Starting phenix.real_space_refine
on Wed Mar 12 03:59:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fjq_31627/03_2025/7fjq_31627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fjq_31627/03_2025/7fjq_31627.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2025/7fjq_31627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2025/7fjq_31627.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2025/7fjq_31627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fjq_31627/03_2025/7fjq_31627.cif"
  }
  resolution = 3.6
  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=   0.002 sd=   0.080
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      44      5.16       5
     C    4570      2.51       5
     N    1203      2.21       5
     O    1269      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7086
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7072
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 973, 7072
          Classifications: {'peptide': 973}
          Incomplete info: {'truncation_to_alanine': 107}
          Link IDs: {'PTRANS': 67, 'TRANS': 905}
          Chain breaks: 9
          Unresolved chain link angles: 6
          Unresolved non-hydrogen bonds: 428
          Unresolved non-hydrogen angles: 534
          Unresolved non-hydrogen dihedrals: 372
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 11, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 13, 'ARG:plan': 14}
          Unresolved non-hydrogen planarities: 260
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'SPM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.71, per 1000 atoms: 0.66
  Number of scatterers: 7086
  At special positions: 0
  Unit cell: (77.9509, 96.6152, 138.335, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      44     16.00
     O    1269      8.00
     N    1203      7.00
     C    4570      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 298 " - pdb=" SG  CYS A 317 " distance=2.03

  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: 1.85
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1816

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      42.4% alpha, 8.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 124
    Processing helix  chain 'A' and resid 195 through 200
    Processing helix  chain 'A' and resid 205 through 216
      removed outlier: 3.623A  pdb=" N   MET A 210 " --> pdb=" O   LEU A 206 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL A 211 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   ALA A 214 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 237
    Processing helix  chain 'A' and resid 242 through 247
    Processing helix  chain 'A' and resid 247 through 252
    Processing helix  chain 'A' and resid 257 through 287
      removed outlier: 4.197A  pdb=" N   SER A 274 " --> pdb=" O   SER A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 411
      removed outlier: 3.736A  pdb=" N   VAL A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 424
    Processing helix  chain 'A' and resid 424 through 436
      removed outlier: 3.850A  pdb=" N   VAL A 429 " --> pdb=" O   SER A 425 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   ALA A 430 " --> pdb=" O   MET A 426 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   VAL A 434 " --> pdb=" O   ALA A 430 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ALA A 436 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 450
    Processing helix  chain 'A' and resid 454 through 469
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.534A  pdb=" N   GLN A 485 " --> pdb=" O   THR A 481 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 486 " --> pdb=" O   LEU A 482 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 505
      removed outlier: 3.782A  pdb=" N   ASN A 502 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 505 " --> pdb=" O   ASN A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 556
      removed outlier: 3.610A  pdb=" N   ALA A 554 " --> pdb=" O   PRO A 550 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   ALA A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 577
      removed outlier: 4.178A  pdb=" N   LYS A 576 " --> pdb=" O   PRO A 572 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   MET A 577 " --> pdb=" O   MET A 573 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 572 through 577'
    Processing helix  chain 'A' and resid 577 through 582
      removed outlier: 4.523A  pdb=" N   THR A 581 " --> pdb=" O   MET A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 662
      removed outlier: 3.535A  pdb=" N   GLY A 662 " --> pdb=" O   GLU A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 678
    Processing helix  chain 'A' and resid 709 through 713
      removed outlier: 3.935A  pdb=" N   VAL A 712 " --> pdb=" O   ARG A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 741
      removed outlier: 3.838A  pdb=" N   ILE A 736 " --> pdb=" O   THR A 732 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   GLN A 737 " --> pdb=" O   THR A 733 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA A 738 " --> pdb=" O   PRO A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 765
      removed outlier: 3.705A  pdb=" N   THR A 759 " --> pdb=" O   GLN A 755 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL A 760 " --> pdb=" O   THR A 756 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   ALA A 761 " --> pdb=" O   ALA A 757 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY A 765 " --> pdb=" O   ALA A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 834
    Processing helix  chain 'A' and resid 840 through 844
    Processing helix  chain 'A' and resid 858 through 866
      removed outlier: 3.719A  pdb=" N   LEU A 862 " --> pdb=" O   GLN A 858 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   CYS A 864 " --> pdb=" O   THR A 860 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 866 " --> pdb=" O   LEU A 862 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 882 through 889
      removed outlier: 4.390A  pdb=" N   LYS A 887 " --> pdb=" O   CYS A 883 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ALA A 888 " --> pdb=" O   GLY A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 921
      removed outlier: 3.607A  pdb=" N   ILE A 920 " --> pdb=" O   VAL A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 931 through 950
      removed outlier: 3.522A  pdb=" N   TYR A 936 " --> pdb=" O   SER A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 959 through 979
      removed outlier: 3.923A  pdb=" N   VAL A 974 " --> pdb=" O   ILE A 970 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA A 975 " --> pdb=" O   THR A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1025
    Processing helix  chain 'A' and resid 1044 through 1065
      removed outlier: 3.943A  pdb=" N   THR A1048 " --> pdb=" O   ASN A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1074 through 1077
    Processing helix  chain 'A' and resid 1078 through 1098
    Processing helix  chain 'A' and resid 1104 through 1108
      removed outlier: 3.969A  pdb=" N   ALA A1107 " --> pdb=" O   GLY A1104 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   LEU A1108 " --> pdb=" O   PRO A1105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1104 through 1108'
    Processing helix  chain 'A' and resid 1116 through 1140
    Processing helix  chain 'A' and resid 1157 through 1169
    Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318
      removed outlier: 6.643A  pdb=" N   LEU A 392 " --> pdb=" O   VAL A 334 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 493 through 495
    Processing sheet with id=AA3, first strand: chain 'A' and resid 792 through 794
      removed outlier: 4.689A  pdb=" N   LEU A 773 " --> pdb=" O   MET A 794 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU A 823 " --> pdb=" O   GLY A 848 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   VAL A 850 " --> pdb=" O   LEU A 823 " (cutoff:3.500A)
      removed outlier: 7.354A  pdb=" N   ALA A 746 " --> pdb=" O   THR A 849 " (cutoff:3.500A)
      removed outlier: 8.585A  pdb=" N   PHE A 851 " --> pdb=" O   ALA A 746 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   MET A 748 " --> pdb=" O   PHE A 851 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   MET A 875 " --> pdb=" O   ILE A 893 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 530
      removed outlier: 5.417A  pdb=" N   VAL A 525 " --> pdb=" O   ARG A 725 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   ARG A 725 " --> pdb=" O   VAL A 525 " (cutoff:3.500A)
      removed outlier: 4.632A  pdb=" N   GLY A 527 " --> pdb=" O   VAL A 723 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   LEU A 718 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   SER A 692 " --> pdb=" O   LEU A 718 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   VAL A 641 " --> pdb=" O   GLU A 650 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   ARG A 636 " --> pdb=" O   PRO A 629 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   SER A 638 " --> pdb=" O   ARG A 627 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ARG A 627 " --> pdb=" O   SER A 638 " (cutoff:3.500A)
      removed outlier: 7.374A  pdb=" N   ALA A 642 " --> pdb=" O   SER A 623 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   SER A 623 " --> pdb=" O   ALA A 642 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 562 through 564
      removed outlier: 3.730A  pdb=" N   LEU A 564 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   THR A 567 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)

    275 hydrogen bonds defined for protein.
    783 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: 2.08

  Time building geometry restraints manager: 2.17 seconds

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

  Histogram of bond lengths:
        1.11 -     1.25: 1025
        1.25 -     1.39: 1712
        1.39 -     1.53: 3693
        1.53 -     1.67: 728
        1.67 -     1.81: 65
  Bond restraints: 7223
  Sorted by residual:
  bond pdb=" CA  TYR A 256 "
       pdb=" C   TYR A 256 "
    ideal  model  delta    sigma   weight residual
    1.523  1.308  0.215 1.34e-02 5.57e+03 2.57e+02
  bond pdb=" CA  HIS A 255 "
       pdb=" C   HIS A 255 "
    ideal  model  delta    sigma   weight residual
    1.523  1.347  0.176 1.34e-02 5.57e+03 1.73e+02
  bond pdb=" CA  ALA A 965 "
       pdb=" C   ALA A 965 "
    ideal  model  delta    sigma   weight residual
    1.524  1.363  0.161 1.27e-02 6.20e+03 1.60e+02
  bond pdb=" C   LEU A 964 "
       pdb=" O   LEU A 964 "
    ideal  model  delta    sigma   weight residual
    1.237  1.106  0.131 1.17e-02 7.31e+03 1.25e+02
  bond pdb=" CA  SER A 941 "
       pdb=" C   SER A 941 "
    ideal  model  delta    sigma   weight residual
    1.524  1.386  0.138 1.27e-02 6.20e+03 1.17e+02
  ... (remaining 7218 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.92: 9458
        4.92 -     9.84: 372
        9.84 -    14.77: 31
       14.77 -    19.69: 6
       19.69 -    24.61: 3
  Bond angle restraints: 9870
  Sorted by residual:
  angle pdb=" N   PRO A1172 "
        pdb=" CA  PRO A1172 "
        pdb=" C   PRO A1172 "
      ideal   model   delta    sigma   weight residual
     110.70   86.09   24.61 1.22e+00 6.72e-01 4.07e+02
  angle pdb=" N   LYS A1117 "
        pdb=" CA  LYS A1117 "
        pdb=" C   LYS A1117 "
      ideal   model   delta    sigma   weight residual
     111.71   98.66   13.05 1.15e+00 7.56e-01 1.29e+02
  angle pdb=" N   ILE A 441 "
        pdb=" CA  ILE A 441 "
        pdb=" C   ILE A 441 "
      ideal   model   delta    sigma   weight residual
     111.56  101.88    9.68 8.60e-01 1.35e+00 1.27e+02
  angle pdb=" N   TRP A 258 "
        pdb=" CA  TRP A 258 "
        pdb=" C   TRP A 258 "
      ideal   model   delta    sigma   weight residual
     111.11  123.97  -12.86 1.20e+00 6.94e-01 1.15e+02
  angle pdb=" N   LEU A1042 "
        pdb=" CA  LEU A1042 "
        pdb=" C   LEU A1042 "
      ideal   model   delta    sigma   weight residual
     109.81  133.44  -23.63 2.21e+00 2.05e-01 1.14e+02
  ... (remaining 9865 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.85: 3961
       16.85 -    33.69: 266
       33.69 -    50.53: 93
       50.53 -    67.37: 17
       67.37 -    84.22: 4
  Dihedral angle restraints: 4341
    sinusoidal: 1536
      harmonic: 2805
  Sorted by residual:
  dihedral pdb=" C   LEU A1042 "
           pdb=" N   LEU A1042 "
           pdb=" CA  LEU A1042 "
           pdb=" CB  LEU A1042 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -152.07   29.47     0      2.50e+00 1.60e-01 1.39e+02
  dihedral pdb=" N   LEU A1042 "
           pdb=" C   LEU A1042 "
           pdb=" CA  LEU A1042 "
           pdb=" CB  LEU A1042 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  151.73  -28.93     0      2.50e+00 1.60e-01 1.34e+02
  dihedral pdb=" N   GLN A 944 "
           pdb=" C   GLN A 944 "
           pdb=" CA  GLN A 944 "
           pdb=" CB  GLN A 944 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  147.79  -24.99     0      2.50e+00 1.60e-01 1.00e+02
  ... (remaining 4338 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.265: 1108
       0.265 -    0.530: 82
       0.530 -    0.795: 26
       0.795 -    1.060: 4
       1.060 -    1.325: 2
  Chirality restraints: 1222
  Sorted by residual:
  chirality pdb=" CA  LEU A1042 "
            pdb=" N   LEU A1042 "
            pdb=" C   LEU A1042 "
            pdb=" CB  LEU A1042 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.19    1.33 2.00e-01 2.50e+01 4.39e+01
  chirality pdb=" CA  GLN A 944 "
            pdb=" N   GLN A 944 "
            pdb=" C   GLN A 944 "
            pdb=" CB  GLN A 944 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.44    1.07 2.00e-01 2.50e+01 2.85e+01
  chirality pdb=" CA  LYS A 935 "
            pdb=" N   LYS A 935 "
            pdb=" C   LYS A 935 "
            pdb=" CB  LYS A 935 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.51    1.00 2.00e-01 2.50e+01 2.51e+01
  ... (remaining 1219 not shown)

  Planarity restraints: 1250
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 966 "   -0.040 2.00e-02 2.50e+03   7.67e-02 5.88e+01
        pdb=" C   ILE A 966 "    0.133 2.00e-02 2.50e+03
        pdb=" O   ILE A 966 "   -0.047 2.00e-02 2.50e+03
        pdb=" N   ASP A 967 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 967 "   -0.039 2.00e-02 2.50e+03   7.29e-02 5.31e+01
        pdb=" C   ASP A 967 "    0.126 2.00e-02 2.50e+03
        pdb=" O   ASP A 967 "   -0.045 2.00e-02 2.50e+03
        pdb=" N   LEU A 968 "   -0.043 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 969 "    0.032 2.00e-02 2.50e+03   6.23e-02 3.89e+01
        pdb=" C   VAL A 969 "   -0.108 2.00e-02 2.50e+03
        pdb=" O   VAL A 969 "    0.039 2.00e-02 2.50e+03
        pdb=" N   ILE A 970 "    0.036 2.00e-02 2.50e+03
  ... (remaining 1247 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 147
        2.56 -     3.15: 5519
        3.15 -     3.73: 10784
        3.73 -     4.32: 14168
        4.32 -     4.90: 22826
  Nonbonded interactions: 53444
  Sorted by model distance:
  nonbonded pdb=" CB  HIS A 255 "
            pdb=" N   TYR A 256 "
     model   vdw
     1.980 2.816
  nonbonded pdb=" CB  TYR A 256 "
            pdb=" N   TYR A 257 "
     model   vdw
     2.063 2.816
  nonbonded pdb=" N   SER A1055 "
            pdb=" OG  SER A1055 "
     model   vdw
     2.181 2.496
  nonbonded pdb=" O   TYR A 256 "
            pdb=" N   TRP A 258 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   TYR A 256 "
            pdb=" C   TYR A 257 "
     model   vdw
     2.294 3.270
  ... (remaining 53439 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.270
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.880
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
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      :  0.019   0.215   7223  Z= 1.242
  Angle     :  2.025  24.610   9870  Z= 1.333
  Chirality :  0.171   1.325   1222
  Planarity :  0.014   0.144   1250
  Dihedral  : 13.671  84.216   2522
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  1.68 %
    Allowed  : 10.18 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  :  9.94 %
    Favored  : 83.29 %
  Cbeta Deviations :  4.85 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (0.24), residues: 953
  helix: -1.36 (0.25), residues: 398
  sheet: -2.71 (0.50), residues: 71
  loop : -3.45 (0.24), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A1171 
 HIS   0.009   0.001   HIS A 255 
 PHE   0.066   0.004   PHE A 945 
 TYR   0.035   0.003   TYR A 940 
 ARG   0.003   0.001   ARG A1158 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 112
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 ILE cc_start: 0.8701 (pp) cc_final: 0.8493 (mm)
REVERT: A  854 MET cc_start: 0.8812 (mmm) cc_final: 0.8491 (mmm)
REVERT: A  918 MET cc_start: 0.8317 (ptp) cc_final: 0.7981 (ptp)
REVERT: A  937 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mmt)
REVERT: A  941 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.9060 (t)
REVERT: A  942 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8803 (mt)
REVERT: A 1008 GLN cc_start: 0.8265 (OUTLIER) cc_final: 0.7960 (tt0)
  outliers start: 49
  outliers final: 25
  residues processed: 156
  average time/residue: 0.1772
  time to fit residues: 38.3570
Evaluate side-chains
  95 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 66
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 LEU
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  480 CYS
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  937 MET
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  941 SER
Chi-restraints excluded: chain A residue  942 LEU
Chi-restraints excluded: chain A residue  950 ILE
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  962 GLN
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue 1008 GLN
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1047 ASN
Chi-restraints excluded: chain A residue 1049 VAL
Chi-restraints excluded: chain A residue 1059 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1079 VAL
Chi-restraints excluded: chain A residue 1080 PRO
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1087 LEU
Chi-restraints excluded: chain A residue 1116 PHE
Chi-restraints excluded: chain A residue 1118 LEU
Chi-restraints excluded: chain A residue 1121 LEU
Chi-restraints excluded: chain A residue 1129 VAL
Chi-restraints excluded: chain A residue 1136 SER
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:   30.0000
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0170
   chunk 56 optimal weight:    4.9990
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
A 497 HIS
A 870 GLN
A1047 ASN
** A1057 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1078 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.176328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.111385 restraints weight = 10629.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.112388 restraints weight = 7121.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113291 restraints weight = 5713.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7223  Z= 0.234
  Angle     :  0.818  11.373   9870  Z= 0.411
  Chirality :  0.049   0.311   1222
  Planarity :  0.008   0.136   1250
  Dihedral  :  9.159  56.297   1091
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  9.65 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 14.78 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.25), residues: 953
  helix: -1.27 (0.26), residues: 385
  sheet: -2.13 (0.50), residues: 74
  loop : -3.03 (0.25), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1171 
 HIS   0.005   0.001   HIS A 255 
 PHE   0.017   0.002   PHE A 963 
 TYR   0.025   0.002   TYR A 936 
 ARG   0.007   0.001   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 75
  time to evaluate  : 0.731 
Fit side-chains
   revert: symmetry clash
REVERT: A  501 ILE cc_start: 0.9103 (mt) cc_final: 0.8891 (mt)
REVERT: A  542 GLU cc_start: 0.6594 (tm-30) cc_final: 0.6091 (pp20)
REVERT: A  875 MET cc_start: 0.8237 (tpt) cc_final: 0.8014 (tpt)
REVERT: A  937 MET cc_start: 0.8636 (tpp) cc_final: 0.8208 (mmm)
REVERT: A 1047 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7738 (t0)
REVERT: A 1093 VAL cc_start: 0.8732 (OUTLIER) cc_final: 0.8496 (p)
REVERT: A 1133 MET cc_start: 0.7344 (mmm) cc_final: 0.6950 (mmp)
  outliers start: 36
  outliers final: 15
  residues processed: 103
  average time/residue: 0.1760
  time to fit residues: 25.5543
Evaluate side-chains
  83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  446 ILE
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  748 MET
Chi-restraints excluded: chain A residue  896 SER
Chi-restraints excluded: chain A residue  933 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  962 GLN
Chi-restraints excluded: chain A residue 1047 ASN
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1067 LYS
Chi-restraints excluded: chain A residue 1083 VAL
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1116 PHE
Chi-restraints excluded: chain A residue 1121 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 78 optimal weight:    0.0970
   chunk 1 optimal weight:   20.0000
   chunk 58 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 26 optimal weight:   50.0000
   chunk 95 optimal weight:    0.0770
   chunk 2 optimal weight:    9.9990
   chunk 36 optimal weight:    0.3980
   chunk 42 optimal weight:   20.0000
   chunk 68 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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 = 0.4273 r_free = 0.4273 target = 0.178206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.114062 restraints weight = 10763.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.114007 restraints weight = 6838.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.115020 restraints weight = 5428.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7223  Z= 0.183
  Angle     :  0.731  11.323   9870  Z= 0.362
  Chirality :  0.046   0.287   1222
  Planarity :  0.006   0.074   1250
  Dihedral  :  7.682  59.428   1057
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  9.34 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.57 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.91 (0.26), residues: 953
  helix: -0.89 (0.26), residues: 394
  sheet: -1.41 (0.57), residues: 66
  loop : -2.99 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1028 
 HIS   0.002   0.000   HIS A 198 
 PHE   0.019   0.001   PHE A 963 
 TYR   0.016   0.001   TYR A 936 
 ARG   0.005   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.748 
Fit side-chains
REVERT: A  235 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7400 (mm-30)
REVERT: A  276 TYR cc_start: 0.7162 (t80) cc_final: 0.6734 (t80)
REVERT: A  542 GLU cc_start: 0.6522 (tm-30) cc_final: 0.5968 (pp20)
REVERT: A  612 LEU cc_start: 0.2590 (OUTLIER) cc_final: 0.2316 (tp)
REVERT: A  637 MET cc_start: 0.8130 (tmm) cc_final: 0.7655 (ttt)
REVERT: A 1133 MET cc_start: 0.7397 (mmm) cc_final: 0.7039 (mmp)
REVERT: A 1140 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.6282 (mp10)
  outliers start: 29
  outliers final: 9
  residues processed: 93
  average time/residue: 0.1342
  time to fit residues: 18.8823
Evaluate side-chains
  71 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 GLU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  748 MET
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0980
   chunk 74 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 70 optimal weight:    4.9990
   chunk 23 optimal weight:   40.0000
   chunk 37 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
A 962 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.176733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111054 restraints weight = 10659.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111905 restraints weight = 6881.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.112806 restraints weight = 5378.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.3304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7223  Z= 0.203
  Angle     :  0.734  11.254   9870  Z= 0.354
  Chirality :  0.046   0.313   1222
  Planarity :  0.007   0.107   1250
  Dihedral  :  6.561  59.003   1043
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.55 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 17.40 %
    Favored  : 78.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.26), residues: 953
  helix: -0.48 (0.27), residues: 394
  sheet: -1.02 (0.59), residues: 66
  loop : -2.84 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 198 
 PHE   0.017   0.001   PHE A 963 
 TYR   0.015   0.001   TYR A 936 
 ARG   0.004   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 68
  time to evaluate  : 0.760 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8631 (t80) cc_final: 0.7849 (t80)
REVERT: A  169 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8042 (mp10)
REVERT: A  276 TYR cc_start: 0.7206 (t80) cc_final: 0.6838 (t80)
REVERT: A  542 GLU cc_start: 0.6337 (tm-30) cc_final: 0.5781 (tm-30)
REVERT: A  612 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.2371 (tp)
REVERT: A  724 MET cc_start: 0.7464 (mmm) cc_final: 0.7206 (mmp)
REVERT: A 1009 MET cc_start: 0.8580 (mmm) cc_final: 0.8310 (tpp)
REVERT: A 1133 MET cc_start: 0.7400 (mmm) cc_final: 0.7032 (mmp)
  outliers start: 31
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1622
  time to fit residues: 21.0400
Evaluate side-chains
  76 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  457 ILE
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  748 MET
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  956 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 52 optimal weight:    6.9990
   chunk 35 optimal weight:    0.0020
   chunk 81 optimal weight:    0.9980
   chunk 55 optimal weight:   20.0000
   chunk 94 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    0.0270
   chunk 27 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   chunk 18 optimal weight:   30.0000
   overall best weight:    0.9248

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

Flipped N/Q/H residues before XYZ refinement:
A 836 HIS
A1047 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.175679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.111160 restraints weight = 10580.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.111150 restraints weight = 7834.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.111636 restraints weight = 5613.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7223  Z= 0.221
  Angle     :  0.728  10.680   9870  Z= 0.353
  Chirality :  0.045   0.244   1222
  Planarity :  0.006   0.097   1250
  Dihedral  :  6.206  55.313   1041
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.23 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.65 %
    Favored  : 77.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.18 (0.27), residues: 953
  helix: -0.23 (0.27), residues: 394
  sheet: -0.78 (0.60), residues: 66
  loop : -2.68 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 198 
 PHE   0.014   0.001   PHE A 963 
 TYR   0.015   0.001   TYR A 936 
 ARG   0.004   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 70
  time to evaluate  : 0.693 
Fit side-chains
REVERT: A  276 TYR cc_start: 0.7206 (t80) cc_final: 0.6999 (t80)
REVERT: A  339 MET cc_start: 0.6200 (tpp) cc_final: 0.5938 (tpp)
REVERT: A  542 GLU cc_start: 0.6290 (tm-30) cc_final: 0.5711 (tm-30)
REVERT: A  612 LEU cc_start: 0.2629 (OUTLIER) cc_final: 0.2414 (tp)
REVERT: A  637 MET cc_start: 0.7912 (ppp) cc_final: 0.7276 (ttt)
REVERT: A 1009 MET cc_start: 0.8650 (mmm) cc_final: 0.8448 (mmm)
REVERT: A 1133 MET cc_start: 0.7450 (mmm) cc_final: 0.7073 (mmp)
  outliers start: 27
  outliers final: 18
  residues processed: 89
  average time/residue: 0.1401
  time to fit residues: 19.0488
Evaluate side-chains
  82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  748 MET
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1116 PHE
Chi-restraints excluded: chain A residue 1118 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 2 optimal weight:    0.0010
   chunk 72 optimal weight:    0.0980
   chunk 41 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 53 optimal weight:    5.9990
   chunk 26 optimal weight:   30.0000
   chunk 95 optimal weight:    0.0670
   chunk 19 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.2724

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 GLN ** 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 = 0.4263 r_free = 0.4263 target = 0.177706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.113158 restraints weight = 10609.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.113920 restraints weight = 6637.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.115115 restraints weight = 5185.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7223  Z= 0.170
  Angle     :  0.698  11.691   9870  Z= 0.334
  Chirality :  0.044   0.329   1222
  Planarity :  0.006   0.086   1250
  Dihedral  :  5.962  49.689   1041
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.92 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.86 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.27), residues: 953
  helix:  0.07 (0.27), residues: 394
  sheet: -0.57 (0.62), residues: 66
  loop : -2.62 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A1171 
 HIS   0.001   0.000   HIS A 198 
 PHE   0.010   0.001   PHE A 963 
 TYR   0.014   0.001   TYR A 166 
 ARG   0.003   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.730 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8594 (t80) cc_final: 0.7823 (t80)
REVERT: A  169 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7992 (mp10)
REVERT: A  276 TYR cc_start: 0.7102 (t80) cc_final: 0.6870 (t80)
REVERT: A  542 GLU cc_start: 0.6408 (tm-30) cc_final: 0.5869 (tm-30)
REVERT: A  612 LEU cc_start: 0.2531 (OUTLIER) cc_final: 0.2287 (tp)
REVERT: A  637 MET cc_start: 0.7718 (ppp) cc_final: 0.6977 (ttt)
REVERT: A  897 GLN cc_start: 0.5944 (pt0) cc_final: 0.5481 (mm-40)
REVERT: A 1133 MET cc_start: 0.7322 (mmm) cc_final: 0.7000 (mmp)
  outliers start: 23
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1415
  time to fit residues: 19.0012
Evaluate side-chains
  82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  482 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1118 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 6 optimal weight:    9.9990
   chunk 40 optimal weight:    7.9990
   chunk 42 optimal weight:    8.9990
   chunk 51 optimal weight:    0.0020
   chunk 62 optimal weight:    3.9990
   chunk 64 optimal weight:    5.9990
   chunk 41 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 7 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    2.1194

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

Flipped N/Q/H residues before XYZ refinement:
** A1016 GLN ** 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 = 0.4248 r_free = 0.4248 target = 0.174581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.130515 restraints weight = 10615.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.114710 restraints weight = 16848.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.112457 restraints weight = 13245.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.3878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   7223  Z= 0.379
  Angle     :  0.804  12.056   9870  Z= 0.391
  Chirality :  0.049   0.328   1222
  Planarity :  0.006   0.090   1250
  Dihedral  :  6.307  46.108   1041
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.76 %
    Favored  : 89.82 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 19.34 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.27), residues: 953
  helix: -0.07 (0.27), residues: 394
  sheet: -0.71 (0.62), residues: 67
  loop : -2.52 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1171 
 HIS   0.004   0.001   HIS A 255 
 PHE   0.017   0.002   PHE A 945 
 TYR   0.019   0.002   TYR A1076 
 ARG   0.005   0.001   ARG A1073 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.745 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8260 (t80) cc_final: 0.7141 (t80)
REVERT: A  169 GLN cc_start: 0.8732 (OUTLIER) cc_final: 0.7452 (mp10)
REVERT: A  542 GLU cc_start: 0.6091 (tm-30) cc_final: 0.5563 (tm-30)
REVERT: A  897 GLN cc_start: 0.5845 (pt0) cc_final: 0.5470 (mm-40)
REVERT: A 1009 MET cc_start: 0.8735 (mmm) cc_final: 0.8533 (mmm)
REVERT: A 1061 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8513 (mt)
REVERT: A 1133 MET cc_start: 0.7691 (mmm) cc_final: 0.7343 (mmp)
  outliers start: 29
  outliers final: 17
  residues processed: 96
  average time/residue: 0.1573
  time to fit residues: 22.2412
Evaluate side-chains
  82 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  468 VAL
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1118 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 48 optimal weight:   30.0000
   chunk 77 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0970
   chunk 18 optimal weight:   20.0000
   chunk 78 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 95 optimal weight:    4.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A1057 GLN ** 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 = 0.4241 r_free = 0.4241 target = 0.175440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.108267 restraints weight = 10619.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.109585 restraints weight = 6992.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.110653 restraints weight = 5388.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7223  Z= 0.192
  Angle     :  0.748  12.467   9870  Z= 0.357
  Chirality :  0.045   0.273   1222
  Planarity :  0.006   0.082   1250
  Dihedral  :  5.910  46.872   1039
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.50 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.17 %
    Favored  : 77.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.28), residues: 953
  helix:  0.19 (0.28), residues: 395
  sheet: -0.62 (0.63), residues: 67
  loop : -2.45 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 198 
 PHE   0.011   0.001   PHE A 945 
 TYR   0.015   0.001   TYR A 166 
 ARG   0.003   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.774 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8554 (t80) cc_final: 0.7437 (t80)
REVERT: A  169 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.7578 (mp10)
REVERT: A  339 MET cc_start: 0.6069 (tpp) cc_final: 0.5781 (tpp)
REVERT: A  542 GLU cc_start: 0.6252 (tm-30) cc_final: 0.5721 (tm-30)
REVERT: A  637 MET cc_start: 0.7822 (ppp) cc_final: 0.7041 (ttt)
REVERT: A  897 GLN cc_start: 0.6026 (pt0) cc_final: 0.5548 (mm-40)
REVERT: A 1133 MET cc_start: 0.7436 (mmm) cc_final: 0.7073 (mmp)
  outliers start: 20
  outliers final: 17
  residues processed: 85
  average time/residue: 0.1516
  time to fit residues: 19.0158
Evaluate side-chains
  83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1116 PHE
Chi-restraints excluded: chain A residue 1118 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 35 optimal weight:    6.9990
   chunk 88 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 9 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:   20.0000
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
A 626 HIS
** A1057 GLN ** 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 = 0.4299 r_free = 0.4299 target = 0.179107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.112369 restraints weight = 10745.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.114957 restraints weight = 6396.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.116327 restraints weight = 4756.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7223  Z= 0.204
  Angle     :  0.737  13.026   9870  Z= 0.349
  Chirality :  0.045   0.286   1222
  Planarity :  0.006   0.084   1250
  Dihedral  :  5.724  45.886   1039
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.71 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.44 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.58 (0.28), residues: 953
  helix:  0.32 (0.28), residues: 395
  sheet: -0.54 (0.65), residues: 66
  loop : -2.39 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1171 
 HIS   0.001   0.000   HIS A 198 
 PHE   0.011   0.001   PHE A 963 
 TYR   0.014   0.001   TYR A 936 
 ARG   0.003   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.785 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8459 (t80) cc_final: 0.7309 (t80)
REVERT: A  169 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.7452 (mp10)
REVERT: A  542 GLU cc_start: 0.6298 (tm-30) cc_final: 0.5739 (tm-30)
REVERT: A  637 MET cc_start: 0.7698 (ppp) cc_final: 0.6806 (ttt)
REVERT: A  897 GLN cc_start: 0.6151 (pt0) cc_final: 0.5697 (mm-40)
REVERT: A 1133 MET cc_start: 0.7326 (mmm) cc_final: 0.7040 (mmp)
  outliers start: 21
  outliers final: 19
  residues processed: 88
  average time/residue: 0.1471
  time to fit residues: 19.1774
Evaluate side-chains
  86 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1116 PHE
Chi-restraints excluded: chain A residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 11 optimal weight:    0.7980
   chunk 13 optimal weight:    0.8980
   chunk 2 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 46 optimal weight:    9.9990
   chunk 19 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 72 optimal weight:    0.2980
   chunk 66 optimal weight:    4.9990
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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 = 0.4283 r_free = 0.4283 target = 0.177658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.119008 restraints weight = 10923.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.113361 restraints weight = 10286.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.115259 restraints weight = 8051.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.4354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7223  Z= 0.253
  Angle     :  0.757  13.330   9870  Z= 0.361
  Chirality :  0.045   0.228   1222
  Planarity :  0.006   0.083   1250
  Dihedral  :  5.805  45.881   1039
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.02 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.86 %
    Favored  : 76.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.55 (0.28), residues: 953
  helix:  0.33 (0.28), residues: 395
  sheet: -0.55 (0.64), residues: 66
  loop : -2.35 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 198 
 PHE   0.012   0.001   PHE A 945 
 TYR   0.016   0.001   TYR A 166 
 ARG   0.002   0.000   ARG A 172 

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

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

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1906 Ramachandran restraints generated.
    953 Oldfield, 0 Emsley, 953 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A  168 PHE cc_start: 0.8130 (t80) cc_final: 0.7040 (t80)
REVERT: A  169 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.7401 (mp10)
REVERT: A  404 LYS cc_start: 0.8273 (tptt) cc_final: 0.7812 (tptp)
REVERT: A  542 GLU cc_start: 0.6086 (tm-30) cc_final: 0.5614 (tm-30)
REVERT: A  897 GLN cc_start: 0.6029 (pt0) cc_final: 0.5602 (mm-40)
REVERT: A 1133 MET cc_start: 0.7435 (mmm) cc_final: 0.7119 (mmp)
  outliers start: 21
  outliers final: 20
  residues processed: 88
  average time/residue: 0.1522
  time to fit residues: 19.7922
Evaluate side-chains
  88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  380 ILE
Chi-restraints excluded: chain A residue  438 LEU
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  514 LYS
Chi-restraints excluded: chain A residue  526 MET
Chi-restraints excluded: chain A residue  744 ILE
Chi-restraints excluded: chain A residue  825 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  907 THR
Chi-restraints excluded: chain A residue  916 VAL
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1061 LEU
Chi-restraints excluded: chain A residue 1116 PHE
Chi-restraints excluded: chain A residue 1118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 91 optimal weight:    0.0050
   chunk 55 optimal weight:   30.0000
   chunk 81 optimal weight:    0.6980
   chunk 72 optimal weight:    0.2980
   chunk 6 optimal weight:    0.3980
   chunk 15 optimal weight:    0.8980
   chunk 35 optimal weight:    0.5980
   chunk 54 optimal weight:   40.0000
   chunk 53 optimal weight:    7.9990
   chunk 7 optimal weight:   30.0000
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A 198 HIS
** A1057 GLN ** 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 = 0.4262 r_free = 0.4262 target = 0.177303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.111072 restraints weight = 10636.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112502 restraints weight = 6784.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.113205 restraints weight = 5156.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.4532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7223  Z= 0.177
  Angle     :  0.719  13.608   9870  Z= 0.341
  Chirality :  0.044   0.275   1222
  Planarity :  0.005   0.081   1250
  Dihedral  :  5.668  50.429   1039
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.60 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.41 %
    Favored  : 76.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.39 (0.28), residues: 953
  helix:  0.53 (0.28), residues: 394
  sheet: -0.41 (0.63), residues: 65
  loop : -2.33 (0.27), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 643 
 HIS   0.001   0.000   HIS A 255 
 PHE   0.010   0.001   PHE A 963 
 TYR   0.011   0.001   TYR A 936 
 ARG   0.002   0.000   ARG A 172 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2575.14 seconds
wall clock time: 45 minutes 12.33 seconds (2712.33 seconds total)