Starting phenix.real_space_refine
on Sun Aug 24 03:29:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iek_35384/08_2025/8iek_35384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iek_35384/08_2025/8iek_35384.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iek_35384/08_2025/8iek_35384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iek_35384/08_2025/8iek_35384.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iek_35384/08_2025/8iek_35384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iek_35384/08_2025/8iek_35384.cif"
  }
  resolution = 3.2
  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=   0.001 sd=   0.054
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: 7
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      1      5.21       5
     S      53      5.16       5
     C    5184      2.51       5
     N    1377      2.21       5
     O    1427      1.98       5
     H    8299      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16344
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "P"
      Number of atoms: 16312
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1036, 16312
          Classifications: {'peptide': 1036}
          Link IDs: {'CIS': 1, 'PTRANS': 72, 'TRANS': 962}
          Chain breaks: 5
    Chain: "P"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.69, per 1000 atoms: 0.23
  Number of scatterers: 16344
  At special positions: 0
  Unit cell: (90.885, 90.885, 135.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      53     16.00
     P       3     15.00
     Mg      1     11.99
     O    1427      8.00
     N    1377      7.00
     C    5184      6.00
     H    8299      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.58
  Conformation dependent library (CDL) restraints added in 619.0 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1936

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      50.3% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.47
  Creating SS restraints...
    Processing helix  chain 'P' and resid 49 through 58
      removed outlier: 3.868A  pdb=" N   VAL P  53 " --> pdb=" O   GLY P  49 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   MET P  57 " --> pdb=" O   VAL P  53 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 61 through 66
    Processing helix  chain 'P' and resid 68 through 75
      removed outlier: 4.424A  pdb=" N   GLY P  72 " --> pdb=" O   LYS P  68 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 194 through 201
    Processing helix  chain 'P' and resid 209 through 217
      removed outlier: 3.811A  pdb=" N   ILE P 215 " --> pdb=" O   VAL P 211 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 227 through 237
      removed outlier: 3.696A  pdb=" N   VAL P 233 " --> pdb=" O   PRO P 229 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ASP P 234 " --> pdb=" O   GLN P 230 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   GLU P 235 " --> pdb=" O   LEU P 231 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU P 237 " --> pdb=" O   VAL P 233 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 238 through 254
    Processing helix  chain 'P' and resid 256 through 289
      removed outlier: 3.770A  pdb=" N   MET P 288 " --> pdb=" O   THR P 284 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   VAL P 289 " --> pdb=" O   LEU P 285 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 308 through 312
    Processing helix  chain 'P' and resid 342 through 347
    Processing helix  chain 'P' and resid 365 through 370
    Processing helix  chain 'P' and resid 398 through 401
    Processing helix  chain 'P' and resid 402 through 413
      removed outlier: 3.728A  pdb=" N   LEU P 407 " --> pdb=" O   ALA P 403 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 422 through 424
      No H-bonds generated for 'chain 'P' and resid 422 through 424'
    Processing helix  chain 'P' and resid 425 through 450
      removed outlier: 3.533A  pdb=" N   LEU P 435 " --> pdb=" O   ALA P 431 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ARG P 449 " --> pdb=" O   PHE P 445 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN P 450 " --> pdb=" O   ILE P 446 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 455 through 469
      removed outlier: 3.805A  pdb=" N   ILE P 459 " --> pdb=" O   ASN P 455 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LEU P 464 " --> pdb=" O   ARG P 460 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   VAL P 465 " --> pdb=" O   ALA P 461 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL P 469 " --> pdb=" O   VAL P 465 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 472 through 491
      removed outlier: 4.083A  pdb=" N   CYS P 480 " --> pdb=" O   ALA P 476 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   THR P 481 " --> pdb=" O   MET P 477 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU P 482 " --> pdb=" O   THR P 478 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 499 through 504
      removed outlier: 4.095A  pdb=" N   LEU P 503 " --> pdb=" O   LEU P 499 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 505 through 507
      No H-bonds generated for 'chain 'P' and resid 505 through 507'
    Processing helix  chain 'P' and resid 549 through 558
    Processing helix  chain 'P' and resid 571 through 582
    Processing helix  chain 'P' and resid 656 through 662
    Processing helix  chain 'P' and resid 672 through 683
      removed outlier: 3.820A  pdb=" N   TYR P 680 " --> pdb=" O   MET P 676 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 696 through 707
    Processing helix  chain 'P' and resid 708 through 713
      removed outlier: 4.405A  pdb=" N   VAL P 712 " --> pdb=" O   THR P 708 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 731 through 742
      removed outlier: 3.512A  pdb=" N   VAL P 735 " --> pdb=" O   GLN P 731 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   THR P 742 " --> pdb=" O   ALA P 738 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 753 through 765
    Processing helix  chain 'P' and resid 827 through 837
      removed outlier: 3.993A  pdb=" N   LYS P 835 " --> pdb=" O   GLY P 831 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 841 through 846
      removed outlier: 3.639A  pdb=" N   VAL P 846 " --> pdb=" O   PRO P 842 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 855 through 868
      removed outlier: 3.905A  pdb=" N   THR P 860 " --> pdb=" O   PRO P 856 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 882 through 889
    Processing helix  chain 'P' and resid 914 through 954
      removed outlier: 3.987A  pdb=" N   MET P 918 " --> pdb=" O   GLU P 914 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ILE P 954 " --> pdb=" O   ILE P 950 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 959 through 969
    Processing helix  chain 'P' and resid 969 through 978
      removed outlier: 3.580A  pdb=" N   VAL P 974 " --> pdb=" O   ILE P 970 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 979 through 981
      No H-bonds generated for 'chain 'P' and resid 979 through 981'
    Processing helix  chain 'P' and resid 998 through 1024
      removed outlier: 3.592A  pdb=" N   LEU P1002 " --> pdb=" O   SER P 998 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   THR P1023 " --> pdb=" O   GLY P1019 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   LEU P1024 " --> pdb=" O   TYR P1020 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1044 through 1067
      removed outlier: 3.804A  pdb=" N   THR P1048 " --> pdb=" O   ASN P1044 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   VAL P1049 " --> pdb=" O   TYR P1045 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE P1056 " --> pdb=" O   SER P1052 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   LEU P1059 " --> pdb=" O   SER P1055 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ALA P1062 " --> pdb=" O   TYR P1058 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1074 through 1077
    Processing helix  chain 'P' and resid 1078 through 1097
      removed outlier: 3.586A  pdb=" N   LEU P1082 " --> pdb=" O   ASN P1078 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1114 through 1119
      removed outlier: 4.704A  pdb=" N   LEU P1118 " --> pdb=" O   THR P1114 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1119 through 1140
    Processing helix  chain 'P' and resid 1141 through 1148
    Processing helix  chain 'P' and resid 1157 through 1169
      removed outlier: 3.662A  pdb=" N   GLN P1161 " --> pdb=" O   LYS P1157 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG P1164 " --> pdb=" O   LYS P1160 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLU P1165 " --> pdb=" O   GLN P1161 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   LEU P1166 " --> pdb=" O   LEU P1162 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   ALA P1167 " --> pdb=" O   GLU P1163 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 39 through 43
    Processing sheet with id=AA2, first strand: chain 'P' and resid 165 through 168
      removed outlier: 3.563A  pdb=" N   ILE P 176 " --> pdb=" O   ALA P 181 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ALA P 181 " --> pdb=" O   ILE P 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 304 through 305
      removed outlier: 4.383A  pdb=" N   CYS P 296 " --> pdb=" O   VAL P 319 " (cutoff:3.500A)
      removed outlier: 5.413A  pdb=" N   CYS P 317 " --> pdb=" O   CYS P 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 352 through 354
      removed outlier: 3.895A  pdb=" N   GLN P 382 " --> pdb=" O   MET P 339 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ASN P 341 " --> pdb=" O   ILE P 380 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   ILE P 380 " --> pdb=" O   ASN P 341 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 493 through 495
      removed outlier: 5.917A  pdb=" N   GLY P 892 " --> pdb=" O   PHE P 906 " (cutoff:3.500A)
      removed outlier: 7.076A  pdb=" N   SER P 908 " --> pdb=" O   GLY P 892 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   SER P 894 " --> pdb=" O   SER P 908 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   VAL P 891 " --> pdb=" O   VAL P 873 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   VAL P 510 " --> pdb=" O   VAL P 747 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   VAL P 749 " --> pdb=" O   VAL P 510 " (cutoff:3.500A)
      removed outlier: 5.635A  pdb=" N   PHE P 512 " --> pdb=" O   VAL P 749 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   THR P 849 " --> pdb=" O   ALA P 746 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   LEU P 823 " --> pdb=" O   THR P 849 " (cutoff:3.500A)
      removed outlier: 6.039A  pdb=" N   PHE P 851 " --> pdb=" O   LEU P 823 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   LEU P 825 " --> pdb=" O   PHE P 851 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   SER P 826 " --> pdb=" O   ILE P 774 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'P' and resid 524 through 530
      removed outlier: 6.091A  pdb=" N   VAL P 723 " --> pdb=" O   MET P 526 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   VAL P 528 " --> pdb=" O   LEU P 721 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU P 721 " --> pdb=" O   VAL P 528 " (cutoff:3.500A)
      removed outlier: 7.849A  pdb=" N   LEU P 719 " --> pdb=" O   PRO P 530 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   LEU P 690 " --> pdb=" O   LEU P 719 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   LEU P 721 " --> pdb=" O   VAL P 688 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   VAL P 688 " --> pdb=" O   LEU P 721 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   VAL P 723 " --> pdb=" O   ARG P 686 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ARG P 686 " --> pdb=" O   VAL P 723 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER P 638 " --> pdb=" O   PHE P 628 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ALA P 642 " --> pdb=" O   VAL P 624 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   VAL P 624 " --> pdb=" O   ALA P 642 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'P' and resid 562 through 564

    379 hydrogen bonds defined for protein.
    1092 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: 4.86

  Time building geometry restraints manager: 2.23 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8272
        1.03 -     1.23: 28
        1.23 -     1.42: 3268
        1.42 -     1.62: 4875
        1.62 -     1.81: 79
  Bond restraints: 16522
  Sorted by residual:
  bond pdb=" C5  ATP P1201 "
       pdb=" N7  ATP P1201 "
    ideal  model  delta    sigma   weight residual
    1.387  1.321  0.066 1.00e-02 1.00e+04 4.40e+01
  bond pdb=" C4  ATP P1201 "
       pdb=" N9  ATP P1201 "
    ideal  model  delta    sigma   weight residual
    1.374  1.310  0.064 1.00e-02 1.00e+04 4.11e+01
  bond pdb=" C4  ATP P1201 "
       pdb=" C5  ATP P1201 "
    ideal  model  delta    sigma   weight residual
    1.388  1.449 -0.061 1.00e-02 1.00e+04 3.66e+01
  bond pdb=" C5  ATP P1201 "
       pdb=" C6  ATP P1201 "
    ideal  model  delta    sigma   weight residual
    1.409  1.452 -0.043 1.00e-02 1.00e+04 1.83e+01
  bond pdb=" C2' ATP P1201 "
       pdb=" C3' ATP P1201 "
    ideal  model  delta    sigma   weight residual
    1.531  1.480  0.051 1.20e-02 6.94e+03 1.81e+01
  ... (remaining 16517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.37: 29989
        4.37 -     8.75: 34
        8.75 -    13.12: 3
       13.12 -    17.50: 1
       17.50 -    21.87: 1
  Bond angle restraints: 30028
  Sorted by residual:
  angle pdb=" PB  ATP P1201 "
        pdb=" O3B ATP P1201 "
        pdb=" PG  ATP P1201 "
      ideal   model   delta    sigma   weight residual
     139.87  118.00   21.87 1.00e+00 1.00e+00 4.78e+02
  angle pdb=" PA  ATP P1201 "
        pdb=" O3A ATP P1201 "
        pdb=" PB  ATP P1201 "
      ideal   model   delta    sigma   weight residual
     136.83  121.71   15.12 1.00e+00 1.00e+00 2.29e+02
  angle pdb=" C5  ATP P1201 "
        pdb=" C4  ATP P1201 "
        pdb=" N3  ATP P1201 "
      ideal   model   delta    sigma   weight residual
     126.80  118.92    7.88 1.00e+00 1.00e+00 6.21e+01
  angle pdb=" N3  ATP P1201 "
        pdb=" C4  ATP P1201 "
        pdb=" N9  ATP P1201 "
      ideal   model   delta    sigma   weight residual
     127.04  135.13   -8.09 1.15e+00 7.59e-01 4.97e+01
  angle pdb=" C5' ATP P1201 "
        pdb=" O5' ATP P1201 "
        pdb=" PA  ATP P1201 "
      ideal   model   delta    sigma   weight residual
     121.27  114.87    6.40 1.00e+00 1.00e+00 4.10e+01
  ... (remaining 30023 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 6939
       17.95 -    35.89: 602
       35.89 -    53.84: 189
       53.84 -    71.79: 51
       71.79 -    89.73: 8
  Dihedral angle restraints: 7789
    sinusoidal: 4352
      harmonic: 3437
  Sorted by residual:
  dihedral pdb=" CA  TRP P  55 "
           pdb=" C   TRP P  55 "
           pdb=" N   MET P  56 "
           pdb=" CA  MET P  56 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.43   20.57     0      5.00e+00 4.00e-02 1.69e+01
  dihedral pdb=" CA  ARG P  93 "
           pdb=" C   ARG P  93 "
           pdb=" N   ASP P  94 "
           pdb=" CA  ASP P  94 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.27   19.73     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CA  LEU P  77 "
           pdb=" C   LEU P  77 "
           pdb=" N   ARG P  78 "
           pdb=" CA  ARG P  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.32  -19.68     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 7786 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 896
       0.030 -    0.060: 263
       0.060 -    0.090: 96
       0.090 -    0.119: 65
       0.119 -    0.149: 9
  Chirality restraints: 1329
  Sorted by residual:
  chirality pdb=" CA  VAL P 620 "
            pdb=" N   VAL P 620 "
            pdb=" C   VAL P 620 "
            pdb=" CB  VAL P 620 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.57e-01
  chirality pdb=" CA  ILE P 223 "
            pdb=" N   ILE P 223 "
            pdb=" C   ILE P 223 "
            pdb=" CB  ILE P 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  chirality pdb=" CA  ILE P 350 "
            pdb=" N   ILE P 350 "
            pdb=" C   ILE P 350 "
            pdb=" CB  ILE P 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1326 not shown)

  Planarity restraints: 2369
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL P1098 "   -0.035 5.00e-02 4.00e+02   5.17e-02 4.27e+00
        pdb=" N   PRO P1099 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO P1099 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO P1099 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU P1042 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO P1043 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO P1043 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO P1043 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' ATP P1201 "    0.021 2.00e-02 2.50e+03   9.50e-03 2.48e+00
        pdb=" C2  ATP P1201 "   -0.010 2.00e-02 2.50e+03
        pdb=" C4  ATP P1201 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5  ATP P1201 "    0.002 2.00e-02 2.50e+03
        pdb=" C6  ATP P1201 "    0.003 2.00e-02 2.50e+03
        pdb=" C8  ATP P1201 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1  ATP P1201 "    0.003 2.00e-02 2.50e+03
        pdb=" N3  ATP P1201 "    0.001 2.00e-02 2.50e+03
        pdb=" N6  ATP P1201 "    0.008 2.00e-02 2.50e+03
        pdb=" N7  ATP P1201 "   -0.005 2.00e-02 2.50e+03
        pdb=" N9  ATP P1201 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2366 not shown)

  Histogram of nonbonded interaction distances:
        1.62 -     2.22: 1350
        2.22 -     2.81: 34204
        2.81 -     3.41: 42686
        3.41 -     4.00: 54516
        4.00 -     4.60: 84524
  Nonbonded interactions: 217280
  Sorted by model distance:
  nonbonded pdb=" OG  SER P  43 "
            pdb=" HE  ARG P  78 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" O   ASP P 189 "
            pdb="HH11 ARG P 192 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" OE1 GLN P 101 "
            pdb=" H   GLN P 101 "
     model   vdw
     1.666 2.450
  nonbonded pdb=" OE1 GLN P 770 "
            pdb=" HE2 HIS P 772 "
     model   vdw
     1.698 2.450
  nonbonded pdb=" O   ARG P 819 "
            pdb="HE21 GLN P1169 "
     model   vdw
     1.720 2.450
  ... (remaining 217275 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             2.610
  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:             0.130
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     19.650
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.060
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6320
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   0.066   8223  Z= 0.203
  Angle     :  0.675  21.873  11207  Z= 0.428
  Chirality :  0.039   0.149   1329
  Planarity :  0.004   0.052   1409
  Dihedral  : 14.693  89.734   3057
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.37 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  : 13.51 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.51 (0.27), residues: 1024
  helix:  2.02 (0.26), residues: 433
  sheet:  0.31 (0.49), residues: 110
  loop : -1.29 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P1148 
 TYR   0.008   0.001   TYR P 241 
 PHE   0.012   0.001   PHE P 934 
 TRP   0.009   0.001   TRP P  45 
 HIS   0.005   0.001   HIS P 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8223)
  covalent geometry    : angle       0.67486 (11207)
  hydrogen bonds       : bond        0.19068 (  379)
  hydrogen bonds       : angle       6.81866 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5261 (tmm) cc_final: 0.4714 (tpp)
REVERT: P   57 MET cc_start: 0.4073 (ppp) cc_final: 0.3669 (ppp)
REVERT: P  100 TRP cc_start: 0.7476 (m-90) cc_final: 0.7204 (m-90)
REVERT: P  297 VAL cc_start: 0.7303 (p) cc_final: 0.6924 (p)
REVERT: P  710 ASP cc_start: 0.7598 (t0) cc_final: 0.7310 (t0)
REVERT: P  724 MET cc_start: 0.7545 (mtt) cc_final: 0.7206 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2362
  time to fit residues: 50.1858
Evaluate side-chains
  101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.3980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.2980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
P 190 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.183112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.144258 restraints weight = 34795.375|
|-----------------------------------------------------------------------------|
r_work (start): 0.4190 rms_B_bonded: 3.37
r_work: 0.4084 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6381
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8223  Z= 0.144
  Angle     :  0.603   6.340  11207  Z= 0.311
  Chirality :  0.042   0.149   1329
  Planarity :  0.005   0.085   1409
  Dihedral  :  6.041  76.374   1157
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.27 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.99 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.44 (0.27), residues: 1024
  helix:  1.85 (0.25), residues: 448
  sheet:  0.29 (0.52), residues: 104
  loop : -1.31 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG P 192 
 TYR   0.009   0.001   TYR P 936 
 PHE   0.010   0.001   PHE P 830 
 TRP   0.014   0.001   TRP P  55 
 HIS   0.016   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 8223)
  covalent geometry    : angle       0.60339 (11207)
  hydrogen bonds       : bond        0.05068 (  379)
  hydrogen bonds       : angle       5.20799 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   55 TRP cc_start: 0.5551 (p-90) cc_final: 0.5242 (p-90)
REVERT: P   56 MET cc_start: 0.5172 (tmm) cc_final: 0.4744 (tpp)
REVERT: P  526 MET cc_start: 0.7969 (mtt) cc_final: 0.7555 (mtm)
REVERT: P  710 ASP cc_start: 0.7616 (t0) cc_final: 0.7364 (t0)
REVERT: P  724 MET cc_start: 0.7581 (mtt) cc_final: 0.7248 (mtt)
REVERT: P  861 GLU cc_start: 0.7457 (tt0) cc_final: 0.7148 (tt0)
  outliers start: 11
  outliers final: 7
  residues processed: 117
  average time/residue: 0.1890
  time to fit residues: 31.0313
Evaluate side-chains
  105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  374 LEU
Chi-restraints excluded: chain P residue  434 VAL
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  634 LEU
Chi-restraints excluded: chain P residue  825 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue 1108 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** P 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P1008 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.171827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.131713 restraints weight = 34868.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.4062 rms_B_bonded: 3.43
r_work: 0.3947 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8223  Z= 0.179
  Angle     :  0.610   8.613  11207  Z= 0.320
  Chirality :  0.042   0.146   1329
  Planarity :  0.005   0.059   1409
  Dihedral  :  5.946  74.593   1157
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.59 %
    Allowed  :  5.57 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.33 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.14 (0.27), residues: 1024
  helix:  1.61 (0.25), residues: 451
  sheet:  0.13 (0.52), residues: 105
  loop : -1.51 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG P 821 
 TYR   0.013   0.001   TYR P 936 
 PHE   0.010   0.001   PHE P1071 
 TRP   0.011   0.001   TRP P  55 
 HIS   0.008   0.001   HIS P 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 8223)
  covalent geometry    : angle       0.61007 (11207)
  hydrogen bonds       : bond        0.05252 (  379)
  hydrogen bonds       : angle       5.02920 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5408 (tmm) cc_final: 0.4893 (tpp)
REVERT: P   57 MET cc_start: 0.3987 (OUTLIER) cc_final: 0.3689 (ppp)
REVERT: P  308 ASP cc_start: 0.7461 (p0) cc_final: 0.7148 (p0)
REVERT: P  316 ASP cc_start: 0.6645 (t0) cc_final: 0.6371 (t0)
REVERT: P  348 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6864 (tp30)
REVERT: P  579 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8145 (mt-10)
REVERT: P  710 ASP cc_start: 0.7583 (t0) cc_final: 0.7363 (t0)
REVERT: P  724 MET cc_start: 0.8094 (mtt) cc_final: 0.7737 (mtt)
REVERT: P  861 GLU cc_start: 0.7419 (tt0) cc_final: 0.7112 (tt0)
REVERT: P  897 GLN cc_start: 0.6560 (tp40) cc_final: 0.6322 (mt0)
REVERT: P  940 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.6501 (t80)
  outliers start: 21
  outliers final: 12
  residues processed: 117
  average time/residue: 0.1887
  time to fit residues: 31.5820
Evaluate side-chains
  110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   57 MET
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  263 ILE
Chi-restraints excluded: chain P residue  274 SER
Chi-restraints excluded: chain P residue  374 LEU
Chi-restraints excluded: chain P residue  434 VAL
Chi-restraints excluded: chain P residue  478 THR
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  829 THR
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1097 LEU
Chi-restraints excluded: chain P residue 1111 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 33 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 100 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** P 369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P 777 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.170205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.131119 restraints weight = 34682.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.4033 rms_B_bonded: 3.30
r_work: 0.3926 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6691
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8223  Z= 0.147
  Angle     :  0.573   5.308  11207  Z= 0.298
  Chirality :  0.041   0.142   1329
  Planarity :  0.005   0.057   1409
  Dihedral  :  6.032  82.563   1157
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.27 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.57 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole: -0.01 (0.26), residues: 1024
  helix:  1.58 (0.25), residues: 454
  sheet: -0.24 (0.50), residues: 107
  loop : -1.63 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG P  74 
 TYR   0.010   0.001   TYR P 936 
 PHE   0.010   0.001   PHE P 445 
 TRP   0.012   0.001   TRP P  55 
 HIS   0.004   0.001   HIS P 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 8223)
  covalent geometry    : angle       0.57334 (11207)
  hydrogen bonds       : bond        0.04575 (  379)
  hydrogen bonds       : angle       4.81576 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5793 (tmm) cc_final: 0.5073 (tpp)
REVERT: P  210 MET cc_start: 0.7785 (mmp) cc_final: 0.7039 (mmm)
REVERT: P  316 ASP cc_start: 0.6825 (t0) cc_final: 0.6553 (t0)
REVERT: P  374 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7259 (mp)
REVERT: P  579 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8171 (mt-10)
REVERT: P  710 ASP cc_start: 0.7606 (t0) cc_final: 0.7368 (t0)
REVERT: P  724 MET cc_start: 0.8295 (mtt) cc_final: 0.7975 (mtt)
REVERT: P  861 GLU cc_start: 0.7484 (tt0) cc_final: 0.7174 (tt0)
REVERT: P  940 TYR cc_start: 0.7740 (OUTLIER) cc_final: 0.6588 (t80)
  outliers start: 18
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1712
  time to fit residues: 29.2316
Evaluate side-chains
  107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   57 MET
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  263 ILE
Chi-restraints excluded: chain P residue  274 SER
Chi-restraints excluded: chain P residue  333 LEU
Chi-restraints excluded: chain P residue  374 LEU
Chi-restraints excluded: chain P residue  410 SER
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1097 LEU
Chi-restraints excluded: chain P residue 1111 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 94 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 0 optimal weight:    8.9990
   chunk 75 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.169955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.130041 restraints weight = 34443.773|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 3.38
r_work: 0.3927 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6639
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8223  Z= 0.120
  Angle     :  0.545   4.930  11207  Z= 0.280
  Chirality :  0.040   0.141   1329
  Planarity :  0.005   0.050   1409
  Dihedral  :  5.801  78.837   1157
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.86 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 18.47 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.02 (0.27), residues: 1024
  helix:  1.64 (0.25), residues: 456
  sheet: -0.37 (0.50), residues: 107
  loop : -1.63 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 686 
 TYR   0.009   0.001   TYR P 936 
 PHE   0.018   0.001   PHE P 934 
 TRP   0.012   0.001   TRP P  55 
 HIS   0.004   0.001   HIS P 190 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8223)
  covalent geometry    : angle       0.54521 (11207)
  hydrogen bonds       : bond        0.04214 (  379)
  hydrogen bonds       : angle       4.65580 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5754 (tmm) cc_final: 0.5345 (tpp)
REVERT: P  210 MET cc_start: 0.7714 (mmp) cc_final: 0.6867 (mmm)
REVERT: P  316 ASP cc_start: 0.6692 (t0) cc_final: 0.6404 (t0)
REVERT: P  327 MET cc_start: 0.7237 (tpt) cc_final: 0.7026 (tpp)
REVERT: P  710 ASP cc_start: 0.7510 (t0) cc_final: 0.7261 (t0)
REVERT: P  861 GLU cc_start: 0.7416 (tt0) cc_final: 0.7095 (tt0)
  outliers start: 16
  outliers final: 13
  residues processed: 108
  average time/residue: 0.1742
  time to fit residues: 27.1609
Evaluate side-chains
  109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  263 ILE
Chi-restraints excluded: chain P residue  274 SER
Chi-restraints excluded: chain P residue  333 LEU
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  513 ASP
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue 1002 LEU
Chi-restraints excluded: chain P residue 1097 LEU
Chi-restraints excluded: chain P residue 1111 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 65 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 77 optimal weight:    0.1980
   chunk 83 optimal weight:    0.5980
   chunk 99 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.7586

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

Flipped N/Q/H residues before XYZ refinement:
** P 369 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 = 0.4366 r_free = 0.4366 target = 0.169058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.129388 restraints weight = 34366.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.30
r_work: 0.3908 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8223  Z= 0.128
  Angle     :  0.551   5.030  11207  Z= 0.284
  Chirality :  0.040   0.141   1329
  Planarity :  0.005   0.054   1409
  Dihedral  :  5.866  81.110   1157
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.86 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 19.71 %
    Favored  : 78.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole: -0.00 (0.27), residues: 1024
  helix:  1.64 (0.25), residues: 457
  sheet: -0.37 (0.52), residues: 107
  loop : -1.68 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG P 384 
 TYR   0.009   0.001   TYR P 936 
 PHE   0.015   0.001   PHE P 934 
 TRP   0.012   0.001   TRP P  55 
 HIS   0.004   0.001   HIS P 822 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8223)
  covalent geometry    : angle       0.55111 (11207)
  hydrogen bonds       : bond        0.04167 (  379)
  hydrogen bonds       : angle       4.62961 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5753 (tmm) cc_final: 0.5349 (tpp)
REVERT: P  311 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7560 (mm-30)
REVERT: P  316 ASP cc_start: 0.6935 (t0) cc_final: 0.6606 (t0)
REVERT: P  710 ASP cc_start: 0.7493 (t0) cc_final: 0.7244 (t0)
REVERT: P  861 GLU cc_start: 0.7488 (tt0) cc_final: 0.7155 (tt0)
REVERT: P  940 TYR cc_start: 0.7737 (OUTLIER) cc_final: 0.6590 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 103
  average time/residue: 0.1721
  time to fit residues: 25.8763
Evaluate side-chains
  100 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  274 SER
Chi-restraints excluded: chain P residue  311 GLU
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1002 LEU
Chi-restraints excluded: chain P residue 1111 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 77 optimal weight:    0.0370
   chunk 21 optimal weight:    0.1980
   chunk 46 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.5260

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.170184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.129678 restraints weight = 34214.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.4041 rms_B_bonded: 3.38
r_work: 0.3927 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6643
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8223  Z= 0.108
  Angle     :  0.536   4.829  11207  Z= 0.274
  Chirality :  0.040   0.140   1329
  Planarity :  0.005   0.051   1409
  Dihedral  :  5.740  82.673   1157
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.25 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 18.69 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.10 (0.27), residues: 1024
  helix:  1.80 (0.26), residues: 453
  sheet: -0.43 (0.51), residues: 107
  loop : -1.66 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 384 
 TYR   0.008   0.001   TYR P 936 
 PHE   0.010   0.001   PHE P 963 
 TRP   0.012   0.001   TRP P  55 
 HIS   0.006   0.001   HIS P 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8223)
  covalent geometry    : angle       0.53632 (11207)
  hydrogen bonds       : bond        0.03898 (  379)
  hydrogen bonds       : angle       4.53137 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5784 (tmm) cc_final: 0.5341 (tpp)
REVERT: P  316 ASP cc_start: 0.6798 (t0) cc_final: 0.6509 (t0)
REVERT: P  562 SER cc_start: 0.6437 (OUTLIER) cc_final: 0.6060 (p)
REVERT: P  680 TYR cc_start: 0.8138 (m-80) cc_final: 0.7630 (m-80)
REVERT: P  710 ASP cc_start: 0.7436 (t0) cc_final: 0.7182 (t0)
REVERT: P  940 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6510 (t80)
REVERT: P  961 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7777 (mp)
REVERT: P 1128 PHE cc_start: 0.7971 (t80) cc_final: 0.7743 (t80)
REVERT: P 1132 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6256 (t80)
  outliers start: 20
  outliers final: 11
  residues processed: 110
  average time/residue: 0.1456
  time to fit residues: 23.5756
Evaluate side-chains
  107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  274 SER
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  513 ASP
Chi-restraints excluded: chain P residue  562 SER
Chi-restraints excluded: chain P residue  564 LEU
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  961 LEU
Chi-restraints excluded: chain P residue 1002 LEU
Chi-restraints excluded: chain P residue 1097 LEU
Chi-restraints excluded: chain P residue 1132 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 83 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0070
   chunk 88 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.6798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.167909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.128079 restraints weight = 34509.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.4015 rms_B_bonded: 3.33
r_work: 0.3904 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6718
moved from start:          0.4863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8223  Z= 0.122
  Angle     :  0.543   4.865  11207  Z= 0.278
  Chirality :  0.040   0.142   1329
  Planarity :  0.005   0.053   1409
  Dihedral  :  5.743  79.590   1157
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.57 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.81 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.13 (0.27), residues: 1024
  helix:  1.83 (0.26), residues: 449
  sheet: -0.42 (0.52), residues: 107
  loop : -1.62 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 686 
 TYR   0.008   0.001   TYR P 936 
 PHE   0.014   0.001   PHE P 445 
 TRP   0.011   0.001   TRP P  55 
 HIS   0.005   0.001   HIS P  84 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 8223)
  covalent geometry    : angle       0.54289 (11207)
  hydrogen bonds       : bond        0.03973 (  379)
  hydrogen bonds       : angle       4.54955 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5947 (tmm) cc_final: 0.5489 (tpp)
REVERT: P  316 ASP cc_start: 0.6939 (t0) cc_final: 0.6621 (t0)
REVERT: P  468 VAL cc_start: 0.8203 (t) cc_final: 0.7999 (t)
REVERT: P  562 SER cc_start: 0.6774 (OUTLIER) cc_final: 0.6384 (p)
REVERT: P  710 ASP cc_start: 0.7429 (t0) cc_final: 0.7162 (t0)
REVERT: P  940 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6514 (t80)
REVERT: P  961 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7808 (mp)
REVERT: P 1132 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6259 (t80)
  outliers start: 17
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1399
  time to fit residues: 23.9084
Evaluate side-chains
  115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue   57 MET
Chi-restraints excluded: chain P residue  202 HIS
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  513 ASP
Chi-restraints excluded: chain P residue  562 SER
Chi-restraints excluded: chain P residue  564 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  961 LEU
Chi-restraints excluded: chain P residue 1002 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Chi-restraints excluded: chain P residue 1132 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 95 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 83 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.167489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.127845 restraints weight = 34439.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.3994 rms_B_bonded: 3.28
r_work: 0.3885 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6773
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8223  Z= 0.140
  Angle     :  0.561   5.220  11207  Z= 0.287
  Chirality :  0.040   0.142   1329
  Planarity :  0.005   0.064   1409
  Dihedral  :  5.801  78.978   1157
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.64 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.26 %
    Favored  : 79.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.08 (0.27), residues: 1024
  helix:  1.84 (0.26), residues: 449
  sheet: -0.50 (0.51), residues: 107
  loop : -1.68 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG P  76 
 TYR   0.009   0.001   TYR P 936 
 PHE   0.008   0.001   PHE P 512 
 TRP   0.012   0.001   TRP P  55 
 HIS   0.006   0.001   HIS P 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8223)
  covalent geometry    : angle       0.56097 (11207)
  hydrogen bonds       : bond        0.04155 (  379)
  hydrogen bonds       : angle       4.60240 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  316 ASP cc_start: 0.7113 (t0) cc_final: 0.6819 (t0)
REVERT: P  562 SER cc_start: 0.6917 (OUTLIER) cc_final: 0.6604 (p)
REVERT: P  710 ASP cc_start: 0.7430 (t0) cc_final: 0.7153 (t0)
REVERT: P  934 PHE cc_start: 0.6727 (m-10) cc_final: 0.6343 (m-80)
REVERT: P  940 TYR cc_start: 0.7817 (OUTLIER) cc_final: 0.6547 (t80)
REVERT: P  961 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7816 (mp)
REVERT: P 1132 PHE cc_start: 0.6923 (OUTLIER) cc_final: 0.6262 (t80)
  outliers start: 14
  outliers final: 10
  residues processed: 112
  average time/residue: 0.1402
  time to fit residues: 23.3191
Evaluate side-chains
  115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  478 THR
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  513 ASP
Chi-restraints excluded: chain P residue  562 SER
Chi-restraints excluded: chain P residue  564 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  961 LEU
Chi-restraints excluded: chain P residue 1002 LEU
Chi-restraints excluded: chain P residue 1111 ILE
Chi-restraints excluded: chain P residue 1132 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0970
   chunk 14 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 89 optimal weight:    0.5980
   chunk 37 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.167490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.127856 restraints weight = 34365.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.4005 rms_B_bonded: 3.31
r_work: 0.3895 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6735
moved from start:          0.5177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8223  Z= 0.117
  Angle     :  0.551   6.243  11207  Z= 0.280
  Chirality :  0.040   0.140   1329
  Planarity :  0.005   0.062   1409
  Dihedral  :  5.769  81.365   1157
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.66 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 19.26 %
    Favored  : 79.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.12 (0.27), residues: 1024
  helix:  1.91 (0.26), residues: 445
  sheet: -0.53 (0.52), residues: 107
  loop : -1.65 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG P 384 
 TYR   0.008   0.001   TYR P 936 
 PHE   0.013   0.001   PHE P 445 
 TRP   0.012   0.001   TRP P  55 
 HIS   0.008   0.001   HIS P 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8223)
  covalent geometry    : angle       0.55082 (11207)
  hydrogen bonds       : bond        0.03949 (  379)
  hydrogen bonds       : angle       4.53641 ( 1092)

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

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

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2048 Ramachandran restraints generated.
    1024 Oldfield, 0 Emsley, 1024 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  316 ASP cc_start: 0.7153 (t0) cc_final: 0.6905 (t0)
REVERT: P  562 SER cc_start: 0.6924 (OUTLIER) cc_final: 0.6609 (p)
REVERT: P  710 ASP cc_start: 0.7451 (t0) cc_final: 0.7199 (t0)
REVERT: P  861 GLU cc_start: 0.7479 (tt0) cc_final: 0.7149 (tt0)
REVERT: P  940 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.6494 (t80)
REVERT: P  961 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7880 (mp)
REVERT: P 1128 PHE cc_start: 0.8003 (t80) cc_final: 0.7771 (t80)
REVERT: P 1132 PHE cc_start: 0.6917 (OUTLIER) cc_final: 0.6290 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 108
  average time/residue: 0.1544
  time to fit residues: 24.2634
Evaluate side-chains
  110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  202 HIS
Chi-restraints excluded: chain P residue  232 LEU
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  491 GLN
Chi-restraints excluded: chain P residue  513 ASP
Chi-restraints excluded: chain P residue  562 SER
Chi-restraints excluded: chain P residue  564 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  961 LEU
Chi-restraints excluded: chain P residue 1002 LEU
Chi-restraints excluded: chain P residue 1132 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 101 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.165857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.126391 restraints weight = 34551.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3975 rms_B_bonded: 3.27
r_work: 0.3864 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6743
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8223  Z= 0.144
  Angle     :  0.568   5.485  11207  Z= 0.292
  Chirality :  0.041   0.142   1329
  Planarity :  0.005   0.061   1409
  Dihedral  :  5.884  76.078   1157
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  7.03 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.37 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 aren not related in a simple way.
  whole:  0.01 (0.27), residues: 1024
  helix:  1.88 (0.26), residues: 442
  sheet: -0.59 (0.51), residues: 107
  loop : -1.77 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG P 686 
 TYR   0.010   0.001   TYR P 173 
 PHE   0.017   0.001   PHE P 963 
 TRP   0.011   0.001   TRP P  55 
 HIS   0.007   0.001   HIS P 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8223)
  covalent geometry    : angle       0.56824 (11207)
  hydrogen bonds       : bond        0.04289 (  379)
  hydrogen bonds       : angle       4.64581 ( 1092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3685.27 seconds
wall clock time: 63 minutes 16.36 seconds (3796.36 seconds total)