_final: 0.8057 (Cg_endo)
REVERT: B  239 GLN cc_start: 0.8576 (tt0) cc_final: 0.8340 (tt0)
  outliers start: 19
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2167
  time to fit residues: 31.4011
Evaluate side-chains
  111 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain B residue  231 ILE
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 73 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0060
   chunk 17 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    0.8002

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.149875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.119648 restraints weight = 8052.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.120741 restraints weight = 5561.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.122519 restraints weight = 4454.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6271  Z= 0.167
  Angle     :  0.542   6.936   8510  Z= 0.275
  Chirality :  0.043   0.143    953
  Planarity :  0.004   0.039   1083
  Dihedral  :  4.496  17.352    914
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 10.03 %
    Favored  : 86.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -2.40 (0.29), residues: 735
  helix: -3.88 (0.68), residues: 20
  sheet: -0.46 (0.35), residues: 235
  loop : -2.21 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.011   0.001   PHE A 486 
 TYR   0.017   0.001   TYR L 140 
 ARG   0.002   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8013 (mm-40)
REVERT: A  515 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8269 (p90)
REVERT: A  538 CYS cc_start: 0.4925 (t) cc_final: 0.4579 (t)
  outliers start: 25
  outliers final: 17
  residues processed: 108
  average time/residue: 0.2067
  time to fit residues: 28.6074
Evaluate side-chains
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 43 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0670
   chunk 68 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.9524

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.149502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.118937 restraints weight = 8028.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.120009 restraints weight = 5795.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.121861 restraints weight = 4525.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6271  Z= 0.187
  Angle     :  0.547   6.381   8510  Z= 0.278
  Chirality :  0.043   0.153    953
  Planarity :  0.004   0.038   1083
  Dihedral  :  4.511  15.680    914
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 10.18 %
    Favored  : 85.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -2.22 (0.29), residues: 735
  helix: -3.68 (0.74), residues: 20
  sheet: -0.28 (0.35), residues: 235
  loop : -2.13 (0.26), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.011   0.001   PHE A 486 
 TYR   0.019   0.001   TYR L 140 
 ARG   0.001   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.672 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8343 (mm-40) cc_final: 0.8031 (mm-40)
REVERT: A  515 PHE cc_start: 0.8704 (OUTLIER) cc_final: 0.8284 (p90)
REVERT: A  538 CYS cc_start: 0.4968 (t) cc_final: 0.4590 (t)
  outliers start: 26
  outliers final: 17
  residues processed: 110
  average time/residue: 0.2173
  time to fit residues: 30.7616
Evaluate side-chains
  107 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 34 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 72 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.150473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.120125 restraints weight = 8067.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.121296 restraints weight = 5643.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.123543 restraints weight = 4437.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6271  Z= 0.163
  Angle     :  0.533   6.806   8510  Z= 0.271
  Chirality :  0.043   0.140    953
  Planarity :  0.004   0.039   1083
  Dihedral  :  4.391  14.628    914
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 11.36 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -2.06 (0.30), residues: 735
  helix: -3.54 (0.78), residues: 20
  sheet: -0.17 (0.35), residues: 237
  loop : -2.03 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.010   0.001   PHE A 486 
 TYR   0.019   0.001   TYR L 140 
 ARG   0.002   0.000   ARG B 190 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.715 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8356 (mm-40) cc_final: 0.8031 (mm-40)
REVERT: A  515 PHE cc_start: 0.8697 (OUTLIER) cc_final: 0.8262 (p90)
REVERT: A  538 CYS cc_start: 0.4963 (t) cc_final: 0.4596 (t)
REVERT: L   81 GLU cc_start: 0.7589 (pt0) cc_final: 0.7362 (pm20)
  outliers start: 22
  outliers final: 17
  residues processed: 109
  average time/residue: 0.2174
  time to fit residues: 30.1315
Evaluate side-chains
  109 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 26 optimal weight:    0.1980
   chunk 42 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0020
   chunk 7 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.7790

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.120176 restraints weight = 8009.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.121133 restraints weight = 5540.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.123445 restraints weight = 4370.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   6271  Z= 0.164
  Angle     :  0.535   6.000   8510  Z= 0.272
  Chirality :  0.043   0.139    953
  Planarity :  0.004   0.039   1083
  Dihedral  :  4.354  15.015    914
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 11.21 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.95 (0.30), residues: 735
  helix: -3.49 (0.82), residues: 20
  sheet: -0.09 (0.35), residues: 237
  loop : -1.96 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.010   0.001   PHE A 486 
 TYR   0.020   0.001   TYR L 140 
 ARG   0.002   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.694 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7963 (mm-40)
REVERT: A  515 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.8245 (p90)
REVERT: A  538 CYS cc_start: 0.5002 (t) cc_final: 0.4597 (t)
REVERT: B  239 GLN cc_start: 0.8590 (tt0) cc_final: 0.8221 (tt0)
REVERT: L   81 GLU cc_start: 0.7581 (pt0) cc_final: 0.7331 (pt0)
  outliers start: 23
  outliers final: 18
  residues processed: 108
  average time/residue: 0.2138
  time to fit residues: 29.4521
Evaluate side-chains
  110 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 9 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 65 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.151904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.120993 restraints weight = 8142.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.122493 restraints weight = 5731.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.124770 restraints weight = 4349.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6271  Z= 0.148
  Angle     :  0.523   5.996   8510  Z= 0.265
  Chirality :  0.042   0.138    953
  Planarity :  0.004   0.038   1083
  Dihedral  :  4.221  14.777    914
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 11.50 %
    Favored  : 85.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.85 (0.30), residues: 735
  helix: -3.46 (0.84), residues: 20
  sheet: -0.00 (0.35), residues: 237
  loop : -1.89 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.014   0.001   PHE B  32 
 TYR   0.020   0.001   TYR L 140 
 ARG   0.002   0.000   ARG B 237 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8384 (mm-40) cc_final: 0.8008 (mm-40)
REVERT: A  515 PHE cc_start: 0.8673 (OUTLIER) cc_final: 0.8243 (p90)
REVERT: A  538 CYS cc_start: 0.5000 (t) cc_final: 0.4599 (t)
REVERT: A  555 SER cc_start: 0.7985 (t) cc_final: 0.7535 (m)
REVERT: A  584 ILE cc_start: 0.8981 (mp) cc_final: 0.8638 (mp)
REVERT: B   34 ARG cc_start: 0.8339 (mmm160) cc_final: 0.8023 (mmm-85)
REVERT: B  239 GLN cc_start: 0.8572 (tt0) cc_final: 0.8189 (tt0)
REVERT: L   81 GLU cc_start: 0.7607 (pt0) cc_final: 0.7352 (pt0)
  outliers start: 21
  outliers final: 18
  residues processed: 110
  average time/residue: 0.2115
  time to fit residues: 29.5844
Evaluate side-chains
  114 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   13 GLN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   18 ARG
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 15 optimal weight:    8.9990
   chunk 12 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.147627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.116414 restraints weight = 8277.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.119060 restraints weight = 5614.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.121171 restraints weight = 4411.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6271  Z= 0.305
  Angle     :  0.616   6.079   8510  Z= 0.318
  Chirality :  0.046   0.353    953
  Planarity :  0.005   0.037   1083
  Dihedral  :  4.782  15.706    914
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 11.65 %
    Favored  : 84.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -2.02 (0.30), residues: 735
  helix: -3.31 (1.00), residues: 14
  sheet: -0.16 (0.35), residues: 237
  loop : -2.03 (0.26), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 436 
 HIS   0.003   0.001   HIS B 207 
 PHE   0.014   0.002   PHE A 377 
 TYR   0.019   0.002   TYR L 140 
 ARG   0.005   0.001   ARG B  34 

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

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

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1470 Ramachandran restraints generated.
    735 Oldfield, 0 Emsley, 735 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A  414 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8045 (mm-40)
REVERT: A  515 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8249 (p90)
REVERT: A  538 CYS cc_start: 0.5129 (t) cc_final: 0.4758 (t)
REVERT: A  555 SER cc_start: 0.8092 (t) cc_final: 0.7686 (m)
REVERT: A  584 ILE cc_start: 0.8998 (mp) cc_final: 0.8665 (mp)
REVERT: L   81 GLU cc_start: 0.7694 (pt0) cc_final: 0.7462 (pt0)
  outliers start: 23
  outliers final: 21
  residues processed: 110
  average time/residue: 0.2154
  time to fit residues: 30.4732
Evaluate side-chains
  116 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 SER
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  515 PHE
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  167 THR
Chi-restraints excluded: chain B residue  207 HIS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  227 VAL
Chi-restraints excluded: chain H residue    3 LEU
Chi-restraints excluded: chain H residue   13 GLN
Chi-restraints excluded: chain H residue   18 LEU
Chi-restraints excluded: chain H residue   78 THR
Chi-restraints excluded: chain H residue  117 THR
Chi-restraints excluded: chain H residue  160 VAL
Chi-restraints excluded: chain L residue   20 THR
Chi-restraints excluded: chain L residue  132 VAL
Chi-restraints excluded: chain L residue  163 VAL
Chi-restraints excluded: chain L residue  172 THR
Chi-restraints excluded: chain L residue  174 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0870
   chunk 21 optimal weight:    0.0870
   chunk 30 optimal weight:    0.0670
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.8478

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.149719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119003 restraints weight = 8191.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.121848 restraints weight = 5176.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.123307 restraints weight = 4391.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6271  Z= 0.174
  Angle     :  0.556   6.059   8510  Z= 0.283
  Chirality :  0.044   0.333    953
  Planarity :  0.004   0.038   1083
  Dihedral  :  4.474  15.889    914
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 12.68 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.90 %
    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: -1.91 (0.30), residues: 735
  helix: -3.38 (0.86), residues: 20
  sheet: -0.07 (0.35), residues: 237
  loop : -1.92 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 436 
 HIS   0.002   0.001   HIS B 207 
 PHE   0.010   0.001   PHE A 486 
 TYR   0.020   0.001   TYR L 140 
 ARG   0.002   0.000   ARG B  34 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2033.17 seconds
wall clock time: 37 minutes 12.90 seconds (2232.90 seconds total)