Starting phenix.real_space_refine
on Tue Mar  3 12:48:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pdh_13338/03_2026/7pdh_13338.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pdh_13338/03_2026/7pdh_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pdh_13338/03_2026/7pdh_13338.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pdh_13338/03_2026/7pdh_13338.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pdh_13338/03_2026/7pdh_13338.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pdh_13338/03_2026/7pdh_13338.map"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 1.15, per 1000 atoms: 0.25
  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: 0.35
  Conformation dependent library (CDL) restraints added in 293.9 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: 0.17
  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: 0.65

  Time building geometry restraints manager: 0.48 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:             2.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.230
  Find NCS groups from input model:        0.020
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.750
-------------------------------------------------------------------------------
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= 0.151
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.003   0.000   ARG B  31 
 TYR   0.011   0.001   TYR A 445 
 PHE   0.010   0.002   PHE A 507 
 TRP   0.036   0.003   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4595)
  covalent geometry    : angle       0.69657 ( 6189)
  hydrogen bonds       : bond        0.13810 (  228)
  hydrogen bonds       : angle       6.78878 (  723)

*********************** 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  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1145 GLU cc_start: 0.8781 (mp0) cc_final: 0.8441 (mp0)
REVERT: A 1157 MET cc_start: 0.7946 (tmm) cc_final: 0.7723 (tmm)
REVERT: A 1238 MET cc_start: 0.8753 (tpp) cc_final: 0.8422 (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: 0.7626 (mmtm)
REVERT: B  109 GLN cc_start: 0.7076 (pt0) cc_final: 0.6853 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0667
  time to fit residues: 6.2173
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  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.104480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.075456 restraints weight = 16458.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.077481 restraints weight = 11456.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.078765 restraints weight = 9118.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.079178 restraints weight = 7881.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.080068 restraints weight = 7290.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.1232

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= 0.129
  Angle     :  0.623   6.508   6189  Z= 0.328
  Chirality :  0.043   0.149    680
  Planarity :  0.004   0.058    803
  Dihedral  :  4.691  18.193    615
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 12.64
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.35), residues: 567
  helix:  0.25 (0.31), residues: 274
  sheet: -0.65 (0.47), residues: 98
  loop : -1.43 (0.46), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  31 
 TYR   0.012   0.001   TYR A 446 
 PHE   0.009   0.001   PHE A 507 
 TRP   0.021   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4595)
  covalent geometry    : angle       0.62341 ( 6189)
  hydrogen bonds       : bond        0.03835 (  228)
  hydrogen bonds       : angle       5.05031 (  723)

*********************** 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
  61 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.8388 (mmm) cc_final: 0.8178 (mmm)
REVERT: A 1080 LYS cc_start: 0.7693 (mttp) cc_final: 0.7323 (mtmm)
REVERT: A 1183 LEU cc_start: 0.8079 (mt) cc_final: 0.7229 (mp)
REVERT: A 1238 MET cc_start: 0.8669 (tpp) cc_final: 0.8260 (tpp)
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.0749
  time to fit residues: 5.8168
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  : 0.188 
-------------------------------------------------------------------------------
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 16 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 6 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0010
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.5986

-------------------------------------------------------------------------------
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 = 0.4212 r_free = 0.4212 target = 0.104517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.079229 restraints weight = 16227.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.080668 restraints weight = 11934.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.081252 restraints weight = 8892.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.081328 restraints weight = 8386.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.081435 restraints weight = 7996.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.1608

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= 0.110
  Angle     :  0.579   6.534   6189  Z= 0.303
  Chirality :  0.041   0.146    680
  Planarity :  0.003   0.053    803
  Dihedral  :  4.504  22.048    615
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.88 %
    Favored  : 86.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.34), residues: 567
  helix:  0.37 (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
 ARG   0.002   0.000   ARG A1215 
 TYR   0.010   0.001   TYR A 446 
 PHE   0.008   0.001   PHE A 507 
 TRP   0.017   0.001   TRP B  56 
 HIS   0.003   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 4595)
  covalent geometry    : angle       0.57931 ( 6189)
  hydrogen bonds       : bond        0.03361 (  228)
  hydrogen bonds       : angle       4.62703 (  723)

*********************** 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
  68 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1080 LYS cc_start: 0.7696 (mttp) cc_final: 0.7432 (mtmm)
  outliers start: 8
  outliers final: 7
  residues processed: 66
  average time/residue: 0.0604
  time to fit residues: 5.3425
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  : 0.100 
-------------------------------------------------------------------------------
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 26 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 21 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0980
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.5586

-------------------------------------------------------------------------------
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 = 0.4172 r_free = 0.4172 target = 0.101851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.073390 restraints weight = 16717.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.075042 restraints weight = 11900.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.076326 restraints weight = 9634.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.077157 restraints weight = 8348.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.077402 restraints weight = 7572.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4595  Z= 0.168
  Angle     :  0.650   6.699   6189  Z= 0.345
  Chirality :  0.043   0.145    680
  Planarity :  0.004   0.053    803
  Dihedral  :  4.827  24.175    615
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 14.38 %
    Favored  : 81.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.35), residues: 567
  helix:  0.29 (0.30), residues: 275
  sheet: -0.55 (0.48), residues: 96
  loop : -1.38 (0.46), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  31 
 TYR   0.016   0.002   TYR A 446 
 PHE   0.013   0.002   PHE A1062 
 TRP   0.024   0.002   TRP B  56 
 HIS   0.004   0.001   HIS A 335 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4595)
  covalent geometry    : angle       0.64981 ( 6189)
  hydrogen bonds       : bond        0.03933 (  228)
  hydrogen bonds       : angle       4.78165 (  723)

*********************** 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
  76 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 57
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  427 ASP cc_start: 0.8974 (p0) cc_final: 0.8749 (p0)
REVERT: A  465 MET cc_start: 0.8606 (mmm) cc_final: 0.8335 (mmm)
REVERT: A 1080 LYS cc_start: 0.7715 (mttp) cc_final: 0.7243 (mtmm)
  outliers start: 19
  outliers final: 12
  residues processed: 72
  average time/residue: 0.0559
  time to fit residues: 5.4164
Evaluate side-chains
  65 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 53
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
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 1141 GLU
Chi-restraints excluded: chain A residue 1159 TRP
Chi-restraints excluded: chain A residue 1166 VAL
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 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 51 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0040
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0670
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.4330

-------------------------------------------------------------------------------
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 = 0.4201 r_free = 0.4201 target = 0.104190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.078759 restraints weight = 16445.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.080474 restraints weight = 12663.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.080765 restraints weight = 8705.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.081046 restraints weight = 8588.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.081078 restraints weight = 7988.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4595  Z= 0.106
  Angle     :  0.583   6.593   6189  Z= 0.304
  Chirality :  0.041   0.147    680
  Planarity :  0.003   0.057    803
  Dihedral  :  4.497  21.666    615
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.46 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.35), residues: 567
  helix:  0.70 (0.31), residues: 269
  sheet: -0.62 (0.47), residues: 98
  loop : -1.26 (0.45), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  31 
 TYR   0.019   0.001   TYR A1072 
 PHE   0.009   0.001   PHE A 507 
 TRP   0.021   0.001   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4595)
  covalent geometry    : angle       0.58323 ( 6189)
  hydrogen bonds       : bond        0.03183 (  228)
  hydrogen bonds       : angle       4.48504 (  723)

*********************** 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
  77 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6158 (tp30) cc_final: 0.5685 (mp0)
REVERT: A  465 MET cc_start: 0.8583 (mmm) cc_final: 0.8262 (mmm)
REVERT: A 1080 LYS cc_start: 0.7724 (mttp) cc_final: 0.7455 (mtmm)
REVERT: A 1157 MET cc_start: 0.7294 (tmm) cc_final: 0.6892 (tmm)
  outliers start: 16
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0590
  time to fit residues: 5.7661
Evaluate side-chains
  63 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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   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 13 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    6.9990
   chunk 51 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 44 optimal weight:    6.9990
   chunk 22 optimal weight:    0.6980
   chunk 50 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.4185 r_free = 0.4185 target = 0.103278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.074728 restraints weight = 16827.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.076689 restraints weight = 11834.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.077933 restraints weight = 9344.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.078810 restraints weight = 8016.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.079167 restraints weight = 7273.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7074
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4595  Z= 0.118
  Angle     :  0.603   6.659   6189  Z= 0.318
  Chirality :  0.041   0.142    680
  Planarity :  0.003   0.057    803
  Dihedral  :  4.547  22.408    615
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.88 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.35), residues: 567
  helix:  0.62 (0.31), residues: 271
  sheet: -0.56 (0.48), residues: 96
  loop : -1.30 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1148 
 TYR   0.017   0.001   TYR A1072 
 PHE   0.009   0.001   PHE A 507 
 TRP   0.027   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4595)
  covalent geometry    : angle       0.60258 ( 6189)
  hydrogen bonds       : bond        0.03351 (  228)
  hydrogen bonds       : angle       4.49375 (  723)

*********************** 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
  76 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6140 (tp30) cc_final: 0.5671 (mp0)
REVERT: A  465 MET cc_start: 0.8486 (mmm) cc_final: 0.8180 (mmm)
REVERT: A 1080 LYS cc_start: 0.7739 (mttp) cc_final: 0.7483 (mtmm)
  outliers start: 16
  outliers final: 14
  residues processed: 72
  average time/residue: 0.0592
  time to fit residues: 5.6415
Evaluate side-chains
  68 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 54
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  359 LYS
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  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  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 3 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0370
   chunk 44 optimal weight:    6.9990
   chunk 43 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 40 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0470
   chunk 49 optimal weight:    0.0060
   overall best weight:    0.3772

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.104368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.079022 restraints weight = 16587.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.080609 restraints weight = 12750.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.080957 restraints weight = 8852.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.081290 restraints weight = 8710.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.081324 restraints weight = 8025.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4595  Z= 0.110
  Angle     :  0.634   9.950   6189  Z= 0.325
  Chirality :  0.041   0.158    680
  Planarity :  0.003   0.056    803
  Dihedral  :  4.484  21.217    615
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.12 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.53 (0.35), residues: 567
  helix:  0.51 (0.31), residues: 277
  sheet: -0.41 (0.51), residues: 86
  loop : -1.43 (0.44), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1215 
 TYR   0.018   0.001   TYR A1072 
 PHE   0.008   0.001   PHE A 507 
 TRP   0.028   0.002   TRP B  56 
 HIS   0.003   0.001   HIS A1135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 4595)
  covalent geometry    : angle       0.63365 ( 6189)
  hydrogen bonds       : bond        0.03266 (  228)
  hydrogen bonds       : angle       4.45061 (  723)

*********************** 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
  70 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 57
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6148 (tp30) cc_final: 0.5823 (pm20)
REVERT: A  465 MET cc_start: 0.8505 (mmm) cc_final: 0.8139 (mmm)
REVERT: A  469 MET cc_start: 0.8781 (tpp) cc_final: 0.8445 (mmt)
REVERT: A 1080 LYS cc_start: 0.7728 (mttp) cc_final: 0.7471 (mtmm)
REVERT: A 1157 MET cc_start: 0.7278 (tmm) cc_final: 0.6878 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 67
  average time/residue: 0.0627
  time to fit residues: 5.6069
Evaluate side-chains
  68 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  359 LYS
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  106 VAL
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 3 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 35 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 45 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4186 r_free = 0.4186 target = 0.103189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.074680 restraints weight = 16659.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.076632 restraints weight = 11667.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.077931 restraints weight = 9217.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.078816 restraints weight = 7890.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.079146 restraints weight = 7159.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7065
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4595  Z= 0.121
  Angle     :  0.654  10.503   6189  Z= 0.334
  Chirality :  0.041   0.152    680
  Planarity :  0.003   0.055    803
  Dihedral  :  4.532  22.080    615
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.75 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.35), residues: 567
  helix:  0.56 (0.31), residues: 271
  sheet: -0.48 (0.49), residues: 96
  loop : -1.28 (0.46), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  31 
 TYR   0.013   0.001   TYR A1072 
 PHE   0.009   0.001   PHE A 507 
 TRP   0.028   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 4595)
  covalent geometry    : angle       0.65422 ( 6189)
  hydrogen bonds       : bond        0.03336 (  228)
  hydrogen bonds       : angle       4.46659 (  723)

*********************** 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
  73 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 57
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  392 GLU cc_start: 0.6100 (tp30) cc_final: 0.5767 (pm20)
REVERT: A  465 MET cc_start: 0.8486 (mmm) cc_final: 0.8121 (mmm)
REVERT: A 1080 LYS cc_start: 0.7730 (mttp) cc_final: 0.7475 (mtmm)
REVERT: A 1157 MET cc_start: 0.7502 (tmm) cc_final: 0.7002 (tmm)
REVERT: A 1198 MET cc_start: 0.6963 (ppp) cc_final: 0.6754 (tmm)
  outliers start: 16
  outliers final: 13
  residues processed: 68
  average time/residue: 0.0593
  time to fit residues: 5.4018
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  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  359 LYS
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
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 38 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0770
   chunk 8 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    1.0144

-------------------------------------------------------------------------------
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 = 0.4168 r_free = 0.4168 target = 0.102116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.077585 restraints weight = 16476.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.079505 restraints weight = 12573.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.079839 restraints weight = 9229.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.079916 restraints weight = 7863.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.080187 restraints weight = 7809.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6963
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4595  Z= 0.133
  Angle     :  0.676  10.340   6189  Z= 0.344
  Chirality :  0.041   0.147    680
  Planarity :  0.004   0.057    803
  Dihedral  :  4.647  22.104    615
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 18.75 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.35), residues: 567
  helix:  0.40 (0.31), residues: 271
  sheet: -0.54 (0.51), residues: 91
  loop : -1.33 (0.45), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  31 
 TYR   0.015   0.001   TYR A1072 
 PHE   0.010   0.001   PHE A1062 
 TRP   0.028   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4595)
  covalent geometry    : angle       0.67627 ( 6189)
  hydrogen bonds       : bond        0.03506 (  228)
  hydrogen bonds       : angle       4.57116 (  723)

*********************** 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
  72 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.8360 (mmm) cc_final: 0.8058 (mmm)
REVERT: A 1080 LYS cc_start: 0.7683 (mttp) cc_final: 0.7439 (mtmm)
REVERT: A 1183 LEU cc_start: 0.8032 (mt) cc_final: 0.7588 (mp)
REVERT: A 1198 MET cc_start: 0.7176 (ppp) cc_final: 0.6893 (tmm)
  outliers start: 15
  outliers final: 11
  residues processed: 68
  average time/residue: 0.0583
  time to fit residues: 5.2758
Evaluate side-chains
  66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  359 LYS
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   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 9 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.4172 r_free = 0.4172 target = 0.102421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.074215 restraints weight = 16340.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.076154 restraints weight = 11359.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.077269 restraints weight = 9010.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.078183 restraints weight = 7830.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.078754 restraints weight = 7039.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7078
moved from start:          0.2925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4595  Z= 0.126
  Angle     :  0.683  10.628   6189  Z= 0.347
  Chirality :  0.041   0.155    680
  Planarity :  0.003   0.056    803
  Dihedral  :  4.610  21.023    615
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.53 %
    Favored  : 93.47 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.58 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.58 (0.35), residues: 567
  helix:  0.43 (0.31), residues: 270
  sheet: -0.76 (0.50), residues: 92
  loop : -1.18 (0.46), residues: 205

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  31 
 TYR   0.015   0.001   TYR A1072 
 PHE   0.010   0.001   PHE A 507 
 TRP   0.031   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 4595)
  covalent geometry    : angle       0.68324 ( 6189)
  hydrogen bonds       : bond        0.03415 (  228)
  hydrogen bonds       : angle       4.54587 (  723)

********************** 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
  66 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 MET cc_start: 0.8366 (mmm) cc_final: 0.8050 (mmm)
REVERT: A 1080 LYS cc_start: 0.7710 (mttp) cc_final: 0.7466 (mtmm)
REVERT: A 1157 MET cc_start: 0.7466 (tmm) cc_final: 0.7003 (tmm)
REVERT: A 1183 LEU cc_start: 0.8039 (mt) cc_final: 0.7578 (mp)
REVERT: A 1198 MET cc_start: 0.7075 (ppp) cc_final: 0.6767 (tmm)
  outliers start: 11
  outliers final: 11
  residues processed: 63
  average time/residue: 0.0557
  time to fit residues: 4.7176
Evaluate side-chains
  65 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 54
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  359 LYS
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   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 33 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    0.7980
   chunk 45 optimal weight:    0.0030
   chunk 47 optimal weight:    3.9990
   chunk 26 optimal weight:    0.3980
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.6190

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.103316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.075128 restraints weight = 16333.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.077119 restraints weight = 11260.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.078398 restraints weight = 8905.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.079243 restraints weight = 7651.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.079782 restraints weight = 6923.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7039
moved from start:          0.3048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   4595  Z= 0.115
  Angle     :  0.665  11.009   6189  Z= 0.336
  Chirality :  0.041   0.153    680
  Planarity :  0.003   0.055    803
  Dihedral  :  4.468  20.253    615
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 19.58 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.35), residues: 567
  helix:  0.54 (0.31), residues: 269
  sheet: -0.48 (0.52), residues: 91
  loop : -1.15 (0.46), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1215 
 TYR   0.014   0.001   TYR A1072 
 PHE   0.009   0.001   PHE A 507 
 TRP   0.030   0.002   TRP B  56 
 HIS   0.003   0.001   HIS B  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 4595)
  covalent geometry    : angle       0.66482 ( 6189)
  hydrogen bonds       : bond        0.03250 (  228)
  hydrogen bonds       : angle       4.43540 (  723)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1045.93 seconds
wall clock time: 18 minutes 38.13 seconds (1118.13 seconds total)