Starting phenix.real_space_refine
on Sun May 18 07:05:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iek_35384/05_2025/8iek_35384.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iek_35384/05_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_35384/05_2025/8iek_35384.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iek_35384/05_2025/8iek_35384.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iek_35384/05_2025/8iek_35384.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iek_35384/05_2025/8iek_35384.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.47, per 1000 atoms: 0.58
  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: 4.23
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  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: 1.44
  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: 6.51

  Time building geometry restraints manager: 5.15 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:             1.850
  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:             0.290
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.110
  Set scattering table:                    0.160
  Process input model:                     39.170
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:3.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.600
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (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
 TRP   0.009   0.001   TRP P  45 
 HIS   0.005   0.001   HIS P 198 
 PHE   0.012   0.001   PHE P 934 
 TYR   0.008   0.001   TYR P 241 
 ARG   0.003   0.000   ARG P1148 

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

*********************** 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  : 1.165 
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: 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: 0.7205 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.4990
  time to fit residues: 106.1825
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.181728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.142271 restraints weight = 34776.864|
|-----------------------------------------------------------------------------|
r_work (start): 0.4176 rms_B_bonded: 3.39
r_work: 0.4068 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6354
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   8223  Z= 0.153
  Angle     :  0.616   6.269  11207  Z= 0.318
  Chirality :  0.042   0.142   1329
  Planarity :  0.005   0.083   1409
  Dihedral  :  6.072  79.118   1157
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.98 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 15.99 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.27), residues: 1024
  helix:  1.77 (0.25), residues: 451
  sheet:  0.51 (0.56), residues: 94
  loop : -1.28 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P  55 
 HIS   0.018   0.001   HIS P 190 
 PHE   0.016   0.001   PHE P 934 
 TYR   0.010   0.001   TYR P 936 
 ARG   0.005   0.001   ARG P 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04950 (  379)
  hydrogen bonds       : angle       5.15973 ( 1092)
  covalent geometry    : bond        0.00351 ( 8223)
  covalent geometry    : angle       0.61635 (11207)

*********************** 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
  126 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 1.237 
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   55 TRP cc_start: 0.5535 (p-90) cc_final: 0.5244 (p-90)
REVERT: P   56 MET cc_start: 0.5188 (tmm) cc_final: 0.4756 (tpp)
REVERT: P  526 MET cc_start: 0.8009 (mtt) cc_final: 0.7573 (mtp)
REVERT: P  710 ASP cc_start: 0.7623 (t0) cc_final: 0.7373 (t0)
REVERT: P  724 MET cc_start: 0.7627 (mtt) cc_final: 0.7254 (mtt)
REVERT: P  861 GLU cc_start: 0.7449 (tt0) cc_final: 0.7131 (tt0)
  outliers start: 12
  outliers final: 7
  residues processed: 123
  average time/residue: 0.4026
  time to fit residues: 70.2183
Evaluate side-chains
  106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
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 45 optimal weight:    0.0670
   chunk 24 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
P1008 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4440 r_free = 0.4440 target = 0.176721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.137558 restraints weight = 34321.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.4122 rms_B_bonded: 3.35
r_work: 0.4015 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.2887

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= 0.131
  Angle     :  0.558   6.332  11207  Z= 0.289
  Chirality :  0.041   0.142   1329
  Planarity :  0.005   0.064   1409
  Dihedral  :  5.810  75.806   1157
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.88 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 16.55 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.27), residues: 1024
  helix:  1.78 (0.25), residues: 452
  sheet:  0.08 (0.51), residues: 107
  loop : -1.44 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP P  55 
 HIS   0.005   0.001   HIS P 822 
 PHE   0.022   0.001   PHE P 934 
 TYR   0.010   0.001   TYR P 936 
 ARG   0.005   0.000   ARG P 743 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04860 (  379)
  hydrogen bonds       : angle       4.91649 ( 1092)
  covalent geometry    : bond        0.00302 ( 8223)
  covalent geometry    : angle       0.55800 (11207)

*********************** 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
  110 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.162 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5388 (tmm) cc_final: 0.4835 (tpp)
REVERT: P   57 MET cc_start: 0.3759 (OUTLIER) cc_final: 0.3249 (ppp)
REVERT: P  163 LEU cc_start: 0.6640 (tp) cc_final: 0.6322 (mm)
REVERT: P  176 ILE cc_start: 0.6763 (pt) cc_final: 0.6519 (pt)
REVERT: P  210 MET cc_start: 0.7044 (mmm) cc_final: 0.6724 (mmp)
REVERT: P  308 ASP cc_start: 0.7495 (p0) cc_final: 0.7160 (p0)
REVERT: P  579 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7952 (mt-10)
REVERT: P  710 ASP cc_start: 0.7566 (t0) cc_final: 0.7338 (t0)
REVERT: P  724 MET cc_start: 0.7937 (mtt) cc_final: 0.7623 (mtt)
REVERT: P  861 GLU cc_start: 0.7475 (tt0) cc_final: 0.7155 (tt0)
  outliers start: 13
  outliers final: 11
  residues processed: 106
  average time/residue: 0.3971
  time to fit residues: 59.3146
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
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  339 MET
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 1097 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0980
   chunk 80 optimal weight:    0.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.4405 r_free = 0.4405 target = 0.173189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.133791 restraints weight = 34255.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 3.36
r_work: 0.3971 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
moved from start:          0.3591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8223  Z= 0.132
  Angle     :  0.563   6.442  11207  Z= 0.291
  Chirality :  0.041   0.143   1329
  Planarity :  0.005   0.056   1409
  Dihedral  :  5.911  86.505   1157
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.98 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.33 %
    Favored  : 81.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.15 (0.27), residues: 1024
  helix:  1.70 (0.25), residues: 455
  sheet: -0.15 (0.52), residues: 102
  loop : -1.54 (0.27), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP P  55 
 HIS   0.012   0.001   HIS P 190 
 PHE   0.013   0.001   PHE P1132 
 TYR   0.010   0.001   TYR P  40 
 ARG   0.007   0.000   ARG P 989 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04173 (  379)
  hydrogen bonds       : angle       4.66447 ( 1092)
  covalent geometry    : bond        0.00305 ( 8223)
  covalent geometry    : angle       0.56349 (11207)

*********************** 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
  115 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5498 (tmm) cc_final: 0.4875 (tpp)
REVERT: P  348 GLU cc_start: 0.7837 (tp30) cc_final: 0.7571 (mm-30)
REVERT: P  526 MET cc_start: 0.7941 (mtt) cc_final: 0.7435 (mtp)
REVERT: P  710 ASP cc_start: 0.7558 (t0) cc_final: 0.7328 (t0)
REVERT: P  724 MET cc_start: 0.8146 (mtt) cc_final: 0.7779 (mtt)
REVERT: P  861 GLU cc_start: 0.7425 (tt0) cc_final: 0.7107 (tt0)
  outliers start: 17
  outliers final: 12
  residues processed: 110
  average time/residue: 0.3766
  time to fit residues: 59.4850
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.126 
-------------------------------------------------------------------------------
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  274 SER
Chi-restraints excluded: chain P residue  333 LEU
Chi-restraints excluded: chain P residue  374 LEU
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  825 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue 1097 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 54 optimal weight:    0.2980
   chunk 75 optimal weight:    0.3980
   chunk 83 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 88 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4400 r_free = 0.4400 target = 0.172356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.132708 restraints weight = 34853.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 3.40
r_work: 0.3960 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.3888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8223  Z= 0.115
  Angle     :  0.540   5.146  11207  Z= 0.277
  Chirality :  0.040   0.141   1329
  Planarity :  0.005   0.052   1409
  Dihedral  :  5.703  81.015   1157
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.27 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.79 %
    Favored  : 80.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.27), residues: 1024
  helix:  1.80 (0.25), residues: 456
  sheet: -0.27 (0.50), residues: 107
  loop : -1.49 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P  55 
 HIS   0.003   0.001   HIS P 822 
 PHE   0.020   0.001   PHE P 934 
 TYR   0.009   0.001   TYR P 936 
 ARG   0.003   0.000   ARG P  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04089 (  379)
  hydrogen bonds       : angle       4.58791 ( 1092)
  covalent geometry    : bond        0.00267 ( 8223)
  covalent geometry    : angle       0.54021 (11207)

*********************** 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
  109 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5353 (tmm) cc_final: 0.4999 (tpp)
REVERT: P  100 TRP cc_start: 0.7325 (m100) cc_final: 0.6626 (m-90)
REVERT: P  210 MET cc_start: 0.7803 (mmp) cc_final: 0.6994 (mmm)
REVERT: P  348 GLU cc_start: 0.7918 (tp30) cc_final: 0.7711 (tp30)
REVERT: P  710 ASP cc_start: 0.7509 (t0) cc_final: 0.7276 (t0)
REVERT: P  724 MET cc_start: 0.8205 (mtt) cc_final: 0.7893 (mtt)
REVERT: P  861 GLU cc_start: 0.7416 (tt0) cc_final: 0.7094 (tt0)
REVERT: P  940 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.6639 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 106
  average time/residue: 0.3532
  time to fit residues: 54.2809
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
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  333 LEU
Chi-restraints excluded: chain P residue  374 LEU
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  825 LEU
Chi-restraints excluded: chain P residue  873 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1097 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 13 optimal weight:    0.3980
   chunk 69 optimal weight:    0.1980
   chunk 59 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0070
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.4598

-------------------------------------------------------------------------------
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 = 0.4398 r_free = 0.4398 target = 0.172321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.133256 restraints weight = 34572.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.4075 rms_B_bonded: 3.35
r_work: 0.3964 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.4096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8223  Z= 0.104
  Angle     :  0.524   4.830  11207  Z= 0.268
  Chirality :  0.040   0.141   1329
  Planarity :  0.005   0.053   1409
  Dihedral  :  5.670  84.784   1157
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.08 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 18.58 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.27), residues: 1024
  helix:  1.90 (0.25), residues: 455
  sheet: -0.28 (0.50), residues: 107
  loop : -1.47 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P  55 
 HIS   0.003   0.001   HIS P  84 
 PHE   0.012   0.001   PHE P1128 
 TYR   0.008   0.001   TYR P 936 
 ARG   0.001   0.000   ARG P 451 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03757 (  379)
  hydrogen bonds       : angle       4.47763 ( 1092)
  covalent geometry    : bond        0.00241 ( 8223)
  covalent geometry    : angle       0.52408 (11207)

*********************** 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
  108 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 1.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.5388 (tmm) cc_final: 0.4984 (tpp)
REVERT: P  100 TRP cc_start: 0.7367 (m100) cc_final: 0.6664 (m-90)
REVERT: P  327 MET cc_start: 0.7114 (tpt) cc_final: 0.6881 (tpp)
REVERT: P  710 ASP cc_start: 0.7435 (t0) cc_final: 0.7204 (t0)
REVERT: P  861 GLU cc_start: 0.7411 (tt0) cc_final: 0.7084 (tt0)
REVERT: P  940 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6679 (t80)
  outliers start: 13
  outliers final: 8
  residues processed: 105
  average time/residue: 0.3695
  time to fit residues: 56.7514
Evaluate side-chains
  100 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  252 LEU
Chi-restraints excluded: chain P residue  274 SER
Chi-restraints excluded: chain P residue  333 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  825 LEU
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 1126 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 85 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0170
   chunk 93 optimal weight:    0.0970
   overall best weight:    0.5416

-------------------------------------------------------------------------------
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 = 0.4396 r_free = 0.4396 target = 0.172083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.132232 restraints weight = 34444.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 3.35
r_work: 0.3961 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6617
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8223  Z= 0.112
  Angle     :  0.530   4.804  11207  Z= 0.271
  Chirality :  0.039   0.142   1329
  Planarity :  0.005   0.051   1409
  Dihedral  :  5.621  82.085   1157
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.18 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 18.36 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.27), residues: 1024
  helix:  1.96 (0.26), residues: 451
  sheet: -0.30 (0.51), residues: 107
  loop : -1.51 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P  55 
 HIS   0.003   0.001   HIS P 822 
 PHE   0.013   0.001   PHE P 445 
 TYR   0.008   0.001   TYR P 936 
 ARG   0.002   0.000   ARG P 294 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03790 (  379)
  hydrogen bonds       : angle       4.47561 ( 1092)
  covalent geometry    : bond        0.00258 ( 8223)
  covalent geometry    : angle       0.53010 (11207)

*********************** 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: 19
    poor density    : 95
  time to evaluate  : 1.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  100 TRP cc_start: 0.7421 (m100) cc_final: 0.6681 (m-90)
REVERT: P  210 MET cc_start: 0.7760 (mmp) cc_final: 0.7111 (mmm)
REVERT: P  327 MET cc_start: 0.7220 (tpt) cc_final: 0.6998 (tpp)
REVERT: P  710 ASP cc_start: 0.7389 (t0) cc_final: 0.7149 (t0)
REVERT: P  861 GLU cc_start: 0.7448 (tt0) cc_final: 0.7120 (tt0)
REVERT: P  940 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6586 (t80)
REVERT: P  961 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7764 (mp)
  outliers start: 19
  outliers final: 13
  residues processed: 109
  average time/residue: 0.3660
  time to fit residues: 58.5428
Evaluate side-chains
  105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  176 ILE
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  478 THR
Chi-restraints excluded: chain P residue  479 VAL
Chi-restraints excluded: chain P residue  562 SER
Chi-restraints excluded: chain P residue  612 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  825 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 1097 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 72 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 4 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4380 r_free = 0.4380 target = 0.170480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.131265 restraints weight = 34521.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.4038 rms_B_bonded: 3.26
r_work: 0.3931 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6722
moved from start:          0.4602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8223  Z= 0.123
  Angle     :  0.542   4.909  11207  Z= 0.277
  Chirality :  0.040   0.142   1329
  Planarity :  0.005   0.052   1409
  Dihedral  :  5.653  80.918   1157
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.37 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 18.81 %
    Favored  : 79.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.27), residues: 1024
  helix:  1.91 (0.26), residues: 452
  sheet: -0.34 (0.50), residues: 107
  loop : -1.59 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P  55 
 HIS   0.004   0.001   HIS P  84 
 PHE   0.018   0.001   PHE P 963 
 TYR   0.009   0.001   TYR P 936 
 ARG   0.002   0.000   ARG P 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03972 (  379)
  hydrogen bonds       : angle       4.53864 ( 1092)
  covalent geometry    : bond        0.00294 ( 8223)
  covalent geometry    : angle       0.54174 (11207)

*********************** 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
  111 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.6568 (tmm) cc_final: 0.6064 (tpp)
REVERT: P  311 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7550 (mm-30)
REVERT: P  562 SER cc_start: 0.6617 (OUTLIER) cc_final: 0.6307 (p)
REVERT: P  680 TYR cc_start: 0.8244 (m-80) cc_final: 0.7777 (m-80)
REVERT: P  710 ASP cc_start: 0.7311 (t0) cc_final: 0.7068 (t0)
REVERT: P  861 GLU cc_start: 0.7525 (tt0) cc_final: 0.7197 (tt0)
REVERT: P  940 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6687 (t80)
REVERT: P  961 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7809 (mp)
  outliers start: 14
  outliers final: 8
  residues processed: 109
  average time/residue: 0.3679
  time to fit residues: 58.5436
Evaluate side-chains
  107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
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  311 GLU
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  653 VAL
Chi-restraints excluded: chain P residue  825 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 1097 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 62 optimal weight:    0.1980
   chunk 41 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 90 optimal weight:    0.1980
   chunk 9 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
P 283 GLN
** P 369 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 = 0.4373 r_free = 0.4373 target = 0.170315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.130571 restraints weight = 34575.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.4045 rms_B_bonded: 3.36
r_work: 0.3930 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.4702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8223  Z= 0.113
  Angle     :  0.546   5.992  11207  Z= 0.277
  Chirality :  0.039   0.140   1329
  Planarity :  0.005   0.051   1409
  Dihedral  :  5.620  81.983   1157
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  5.18 %
    Favored  : 94.53 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.27), residues: 1024
  helix:  1.97 (0.26), residues: 451
  sheet: -0.36 (0.50), residues: 107
  loop : -1.58 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P  55 
 HIS   0.003   0.001   HIS P 777 
 PHE   0.021   0.001   PHE P 963 
 TYR   0.009   0.001   TYR P 936 
 ARG   0.008   0.000   ARG P  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03853 (  379)
  hydrogen bonds       : angle       4.49961 ( 1092)
  covalent geometry    : bond        0.00265 ( 8223)
  covalent geometry    : angle       0.54614 (11207)

*********************** 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
  106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 1.303 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   56 MET cc_start: 0.6598 (tmm) cc_final: 0.6178 (tpp)
REVERT: P  210 MET cc_start: 0.7690 (mmp) cc_final: 0.7046 (mmm)
REVERT: P  311 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7502 (mm-30)
REVERT: P  562 SER cc_start: 0.6438 (OUTLIER) cc_final: 0.6060 (p)
REVERT: P  680 TYR cc_start: 0.8172 (m-80) cc_final: 0.7762 (m-80)
REVERT: P  710 ASP cc_start: 0.7386 (t0) cc_final: 0.7157 (t0)
REVERT: P  861 GLU cc_start: 0.7450 (tt0) cc_final: 0.7115 (tt0)
REVERT: P  940 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.6441 (t80)
REVERT: P  961 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7770 (mp)
  outliers start: 13
  outliers final: 8
  residues processed: 104
  average time/residue: 0.3772
  time to fit residues: 56.3874
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 1.178 
-------------------------------------------------------------------------------
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  311 GLU
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  612 LEU
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  825 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 62 optimal weight:    0.2980
   chunk 53 optimal weight:    0.0980
   chunk 59 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4380 r_free = 0.4380 target = 0.170479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.130785 restraints weight = 34618.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.4031 rms_B_bonded: 3.29
r_work: 0.3925 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6721
moved from start:          0.4837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8223  Z= 0.108
  Angle     :  0.541   6.169  11207  Z= 0.273
  Chirality :  0.039   0.140   1329
  Planarity :  0.005   0.052   1409
  Dihedral  :  5.583  82.907   1157
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.57 %
    Favored  : 94.04 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 19.26 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.27), residues: 1024
  helix:  1.99 (0.26), residues: 453
  sheet: -0.32 (0.51), residues: 107
  loop : -1.56 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP P  55 
 HIS   0.002   0.001   HIS P 822 
 PHE   0.015   0.001   PHE P1128 
 TYR   0.008   0.001   TYR P 936 
 ARG   0.001   0.000   ARG P 544 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  379)
  hydrogen bonds       : angle       4.45627 ( 1092)
  covalent geometry    : bond        0.00257 ( 8223)
  covalent geometry    : angle       0.54087 (11207)

********************** 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
  107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.477 
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   56 MET cc_start: 0.6599 (tmm) cc_final: 0.6167 (tpp)
REVERT: P  562 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.6200 (p)
REVERT: P  710 ASP cc_start: 0.7329 (t0) cc_final: 0.7074 (t0)
REVERT: P  934 PHE cc_start: 0.6513 (m-10) cc_final: 0.6182 (m-80)
REVERT: P  940 TYR cc_start: 0.7847 (OUTLIER) cc_final: 0.6505 (t80)
REVERT: P  961 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7797 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 107
  average time/residue: 0.3834
  time to fit residues: 59.2521
Evaluate side-chains
  105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
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  479 VAL
Chi-restraints excluded: chain P residue  513 ASP
Chi-restraints excluded: chain P residue  562 SER
Chi-restraints excluded: chain P residue  653 VAL
Chi-restraints excluded: chain P residue  825 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 34 optimal weight:    0.4980
   chunk 83 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4349 r_free = 0.4349 target = 0.168853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.128919 restraints weight = 34478.119|
|-----------------------------------------------------------------------------|
r_work (start): 0.4032 rms_B_bonded: 3.36
r_work: 0.3917 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6656
moved from start:          0.4991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8223  Z= 0.120
  Angle     :  0.550   5.997  11207  Z= 0.279
  Chirality :  0.040   0.140   1329
  Planarity :  0.005   0.066   1409
  Dihedral  :  5.603  80.387   1157
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  6.15 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 19.26 %
    Favored  : 79.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.27), residues: 1024
  helix:  2.03 (0.26), residues: 447
  sheet: -0.35 (0.51), residues: 107
  loop : -1.52 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P  55 
 HIS   0.003   0.001   HIS P 822 
 PHE   0.015   0.001   PHE P1128 
 TYR   0.009   0.001   TYR P 936 
 ARG   0.007   0.000   ARG P 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03865 (  379)
  hydrogen bonds       : angle       4.51683 ( 1092)
  covalent geometry    : bond        0.00287 ( 8223)
  covalent geometry    : angle       0.55001 (11207)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7732.21 seconds
wall clock time: 133 minutes 27.17 seconds (8007.17 seconds total)