Starting phenix.real_space_refine
on Mon Nov 17 17:50:49 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fjq_31627/11_2025/7fjq_31627.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fjq_31627/11_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_31627/11_2025/7fjq_31627.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fjq_31627/11_2025/7fjq_31627.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fjq_31627/11_2025/7fjq_31627.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fjq_31627/11_2025/7fjq_31627.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: {'PHE:plan': 4, 'ARG:plan': 14, 'TRP:plan': 4, 'GLU:plan': 13, 'GLN:plan1': 11, 'ASP:plan': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2}
          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: 1.85, per 1000 atoms: 0.26
  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: 0.55
  Conformation dependent library (CDL) restraints added in 368.6 milliseconds
  

  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: 0.28
  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: 1.22

  Time building geometry restraints manager: 0.70 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:             1.050
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.210
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.760
-------------------------------------------------------------------------------
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   7224  Z= 1.371
  Angle     :  2.025  24.610   9872  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -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
 ARG   0.003   0.001   ARG A1158 
 TYR   0.035   0.003   TYR A 940 
 PHE   0.066   0.004   PHE A 945 
 TRP   0.008   0.002   TRP A1171 
 HIS   0.009   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.01897 ( 7223)
  covalent geometry    : angle       2.02513 ( 9870)
  SS BOND              : bond        0.00208 (    1)
  SS BOND              : angle       1.03296 (    2)
  hydrogen bonds       : bond        0.24116 (  275)
  hydrogen bonds       : angle       9.55292 (  783)

*********************** 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  : 0.261 
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: 0.0743
  time to fit residues: 16.1625
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  : 0.266 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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
A1078 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.175349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.113600 restraints weight = 10917.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.114062 restraints weight = 6597.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.113093 restraints weight = 5049.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.113319 restraints weight = 5198.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.113465 restraints weight = 4777.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7224  Z= 0.170
  Angle     :  0.826  11.458   9872  Z= 0.416
  Chirality :  0.049   0.307   1222
  Planarity :  0.008   0.136   1250
  Dihedral  :  9.194  56.481   1091
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.52 %
    Allowed  :  9.55 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  5.25 %
    Allowed  : 14.92 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.29 (0.25), residues: 953
  helix: -1.27 (0.26), residues: 384
  sheet: -2.10 (0.51), residues: 74
  loop : -3.04 (0.25), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 172 
 TYR   0.022   0.002   TYR A 936 
 PHE   0.016   0.002   PHE A 963 
 TRP   0.012   0.002   TRP A1171 
 HIS   0.005   0.001   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 7223)
  covalent geometry    : angle       0.82605 ( 9870)
  SS BOND              : bond        0.00478 (    1)
  SS BOND              : angle       0.79297 (    2)
  hydrogen bonds       : bond        0.06177 (  275)
  hydrogen bonds       : angle       6.08020 (  783)

*********************** 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
  114 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 76
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  542 GLU cc_start: 0.6492 (tm-30) cc_final: 0.6019 (pp20)
REVERT: A  875 MET cc_start: 0.8230 (tpt) cc_final: 0.8004 (tpt)
REVERT: A  937 MET cc_start: 0.8646 (tpp) cc_final: 0.8179 (mmm)
REVERT: A 1047 ASN cc_start: 0.8108 (OUTLIER) cc_final: 0.7821 (t0)
REVERT: A 1133 MET cc_start: 0.7348 (mmm) cc_final: 0.6979 (mmp)
REVERT: A 1140 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6045 (mp10)
  outliers start: 38
  outliers final: 17
  residues processed: 107
  average time/residue: 0.0774
  time to fit residues: 11.7674
Evaluate side-chains
  83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  440 THR
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  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  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
Chi-restraints excluded: chain A residue 1140 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 43 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 57 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.4250 r_free = 0.4250 target = 0.175983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.110917 restraints weight = 10582.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.111424 restraints weight = 6831.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112296 restraints weight = 5352.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.112580 restraints weight = 4448.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112898 restraints weight = 4550.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7224  Z= 0.147
  Angle     :  0.758  11.668   9872  Z= 0.374
  Chirality :  0.046   0.299   1222
  Planarity :  0.006   0.073   1250
  Dihedral  :  7.752  59.127   1057
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.34 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 16.99 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.26), residues: 953
  helix: -0.90 (0.26), residues: 393
  sheet: -1.38 (0.57), residues: 66
  loop : -2.98 (0.26), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 172 
 TYR   0.016   0.002   TYR A 936 
 PHE   0.017   0.001   PHE A 963 
 TRP   0.006   0.001   TRP A 643 
 HIS   0.002   0.000   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7223)
  covalent geometry    : angle       0.75800 ( 9870)
  SS BOND              : bond        0.00517 (    1)
  SS BOND              : angle       0.50213 (    2)
  hydrogen bonds       : bond        0.05176 (  275)
  hydrogen bonds       : angle       5.49364 (  783)

*********************** 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
  97 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 69
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7304 (mm-30)
REVERT: A  276 TYR cc_start: 0.7250 (t80) cc_final: 0.6852 (t80)
REVERT: A  542 GLU cc_start: 0.6367 (tm-30) cc_final: 0.5779 (pp20)
REVERT: A  612 LEU cc_start: 0.2667 (OUTLIER) cc_final: 0.2409 (tp)
REVERT: A  961 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8591 (tp)
REVERT: A 1009 MET cc_start: 0.8553 (mmm) cc_final: 0.8340 (mmm)
REVERT: A 1133 MET cc_start: 0.7457 (mmm) cc_final: 0.7080 (mmp)
  outliers start: 28
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0606
  time to fit residues: 8.1805
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  : 0.236 
-------------------------------------------------------------------------------
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  353 LEU
Chi-restraints excluded: chain A residue  457 ILE
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  748 MET
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  940 TYR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1061 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 31 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 56 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 82 optimal weight:    0.5980
   chunk 12 optimal weight:    0.0870
   chunk 80 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A 962 GLN
** A1016 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 = 0.4263 r_free = 0.4263 target = 0.177385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.114046 restraints weight = 10746.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112976 restraints weight = 7614.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113132 restraints weight = 6548.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.113396 restraints weight = 5283.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113578 restraints weight = 5161.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3463
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7224  Z= 0.132
  Angle     :  0.725  10.501   9872  Z= 0.352
  Chirality :  0.046   0.314   1222
  Planarity :  0.006   0.106   1250
  Dihedral  :  6.797  59.013   1045
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.44 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 18.37 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.50 (0.26), residues: 953
  helix: -0.53 (0.27), residues: 394
  sheet: -1.01 (0.59), residues: 66
  loop : -2.82 (0.26), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 172 
 TYR   0.015   0.001   TYR A 936 
 PHE   0.016   0.001   PHE A 963 
 TRP   0.009   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 7223)
  covalent geometry    : angle       0.72502 ( 9870)
  SS BOND              : bond        0.00490 (    1)
  SS BOND              : angle       0.44609 (    2)
  hydrogen bonds       : bond        0.04486 (  275)
  hydrogen bonds       : angle       5.17770 (  783)

*********************** 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
  94 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 67
  time to evaluate  : 0.285 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8579 (t80) cc_final: 0.7526 (t80)
REVERT: A  169 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.7662 (mp10)
REVERT: A  276 TYR cc_start: 0.7245 (t80) cc_final: 0.6893 (t80)
REVERT: A  526 MET cc_start: 0.7509 (mpp) cc_final: 0.7129 (mpp)
REVERT: A  542 GLU cc_start: 0.6396 (tm-30) cc_final: 0.5862 (tm-30)
REVERT: A  612 LEU cc_start: 0.2654 (OUTLIER) cc_final: 0.2404 (tp)
REVERT: A  724 MET cc_start: 0.7526 (mmm) cc_final: 0.7096 (mmp)
REVERT: A 1133 MET cc_start: 0.7409 (mmm) cc_final: 0.7040 (mmp)
  outliers start: 27
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0708
  time to fit residues: 8.7590
Evaluate side-chains
  75 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  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  748 MET
Chi-restraints excluded: chain A residue  863 VAL
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  952 TYR
Chi-restraints excluded: chain A residue  956 THR
Chi-restraints excluded: chain A residue 1116 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   chunk 74 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 64 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   chunk 1 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 836 HIS
** A1016 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 = 0.4257 r_free = 0.4257 target = 0.176686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113261 restraints weight = 10614.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.111992 restraints weight = 7401.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.112299 restraints weight = 5797.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112244 restraints weight = 5467.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.112423 restraints weight = 5067.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.3590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7224  Z= 0.130
  Angle     :  0.706  10.684   9872  Z= 0.343
  Chirality :  0.044   0.247   1222
  Planarity :  0.006   0.104   1250
  Dihedral  :  6.184  55.970   1041
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  9.23 %
    Favored  : 90.45 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.34 %
    Favored  : 77.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.27), residues: 953
  helix: -0.26 (0.27), residues: 394
  sheet: -0.74 (0.61), residues: 66
  loop : -2.69 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 172 
 TYR   0.014   0.001   TYR A 936 
 PHE   0.013   0.001   PHE A 963 
 TRP   0.008   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 7223)
  covalent geometry    : angle       0.70640 ( 9870)
  SS BOND              : bond        0.00457 (    1)
  SS BOND              : angle       0.39205 (    2)
  hydrogen bonds       : bond        0.04364 (  275)
  hydrogen bonds       : angle       5.04341 (  783)

*********************** 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
  93 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A  276 TYR cc_start: 0.7195 (t80) cc_final: 0.6978 (t80)
REVERT: A  526 MET cc_start: 0.7948 (mpp) cc_final: 0.7628 (mpp)
REVERT: A  542 GLU cc_start: 0.6373 (tm-30) cc_final: 0.5785 (tm-30)
REVERT: A  612 LEU cc_start: 0.2621 (OUTLIER) cc_final: 0.2399 (tp)
REVERT: A  637 MET cc_start: 0.7831 (ppp) cc_final: 0.6928 (ttt)
REVERT: A 1133 MET cc_start: 0.7417 (mmm) cc_final: 0.7049 (mmp)
  outliers start: 25
  outliers final: 18
  residues processed: 86
  average time/residue: 0.0587
  time to fit residues: 7.7844
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  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  748 MET
Chi-restraints excluded: chain A residue  863 VAL
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  952 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 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 18 optimal weight:   20.0000
   chunk 4 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 93 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 91 optimal weight:    0.2980
   chunk 63 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0020
   chunk 31 optimal weight:    0.0170
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.4028

-------------------------------------------------------------------------------
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 = 0.4263 r_free = 0.4263 target = 0.177532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.112748 restraints weight = 10682.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.113381 restraints weight = 6860.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.114384 restraints weight = 5244.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.114915 restraints weight = 4433.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.115246 restraints weight = 4436.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7224  Z= 0.119
  Angle     :  0.703  11.575   9872  Z= 0.336
  Chirality :  0.045   0.337   1222
  Planarity :  0.006   0.094   1250
  Dihedral  :  5.971  51.236   1041
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.71 %
    Favored  : 90.98 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.93 (0.27), residues: 953
  helix:  0.00 (0.27), residues: 394
  sheet: -0.53 (0.63), residues: 66
  loop : -2.58 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 172 
 TYR   0.014   0.001   TYR A 166 
 PHE   0.011   0.001   PHE A 963 
 TRP   0.006   0.001   TRP A1171 
 HIS   0.001   0.000   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 7223)
  covalent geometry    : angle       0.70280 ( 9870)
  SS BOND              : bond        0.00435 (    1)
  SS BOND              : angle       0.36736 (    2)
  hydrogen bonds       : bond        0.04000 (  275)
  hydrogen bonds       : angle       4.89106 (  783)

*********************** 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
  92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8583 (t80) cc_final: 0.7784 (t80)
REVERT: A  169 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.7963 (mp10)
REVERT: A  276 TYR cc_start: 0.7100 (t80) cc_final: 0.6882 (t80)
REVERT: A  526 MET cc_start: 0.8053 (mpp) cc_final: 0.7846 (mpp)
REVERT: A  542 GLU cc_start: 0.6403 (tm-30) cc_final: 0.5867 (tm-30)
REVERT: A  612 LEU cc_start: 0.2571 (OUTLIER) cc_final: 0.2322 (tp)
REVERT: A  637 MET cc_start: 0.7409 (ppp) cc_final: 0.6904 (ttt)
REVERT: A 1009 MET cc_start: 0.8507 (mmm) cc_final: 0.8199 (tpp)
REVERT: A 1133 MET cc_start: 0.7349 (mmm) cc_final: 0.7024 (mmp)
  outliers start: 23
  outliers final: 17
  residues processed: 86
  average time/residue: 0.0599
  time to fit residues: 8.0007
Evaluate side-chains
  83 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
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  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  482 LEU
Chi-restraints excluded: chain A residue  612 LEU
Chi-restraints excluded: chain A residue  744 ILE
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  952 TYR
Chi-restraints excluded: chain A residue  964 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1116 PHE
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 26 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 51 optimal weight:   40.0000
   chunk 18 optimal weight:   30.0000
   chunk 87 optimal weight:    0.6980
   chunk 50 optimal weight:    5.9990
   chunk 89 optimal weight:    0.5980
   chunk 37 optimal weight:    0.2980
   chunk 32 optimal weight:    0.7980
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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**
A1047 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.178029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.112840 restraints weight = 10777.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.113693 restraints weight = 6760.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.114447 restraints weight = 5447.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.114599 restraints weight = 4735.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.114741 restraints weight = 4706.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   7224  Z= 0.152
  Angle     :  0.730  12.288   9872  Z= 0.351
  Chirality :  0.046   0.334   1222
  Planarity :  0.006   0.090   1250
  Dihedral  :  5.919  45.783   1041
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.23 %
    Favored  : 90.35 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.27), residues: 953
  helix:  0.08 (0.27), residues: 396
  sheet: -0.60 (0.63), residues: 67
  loop : -2.53 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 172 
 TYR   0.015   0.001   TYR A1076 
 PHE   0.012   0.001   PHE A 963 
 TRP   0.008   0.001   TRP A1171 
 HIS   0.002   0.000   HIS A 255 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 7223)
  covalent geometry    : angle       0.73029 ( 9870)
  SS BOND              : bond        0.00456 (    1)
  SS BOND              : angle       0.28060 (    2)
  hydrogen bonds       : bond        0.04489 (  275)
  hydrogen bonds       : angle       5.00289 (  783)

*********************** 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
  90 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8521 (t80) cc_final: 0.7421 (t80)
REVERT: A  169 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7534 (mp10)
REVERT: A  276 TYR cc_start: 0.7114 (t80) cc_final: 0.6855 (t80)
REVERT: A  339 MET cc_start: 0.6171 (tpp) cc_final: 0.5921 (tpp)
REVERT: A  526 MET cc_start: 0.7988 (mpp) cc_final: 0.7396 (mpp)
REVERT: A  542 GLU cc_start: 0.6325 (tm-30) cc_final: 0.5793 (tm-30)
REVERT: A  612 LEU cc_start: 0.2564 (OUTLIER) cc_final: 0.2356 (tp)
REVERT: A  897 GLN cc_start: 0.5861 (pt0) cc_final: 0.5489 (mm-40)
REVERT: A 1133 MET cc_start: 0.7335 (mmm) cc_final: 0.7041 (mmp)
  outliers start: 21
  outliers final: 15
  residues processed: 86
  average time/residue: 0.0654
  time to fit residues: 8.5775
Evaluate side-chains
  84 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 67
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  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  612 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  952 TYR
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1015 VAL
Chi-restraints excluded: chain A residue 1093 VAL
Chi-restraints excluded: chain A residue 1116 PHE
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 70 optimal weight:    0.9980
   chunk 4 optimal weight:   20.0000
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 66 optimal weight:    0.5980
   chunk 29 optimal weight:    9.9990
   chunk 93 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 46 optimal weight:    0.3980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 = 0.4262 r_free = 0.4262 target = 0.177273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.110970 restraints weight = 10874.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.111477 restraints weight = 7294.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112573 restraints weight = 5935.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.112905 restraints weight = 4813.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113229 restraints weight = 4742.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.4123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7224  Z= 0.122
  Angle     :  0.719  12.985   9872  Z= 0.342
  Chirality :  0.044   0.274   1222
  Planarity :  0.006   0.086   1250
  Dihedral  :  5.580  44.646   1039
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.39 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.30 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.65 (0.28), residues: 953
  helix:  0.30 (0.28), residues: 394
  sheet: -0.56 (0.64), residues: 67
  loop : -2.46 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 172 
 TYR   0.015   0.001   TYR A 166 
 PHE   0.011   0.001   PHE A 168 
 TRP   0.005   0.001   TRP A 643 
 HIS   0.001   0.000   HIS A 198 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7223)
  covalent geometry    : angle       0.71890 ( 9870)
  SS BOND              : bond        0.00417 (    1)
  SS BOND              : angle       0.21923 (    2)
  hydrogen bonds       : bond        0.03924 (  275)
  hydrogen bonds       : angle       4.79478 (  783)

*********************** 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
  92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8530 (t80) cc_final: 0.7730 (t80)
REVERT: A  169 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.7900 (mp10)
REVERT: A  273 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7948 (mm)
REVERT: A  276 TYR cc_start: 0.7074 (t80) cc_final: 0.6795 (t80)
REVERT: A  293 MET cc_start: 0.8122 (tmm) cc_final: 0.7501 (ppp)
REVERT: A  526 MET cc_start: 0.8046 (mpp) cc_final: 0.7435 (mpp)
REVERT: A  542 GLU cc_start: 0.6228 (tm-30) cc_final: 0.5705 (tm-30)
REVERT: A  612 LEU cc_start: 0.2612 (OUTLIER) cc_final: 0.2373 (tp)
REVERT: A  637 MET cc_start: 0.7571 (ppp) cc_final: 0.6975 (ttt)
REVERT: A  897 GLN cc_start: 0.6131 (pt0) cc_final: 0.5708 (mm-40)
REVERT: A 1133 MET cc_start: 0.7300 (mmm) cc_final: 0.6992 (mmp)
  outliers start: 23
  outliers final: 16
  residues processed: 89
  average time/residue: 0.0610
  time to fit residues: 8.3046
Evaluate side-chains
  85 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
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  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  612 LEU
Chi-restraints excluded: chain A residue  744 ILE
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  952 TYR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1015 VAL
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 88 optimal weight:    0.0770
   chunk 7 optimal weight:    8.9990
   chunk 71 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9980
   chunk 81 optimal weight:    0.3980
   chunk 58 optimal weight:    3.9990
   chunk 22 optimal weight:   20.0000
   chunk 96 optimal weight:    1.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 198 HIS
A 497 HIS
A 626 HIS
** A1016 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.177632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.112993 restraints weight = 10740.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.112749 restraints weight = 7888.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113684 restraints weight = 5955.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113734 restraints weight = 5150.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.114043 restraints weight = 5128.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.4265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7224  Z= 0.122
  Angle     :  0.721  13.308   9872  Z= 0.340
  Chirality :  0.044   0.267   1222
  Planarity :  0.006   0.084   1250
  Dihedral  :  5.451  43.581   1039
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.50 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.28), residues: 953
  helix:  0.41 (0.28), residues: 394
  sheet: -0.53 (0.64), residues: 67
  loop : -2.39 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 172 
 TYR   0.012   0.001   TYR A1076 
 PHE   0.010   0.001   PHE A 963 
 TRP   0.005   0.001   TRP A 643 
 HIS   0.001   0.000   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 7223)
  covalent geometry    : angle       0.72086 ( 9870)
  SS BOND              : bond        0.00393 (    1)
  SS BOND              : angle       0.16534 (    2)
  hydrogen bonds       : bond        0.03848 (  275)
  hydrogen bonds       : angle       4.73238 (  783)

*********************** 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
  88 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8480 (t80) cc_final: 0.7684 (t80)
REVERT: A  169 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7885 (mp10)
REVERT: A  273 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7951 (mm)
REVERT: A  276 TYR cc_start: 0.7031 (t80) cc_final: 0.6772 (t80)
REVERT: A  293 MET cc_start: 0.8107 (tmm) cc_final: 0.7445 (ppp)
REVERT: A  526 MET cc_start: 0.7992 (mpp) cc_final: 0.7374 (mpp)
REVERT: A  542 GLU cc_start: 0.6292 (tm-30) cc_final: 0.5743 (tm-30)
REVERT: A  612 LEU cc_start: 0.2572 (OUTLIER) cc_final: 0.2354 (tp)
REVERT: A  637 MET cc_start: 0.7448 (ppp) cc_final: 0.6746 (ttt)
REVERT: A  897 GLN cc_start: 0.6172 (pt0) cc_final: 0.5721 (mm-40)
REVERT: A 1133 MET cc_start: 0.7334 (mmm) cc_final: 0.7030 (mmp)
  outliers start: 20
  outliers final: 17
  residues processed: 85
  average time/residue: 0.0597
  time to fit residues: 7.7675
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  : 0.268 
-------------------------------------------------------------------------------
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  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  612 LEU
Chi-restraints excluded: chain A residue  744 ILE
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  952 TYR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1015 VAL
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 52 optimal weight:    9.9990
   chunk 45 optimal weight:    8.9990
   chunk 81 optimal weight:    0.7980
   chunk 93 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9990
   chunk 84 optimal weight:    0.7980
   chunk 2 optimal weight:   20.0000
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    9.9990
   chunk 6 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0570
   overall best weight:    0.7100

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.176415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.110034 restraints weight = 10641.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.111633 restraints weight = 6922.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112144 restraints weight = 5542.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.112291 restraints weight = 4832.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112545 restraints weight = 4728.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3446
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.4355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7224  Z= 0.129
  Angle     :  0.721  13.609   9872  Z= 0.341
  Chirality :  0.045   0.249   1222
  Planarity :  0.006   0.084   1250
  Dihedral  :  5.416  43.830   1039
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.08 %
    Favored  : 91.61 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 20.99 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.38 (0.28), residues: 953
  helix:  0.56 (0.28), residues: 388
  sheet: -0.50 (0.65), residues: 66
  loop : -2.29 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 172 
 TYR   0.015   0.001   TYR A 166 
 PHE   0.011   0.001   PHE A 963 
 TRP   0.006   0.001   TRP A1171 
 HIS   0.001   0.000   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7223)
  covalent geometry    : angle       0.72103 ( 9870)
  SS BOND              : bond        0.00399 (    1)
  SS BOND              : angle       0.25203 (    2)
  hydrogen bonds       : bond        0.03970 (  275)
  hydrogen bonds       : angle       4.73898 (  783)

********************** 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
  92 residues out of total 831 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  168 PHE cc_start: 0.8554 (t80) cc_final: 0.7747 (t80)
REVERT: A  169 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7928 (mp10)
REVERT: A  273 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7931 (mm)
REVERT: A  276 TYR cc_start: 0.7038 (t80) cc_final: 0.6774 (t80)
REVERT: A  293 MET cc_start: 0.8204 (tmm) cc_final: 0.7541 (ppp)
REVERT: A  526 MET cc_start: 0.8053 (mpp) cc_final: 0.7316 (mpp)
REVERT: A  542 GLU cc_start: 0.6217 (tm-30) cc_final: 0.5670 (tm-30)
REVERT: A  637 MET cc_start: 0.7102 (ppp) cc_final: 0.6729 (ttt)
REVERT: A  897 GLN cc_start: 0.6201 (pt0) cc_final: 0.5660 (mm-40)
REVERT: A 1061 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8120 (mt)
REVERT: A 1133 MET cc_start: 0.7362 (mmm) cc_final: 0.7062 (mmp)
  outliers start: 21
  outliers final: 17
  residues processed: 89
  average time/residue: 0.0682
  time to fit residues: 9.0005
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  : 0.259 
-------------------------------------------------------------------------------
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  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  744 ILE
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  952 TYR
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1012 VAL
Chi-restraints excluded: chain A residue 1015 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 64 optimal weight:    0.9980
   chunk 6 optimal weight:    7.9990
   chunk 47 optimal weight:    8.9990
   chunk 10 optimal weight:    0.2980
   chunk 61 optimal weight:    0.6980
   chunk 72 optimal weight:    0.6980
   chunk 85 optimal weight:    0.0270
   chunk 93 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.4838

-------------------------------------------------------------------------------
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 = 0.4267 r_free = 0.4267 target = 0.177822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.112130 restraints weight = 10678.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113285 restraints weight = 6827.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.114242 restraints weight = 5271.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.114520 restraints weight = 4493.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.114833 restraints weight = 4483.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7224  Z= 0.120
  Angle     :  0.713  13.543   9872  Z= 0.337
  Chirality :  0.044   0.262   1222
  Planarity :  0.006   0.083   1250
  Dihedral  :  5.294  42.662   1039
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  8.60 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.82 %
    Favored  : 75.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.26 (0.28), residues: 953
  helix:  0.66 (0.28), residues: 389
  sheet: -0.44 (0.64), residues: 66
  loop : -2.22 (0.27), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 172 
 TYR   0.012   0.001   TYR A 936 
 PHE   0.010   0.001   PHE A 963 
 TRP   0.005   0.001   TRP A 643 
 HIS   0.001   0.000   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7223)
  covalent geometry    : angle       0.71319 ( 9870)
  SS BOND              : bond        0.00390 (    1)
  SS BOND              : angle       0.17713 (    2)
  hydrogen bonds       : bond        0.03739 (  275)
  hydrogen bonds       : angle       4.61665 (  783)
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 1431.75 seconds
wall clock time: 25 minutes 20.86 seconds (1520.86 seconds total)