Starting phenix.real_space_refine
on Tue Feb 11 07:00:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdh_13338/02_2025/7pdh_13338.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdh_13338/02_2025/7pdh_13338.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdh_13338/02_2025/7pdh_13338.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdh_13338/02_2025/7pdh_13338.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdh_13338/02_2025/7pdh_13338.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdh_13338/02_2025/7pdh_13338.cif"
  }
  resolution = 4.0
  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=   0.000
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      33      5.16       5
     C    2847      2.51       5
     N     772      2.21       5
     O     864      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 4516
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3550
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3550
          Classifications: {'peptide': 449}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 9, 'TRANS': 439}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 966
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 3, 'TRANS': 124}
  Time building chain proxies: 3.78, per 1000 atoms: 0.84
  Number of scatterers: 4516
  At special positions: 0
  Unit cell: (95.598, 77.97, 77.97, 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      33     16.00
     O     864      8.00
     N     772      7.00
     C    2847      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: 1.17
  Conformation dependent library (CDL) restraints added in 554.3 milliseconds
  

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1058

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 4 sheets defined
      49.7% alpha, 29.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 320 through 336
      removed outlier: 3.688A  pdb=" N   GLU A 324 " --> pdb=" O   GLY A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 351 through 359
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 413 through 434
    Processing helix  chain 'A' and resid 457 through 481
    Processing helix  chain 'A' and resid 511 through 523
      removed outlier: 4.101A  pdb=" N   ASN A 515 " --> pdb=" O   SER A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 537
    Processing helix  chain 'A' and resid 1021 through 1037
    Processing helix  chain 'A' and resid 1038 through 1046
      removed outlier: 3.581A  pdb=" N   LYS A1046 " --> pdb=" O   ALA A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1068 through 1072
    Processing helix  chain 'A' and resid 1079 through 1097
      removed outlier: 3.924A  pdb=" N   TYR A1083 " --> pdb=" O   GLY A1079 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A1097 " --> pdb=" O   PHE A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1133 through 1157
      removed outlier: 4.308A  pdb=" N   GLN A1137 " --> pdb=" O   GLN A1133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1189 through 1201
      removed outlier: 4.063A  pdb=" N   ASN A1193 " --> pdb=" O   GLY A1189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1210 through 1219
      removed outlier: 4.192A  pdb=" N   LYS A1219 " --> pdb=" O   ARG A1215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 12 through 25
      removed outlier: 3.587A  pdb=" N   LYS B  16 " --> pdb=" O   SER B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 35
      removed outlier: 3.688A  pdb=" N   VAL B  30 " --> pdb=" O   GLN B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 58
    Processing helix  chain 'B' and resid 59 through 70
    Processing helix  chain 'B' and resid 82 through 91
    Processing helix  chain 'B' and resid 92 through 101
    Processing helix  chain 'B' and resid 115 through 123
      removed outlier: 3.735A  pdb=" N   LEU B 119 " --> pdb=" O   THR B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 133
      removed outlier: 4.157A  pdb=" N   ALA B 129 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 436 through 441
      removed outlier: 3.788A  pdb=" N   ILE A 438 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   THR A 440 " --> pdb=" O   CYS A 444 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   CYS A 444 " --> pdb=" O   THR A 440 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER A 394 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   GLY A 493 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   SER A 394 " --> pdb=" O   HIS A 491 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   HIS A 491 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU A 396 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   GLY A 489 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ALA A 398 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ARG A 487 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ILE A 400 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASN A 485 " --> pdb=" O   ILE A 400 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 441
      removed outlier: 3.788A  pdb=" N   ILE A 438 " --> pdb=" O   TYR A 446 " (cutoff:3.500A)
      removed outlier: 7.942A  pdb=" N   TYR A 446 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   THR A 440 " --> pdb=" O   CYS A 444 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   CYS A 444 " --> pdb=" O   THR A 440 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   SER A 394 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   GLY A 493 " --> pdb=" O   GLU A 392 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   SER A 394 " --> pdb=" O   HIS A 491 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   HIS A 491 " --> pdb=" O   SER A 394 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU A 396 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   GLY A 489 " --> pdb=" O   LEU A 396 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ALA A 398 " --> pdb=" O   ARG A 487 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ARG A 487 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   ILE A 400 " --> pdb=" O   ASN A 485 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   ASN A 485 " --> pdb=" O   ILE A 400 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   HIS A 530 " --> pdb=" O   MET A 486 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   VAL A 488 " --> pdb=" O   HIS A 530 " (cutoff:3.500A)
      removed outlier: 8.799A  pdb=" N   SER A 532 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
      removed outlier: 8.314A  pdb=" N   VAL A 490 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1109
      removed outlier: 7.386A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A1119 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A1057 " --> pdb=" O   GLY A1171 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1109
      removed outlier: 7.386A  pdb=" N   MET A1116 " --> pdb=" O   ILE A1108 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   SER A1119 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1119 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   SER A1057 " --> pdb=" O   GLY A1171 " (cutoff:3.500A)
      removed outlier: 6.084A  pdb=" N   GLY A1171 " --> pdb=" O   SER A1057 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   GLY A1059 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 6.762A  pdb=" N   ASN A1169 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   ILE A1061 " --> pdb=" O   GLY A1167 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   GLY A1167 " --> pdb=" O   ILE A1061 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   ALA A1063 " --> pdb=" O   ARG A1165 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG A1165 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR A1241 " --> pdb=" O   VAL A1209 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLY A1228 " --> pdb=" O   THR A1240 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1226 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   TYR A1226 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    723 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: 1.32

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1515
        1.34 -     1.46: 958
        1.46 -     1.58: 2068
        1.58 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 4595
  Sorted by residual:
  bond pdb=" C   CYS A 451 "
       pdb=" N   PRO A 452 "
    ideal  model  delta    sigma   weight residual
    1.336  1.356 -0.020 1.20e-02 6.94e+03 2.79e+00
  bond pdb=" C   ILE A 334 "
       pdb=" N   HIS A 335 "
    ideal  model  delta    sigma   weight residual
    1.334  1.321  0.013 1.38e-02 5.25e+03 8.76e-01
  bond pdb=" CG  GLU A 431 "
       pdb=" CD  GLU A 431 "
    ideal  model  delta    sigma   weight residual
    1.516  1.494  0.022 2.50e-02 1.60e+03 7.77e-01
  bond pdb=" CD  GLU A 432 "
       pdb=" OE1 GLU A 432 "
    ideal  model  delta    sigma   weight residual
    1.249  1.232  0.017 1.90e-02 2.77e+03 7.58e-01
  bond pdb=" CG  LEU A1032 "
       pdb=" CD2 LEU A1032 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.028 3.30e-02 9.18e+02 7.41e-01
  ... (remaining 4590 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 5948
        1.49 -     2.98: 183
        2.98 -     4.47: 36
        4.47 -     5.96: 17
        5.96 -     7.46: 5
  Bond angle restraints: 6189
  Sorted by residual:
  angle pdb=" N   VAL A 337 "
        pdb=" CA  VAL A 337 "
        pdb=" C   VAL A 337 "
      ideal   model   delta    sigma   weight residual
     113.20  109.42    3.78 9.60e-01 1.09e+00 1.55e+01
  angle pdb=" C   ILE A 334 "
        pdb=" N   HIS A 335 "
        pdb=" CA  HIS A 335 "
      ideal   model   delta    sigma   weight residual
     121.18  114.78    6.40 1.98e+00 2.55e-01 1.05e+01
  angle pdb=" N   GLU A 431 "
        pdb=" CA  GLU A 431 "
        pdb=" CB  GLU A 431 "
      ideal   model   delta    sigma   weight residual
     110.12  114.84   -4.72 1.47e+00 4.63e-01 1.03e+01
  angle pdb=" N   GLU A1141 "
        pdb=" CA  GLU A1141 "
        pdb=" CB  GLU A1141 "
      ideal   model   delta    sigma   weight residual
     110.01  114.55   -4.54 1.45e+00 4.76e-01 9.81e+00
  angle pdb=" C   THR A1181 "
        pdb=" N   LYS A1182 "
        pdb=" CA  LYS A1182 "
      ideal   model   delta    sigma   weight residual
     122.59  127.41   -4.82 1.57e+00 4.06e-01 9.43e+00
  ... (remaining 6184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.46: 2461
       17.46 -    34.92: 251
       34.92 -    52.38: 31
       52.38 -    69.84: 1
       69.84 -    87.30: 8
  Dihedral angle restraints: 2752
    sinusoidal: 1102
      harmonic: 1650
  Sorted by residual:
  dihedral pdb=" CA  TRP A1159 "
           pdb=" C   TRP A1159 "
           pdb=" N   PHE A1160 "
           pdb=" CA  PHE A1160 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.10   18.90     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  THR A1180 "
           pdb=" C   THR A1180 "
           pdb=" N   THR A1181 "
           pdb=" CA  THR A1181 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.24  -16.76     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  MET A 338 "
           pdb=" C   MET A 338 "
           pdb=" N   PRO A 339 "
           pdb=" CA  PRO A 339 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.30  -16.70     0      5.00e+00 4.00e-02 1.11e+01
  ... (remaining 2749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 409
       0.031 -    0.062: 170
       0.062 -    0.093: 60
       0.093 -    0.123: 32
       0.123 -    0.154: 9
  Chirality restraints: 680
  Sorted by residual:
  chirality pdb=" CA  PRO A 339 "
            pdb=" N   PRO A 339 "
            pdb=" C   PRO A 339 "
            pdb=" CB  PRO A 339 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.15 2.00e-01 2.50e+01 5.96e-01
  chirality pdb=" CA  ASP A 541 "
            pdb=" N   ASP A 541 "
            pdb=" C   ASP A 541 "
            pdb=" CB  ASP A 541 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.85e-01
  chirality pdb=" CA  GLU A1141 "
            pdb=" N   GLU A1141 "
            pdb=" C   GLU A1141 "
            pdb=" CB  GLU A1141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.74e-01
  ... (remaining 677 not shown)

  Planarity restraints: 803
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  56 "    0.017 2.00e-02 2.50e+03   1.34e-02 4.52e+00
        pdb=" CG  TRP B  56 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  56 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  56 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  56 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  56 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  56 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1037 "    0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO A1038 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A1038 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A1038 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1141 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.84e+00
        pdb=" C   GLU A1141 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLU A1141 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A1142 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 800 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 196
        2.72 -     3.26: 4863
        3.26 -     3.81: 7475
        3.81 -     4.35: 8807
        4.35 -     4.90: 14458
  Nonbonded interactions: 35799
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 420 "
            pdb=" O   ILE A1178 "
     model   vdw
     2.169 3.120
  nonbonded pdb=" O   ASP A 351 "
            pdb=" OG  SER A 354 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   ALA A 534 "
            pdb=" NZ  LYS A 537 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   SER A 532 "
            pdb=" OG1 THR A 535 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG1 THR B  49 "
            pdb=" ND1 HIS B  52 "
     model   vdw
     2.267 3.120
  ... (remaining 35794 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.130
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.600
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7005
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4595  Z= 0.202
  Angle     :  0.697   7.456   6189  Z= 0.379
  Chirality :  0.044   0.154    680
  Planarity :  0.004   0.049    803
  Dihedral  : 14.156  87.304   1694
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.42 %
    Favored  : 99.58 %
  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: -1.07 (0.35), residues: 567
  helix:  0.05 (0.32), residues: 273
  sheet: -0.78 (0.45), residues: 104
  loop : -1.63 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.010   0.002   PHE A 507 
 TYR   0.011   0.001   TYR A 445 
 ARG   0.003   0.000   ARG B  31 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1145 GLU cc_start: 0.8781 (mp0) cc_final: 0.8507 (mp0)
REVERT: A 1157 MET cc_start: 0.7946 (tmm) cc_final: 0.7725 (tmm)
REVERT: A 1238 MET cc_start: 0.8753 (tpp) cc_final: 0.8424 (tpp)
REVERT: B   78 TRP cc_start: 0.7358 (t60) cc_final: 0.7155 (t60)
REVERT: B  101 LYS cc_start: 0.7836 (mmpt) cc_final: 0.7627 (mmtm)
REVERT: B  109 GLN cc_start: 0.7076 (pt0) cc_final: 0.6852 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1516
  time to fit residues: 14.0001
Evaluate side-chains
  55 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A1067 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  48 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.104382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.078231 restraints weight = 16273.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.079023 restraints weight = 12910.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.079704 restraints weight = 9892.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7014
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4595  Z= 0.180
  Angle     :  0.626   6.495   6189  Z= 0.329
  Chirality :  0.043   0.150    680
  Planarity :  0.004   0.058    803
  Dihedral  :  4.683  18.211    615
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.21 %
    Favored  : 88.75 %
  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: -0.86 (0.34), residues: 567
  helix:  0.17 (0.31), residues: 274
  sheet: -0.54 (0.48), residues: 94
  loop : -1.51 (0.45), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.009   0.001   PHE A1062 
 TYR   0.012   0.001   TYR A 446 
 ARG   0.003   0.000   ARG B  31 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: A 1080 LYS cc_start: 0.7684 (mttp) cc_final: 0.7421 (mtmm)
REVERT: A 1147 MET cc_start: 0.8597 (ptt) cc_final: 0.7464 (ttm)
REVERT: A 1183 LEU cc_start: 0.7998 (mt) cc_final: 0.7152 (mp)
REVERT: A 1238 MET cc_start: 0.8739 (tpp) cc_final: 0.8293 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 61
  average time/residue: 0.1701
  time to fit residues: 13.4492
Evaluate side-chains
  55 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 51
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain B residue   49 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 11 optimal weight:    0.4980
   chunk 46 optimal weight:    5.9990
   chunk 37 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 4 optimal weight:    0.2980
   chunk 23 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.104799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.078966 restraints weight = 16205.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.080034 restraints weight = 11877.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.080696 restraints weight = 9518.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4595  Z= 0.152
  Angle     :  0.585   6.542   6189  Z= 0.306
  Chirality :  0.041   0.145    680
  Planarity :  0.004   0.055    803
  Dihedral  :  4.532  22.009    615
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.04 %
    Favored  : 86.88 %
  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: -0.73 (0.34), residues: 567
  helix:  0.31 (0.30), residues: 281
  sheet: -0.50 (0.50), residues: 88
  loop : -1.52 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  56 
 HIS   0.003   0.001   HIS A 335 
 PHE   0.009   0.001   PHE A 507 
 TYR   0.010   0.001   TYR A 446 
 ARG   0.002   0.000   ARG A1215 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 ASP cc_start: 0.8975 (p0) cc_final: 0.8768 (p0)
REVERT: A  465 MET cc_start: 0.8639 (mmm) cc_final: 0.8377 (mmm)
REVERT: A 1080 LYS cc_start: 0.7693 (mttp) cc_final: 0.7429 (mtmm)
REVERT: A 1147 MET cc_start: 0.8610 (ptt) cc_final: 0.7335 (ttp)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1614
  time to fit residues: 13.8068
Evaluate side-chains
  59 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    0.3980
   chunk 4 optimal weight:    0.1980
   chunk 36 optimal weight:    4.9990
   chunk 44 optimal weight:    7.9990
   chunk 3 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
A1054 ASN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.103829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.078382 restraints weight = 16754.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.080486 restraints weight = 12274.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.080766 restraints weight = 9014.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6962
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4595  Z= 0.152
  Angle     :  0.581   6.640   6189  Z= 0.305
  Chirality :  0.041   0.142    680
  Planarity :  0.003   0.051    803
  Dihedral  :  4.445  22.277    615
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.17 %
    Favored  : 82.71 %
  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: -0.39 (0.35), residues: 567
  helix:  0.58 (0.31), residues: 275
  sheet: -0.49 (0.47), residues: 98
  loop : -1.22 (0.46), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B  56 
 HIS   0.003   0.001   HIS A 335 
 PHE   0.008   0.001   PHE A 507 
 TYR   0.014   0.001   TYR A1072 
 ARG   0.002   0.000   ARG B  31 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.528 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.5980 (tp30) cc_final: 0.5609 (mp0)
REVERT: A  465 MET cc_start: 0.8558 (mmm) cc_final: 0.8074 (mmm)
REVERT: A  469 MET cc_start: 0.8682 (tpp) cc_final: 0.8345 (mmt)
REVERT: A 1080 LYS cc_start: 0.7657 (mttp) cc_final: 0.7400 (mtmm)
REVERT: A 1147 MET cc_start: 0.8588 (ptt) cc_final: 0.7369 (ttp)
  outliers start: 15
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1502
  time to fit residues: 13.7223
Evaluate side-chains
  61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  107 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 45 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.103847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.074563 restraints weight = 17088.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.076629 restraints weight = 11865.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.077956 restraints weight = 9395.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4595  Z= 0.172
  Angle     :  0.604   6.619   6189  Z= 0.316
  Chirality :  0.041   0.139    680
  Planarity :  0.003   0.050    803
  Dihedral  :  4.514  22.966    615
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 15.21 %
    Favored  : 81.25 %
  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: -0.38 (0.35), residues: 567
  helix:  0.62 (0.31), residues: 270
  sheet: -0.62 (0.47), residues: 100
  loop : -1.15 (0.46), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.010   0.001   PHE A1062 
 TYR   0.013   0.001   TYR A1072 
 ARG   0.002   0.000   ARG A1215 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6176 (tp30) cc_final: 0.5716 (mp0)
REVERT: A  419 LEU cc_start: 0.9178 (mt) cc_final: 0.8952 (mm)
REVERT: A  465 MET cc_start: 0.8454 (mmm) cc_final: 0.8069 (mmm)
REVERT: A 1080 LYS cc_start: 0.7755 (mttp) cc_final: 0.7284 (mtmm)
REVERT: A 1147 MET cc_start: 0.8720 (ptt) cc_final: 0.7292 (ttp)
REVERT: A 1183 LEU cc_start: 0.8001 (mt) cc_final: 0.7135 (mp)
  outliers start: 17
  outliers final: 12
  residues processed: 71
  average time/residue: 0.1566
  time to fit residues: 14.5801
Evaluate side-chains
  66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 54
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  112 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 27 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0770
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.103602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.074627 restraints weight = 16814.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.076666 restraints weight = 11729.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.077995 restraints weight = 9271.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7096
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4595  Z= 0.159
  Angle     :  0.599   6.635   6189  Z= 0.313
  Chirality :  0.041   0.145    680
  Planarity :  0.003   0.049    803
  Dihedral  :  4.502  22.211    615
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.04 %
    Favored  : 81.04 %
  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: -0.48 (0.34), residues: 567
  helix:  0.55 (0.31), residues: 276
  sheet: -0.41 (0.51), residues: 86
  loop : -1.40 (0.43), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.008   0.001   PHE A 507 
 TYR   0.013   0.001   TYR A1072 
 ARG   0.002   0.000   ARG A1227 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6096 (tp30) cc_final: 0.5699 (mp0)
REVERT: A  465 MET cc_start: 0.8450 (mmm) cc_final: 0.8055 (mmm)
REVERT: A 1080 LYS cc_start: 0.7771 (mttp) cc_final: 0.7515 (mtmm)
REVERT: A 1147 MET cc_start: 0.8768 (ptt) cc_final: 0.7588 (ttt)
REVERT: A 1157 MET cc_start: 0.7482 (tmm) cc_final: 0.6972 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 67
  average time/residue: 0.1489
  time to fit residues: 13.1946
Evaluate side-chains
  63 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 52
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   97 GLU
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  112 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 54 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 19 optimal weight:    0.0060
   chunk 21 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 32 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    0.9200

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.4191 r_free = 0.4191 target = 0.103524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.073592 restraints weight = 17332.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.075721 restraints weight = 11923.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.077037 restraints weight = 9428.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4595  Z= 0.178
  Angle     :  0.625   9.951   6189  Z= 0.325
  Chirality :  0.041   0.142    680
  Planarity :  0.003   0.050    803
  Dihedral  :  4.583  22.878    615
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.50 %
    Favored  : 79.79 %
  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: -0.42 (0.35), residues: 567
  helix:  0.59 (0.31), residues: 270
  sheet: -0.48 (0.48), residues: 96
  loop : -1.27 (0.45), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.010   0.001   PHE A 507 
 TYR   0.016   0.001   TYR A1072 
 ARG   0.002   0.000   ARG B  31 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6166 (tp30) cc_final: 0.5719 (mp0)
REVERT: A  465 MET cc_start: 0.8510 (mmm) cc_final: 0.8093 (mmm)
REVERT: A 1080 LYS cc_start: 0.7758 (mttp) cc_final: 0.7293 (mtmm)
REVERT: A 1183 LEU cc_start: 0.8016 (mt) cc_final: 0.7140 (mp)
REVERT: A 1198 MET cc_start: 0.6945 (ppp) cc_final: 0.6705 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1560
  time to fit residues: 14.1565
Evaluate side-chains
  67 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 55
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  395 ILE
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  112 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 23 optimal weight:    0.1980
   chunk 50 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.4204 r_free = 0.4204 target = 0.104045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.074222 restraints weight = 17063.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.076378 restraints weight = 11649.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.077736 restraints weight = 9160.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4595  Z= 0.167
  Angle     :  0.632   9.472   6189  Z= 0.324
  Chirality :  0.041   0.144    680
  Planarity :  0.003   0.050    803
  Dihedral  :  4.540  21.799    615
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.54 %
    Favored  : 78.75 %
  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: -0.40 (0.35), residues: 567
  helix:  0.61 (0.31), residues: 270
  sheet: -0.49 (0.48), residues: 96
  loop : -1.25 (0.46), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.009   0.001   PHE A 507 
 TYR   0.015   0.001   TYR A1072 
 ARG   0.002   0.000   ARG B  31 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 56
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6102 (tp30) cc_final: 0.5791 (pm20)
REVERT: A  465 MET cc_start: 0.8458 (mmm) cc_final: 0.8058 (mmm)
REVERT: A 1080 LYS cc_start: 0.7747 (mttp) cc_final: 0.7497 (mtmm)
REVERT: A 1157 MET cc_start: 0.7573 (tmm) cc_final: 0.7153 (tmm)
REVERT: A 1198 MET cc_start: 0.6924 (ppp) cc_final: 0.6585 (tmm)
  outliers start: 13
  outliers final: 13
  residues processed: 66
  average time/residue: 0.1574
  time to fit residues: 13.9053
Evaluate side-chains
  67 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 54
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  112 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 24 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0980
   chunk 32 optimal weight:    0.0060
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.4196

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 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 = 0.4219 r_free = 0.4219 target = 0.105290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.075341 restraints weight = 16899.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.077482 restraints weight = 11540.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.078994 restraints weight = 9052.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4595  Z= 0.146
  Angle     :  0.616   9.488   6189  Z= 0.314
  Chirality :  0.040   0.143    680
  Planarity :  0.003   0.048    803
  Dihedral  :  4.349  20.275    615
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 18.33 %
    Favored  : 78.75 %
  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: -0.46 (0.35), residues: 567
  helix:  0.59 (0.31), residues: 276
  sheet: -0.41 (0.55), residues: 81
  loop : -1.39 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.008   0.001   PHE A 507 
 TYR   0.015   0.001   TYR A1072 
 ARG   0.002   0.000   ARG A1215 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6078 (tp30) cc_final: 0.5775 (mp0)
REVERT: A  465 MET cc_start: 0.8484 (mmm) cc_final: 0.8082 (mmm)
REVERT: A 1080 LYS cc_start: 0.7760 (mttp) cc_final: 0.7512 (mtmm)
REVERT: A 1157 MET cc_start: 0.7421 (tmm) cc_final: 0.6919 (tmm)
REVERT: A 1198 MET cc_start: 0.6808 (ppp) cc_final: 0.6425 (tmm)
  outliers start: 14
  outliers final: 13
  residues processed: 69
  average time/residue: 0.1501
  time to fit residues: 13.6810
Evaluate side-chains
  68 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue  486 MET
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  106 VAL
Chi-restraints excluded: chain B residue  107 ASN
Chi-restraints excluded: chain B residue  112 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 53 optimal weight:    0.0060
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 12 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.103240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.073705 restraints weight = 16926.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.075740 restraints weight = 11949.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.077016 restraints weight = 9520.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4595  Z= 0.175
  Angle     :  0.660  10.432   6189  Z= 0.334
  Chirality :  0.041   0.146    680
  Planarity :  0.003   0.048    803
  Dihedral  :  4.492  21.370    615
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 19.79 %
    Favored  : 77.71 %
  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: -0.58 (0.35), residues: 567
  helix:  0.48 (0.31), residues: 276
  sheet: -0.45 (0.55), residues: 81
  loop : -1.43 (0.43), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.009   0.001   PHE A 507 
 TYR   0.012   0.001   TYR A 446 
 ARG   0.002   0.000   ARG B  23 

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

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

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1134 Ramachandran restraints generated.
    567 Oldfield, 0 Emsley, 567 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6023 (tp30) cc_final: 0.5777 (pm20)
REVERT: A  465 MET cc_start: 0.8395 (mmm) cc_final: 0.8037 (mmm)
REVERT: A 1080 LYS cc_start: 0.7750 (mttp) cc_final: 0.7502 (mtmm)
REVERT: A 1157 MET cc_start: 0.7481 (tmm) cc_final: 0.7010 (tmm)
REVERT: A 1198 MET cc_start: 0.6878 (ppp) cc_final: 0.6457 (tmm)
  outliers start: 12
  outliers final: 10
  residues processed: 66
  average time/residue: 0.1478
  time to fit residues: 13.0120
Evaluate side-chains
  66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  390 ILE
Chi-restraints excluded: chain A residue 1110 THR
Chi-restraints excluded: chain A residue 1141 GLU
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1214 TYR
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue  101 LYS
Chi-restraints excluded: chain B residue  106 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 20 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0170
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0470
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
A 420 ASN
** A1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.102876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.073721 restraints weight = 16620.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.075580 restraints weight = 11920.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.076832 restraints weight = 9638.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4595  Z= 0.189
  Angle     :  0.668   9.138   6189  Z= 0.342
  Chirality :  0.042   0.146    680
  Planarity :  0.003   0.056    803
  Dihedral  :  4.581  21.542    615
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 20.42 %
    Favored  : 77.29 %
  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: -0.58 (0.35), residues: 567
  helix:  0.39 (0.31), residues: 271
  sheet: -0.53 (0.51), residues: 91
  loop : -1.25 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 
 PHE   0.010   0.001   PHE A1062 
 TYR   0.011   0.001   TYR A 445 
 ARG   0.002   0.000   ARG B  31 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2063.02 seconds
wall clock time: 37 minutes 31.13 seconds (2251.13 seconds total)