Starting phenix.real_space_refine
on Mon Jan 20 06:34:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8b9k_15934/01_2025/8b9k_15934.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8b9k_15934/01_2025/8b9k_15934.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8b9k_15934/01_2025/8b9k_15934.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8b9k_15934/01_2025/8b9k_15934.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8b9k_15934/01_2025/8b9k_15934.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8b9k_15934/01_2025/8b9k_15934.cif"
  }
  resolution = 4.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7434 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     P      42      5.49       5
     S      47      5.16       5
     C    5161      2.51       5
     N    1447      2.21       5
     O    1688      1.98       5
     F       4      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.83s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 8390
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7511
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 951, 7500
          Classifications: {'peptide': 951}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 903}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
      Conformer: "B"
        Number of residues, atoms: 951, 7500
          Classifications: {'peptide': 951}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 903}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
          bond proxies already assigned to first conformer: 7633
    Chain: "B"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 847
          Classifications: {'RNA': 40}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 19, 'rna3p_pyr': 18}
          Link IDs: {'rna2p': 2, 'rna3p': 37}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'ADP': 1, 'ALF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 9.51, per 1000 atoms: 1.13
  Number of scatterers: 8390
  At special positions: 0
  Unit cell: (73.98, 106.038, 139.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      47     16.00
     P      42     15.00
     Al      1     13.00
     F       4      9.00
     O    1688      8.00
     N    1447      7.00
     C    5161      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1818

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 7 sheets defined
      47.3% alpha, 10.4% beta
      17 base pairs and 29 stacking pairs defined.
    Time for finding SS restraints: 2.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 170 through 182
      removed outlier: 4.157A  pdb=" N   LEU A 174 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 242
    Processing helix  chain 'A' and resid 268 through 282
    Processing helix  chain 'A' and resid 352 through 371
    Processing helix  chain 'A' and resid 371 through 384
    Processing helix  chain 'A' and resid 385 through 388
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.681A  pdb=" N   ILE A 397 " --> pdb=" O   ILE A 393 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ASN A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 428
      removed outlier: 4.316A  pdb=" N   ALA A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   GLN A 419 " --> pdb=" O   THR A 415 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   SER A 428 " --> pdb=" O   ASP A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 434
    Processing helix  chain 'A' and resid 442 through 457
    Processing helix  chain 'A' and resid 487 through 494
    Processing helix  chain 'A' and resid 513 through 530
      removed outlier: 3.905A  pdb=" N   ASP A 525 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 551
      removed outlier: 3.510A  pdb=" N   PHE A 551 " --> pdb=" O   PHE A 547 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 579
      removed outlier: 3.527A  pdb=" N   ASP A 579 " --> pdb=" O   ILE A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 614
    Processing helix  chain 'A' and resid 621 through 629
    Processing helix  chain 'A' and resid 636 through 651
      removed outlier: 4.085A  pdb=" N   LEU A 640 " --> pdb=" O   SER A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 676
    Processing helix  chain 'A' and resid 695 through 703
      removed outlier: 3.778A  pdb=" N   GLN A 699 " --> pdb=" O   PRO A 695 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE A 703 " --> pdb=" O   GLN A 699 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 722
      removed outlier: 3.828A  pdb=" N   GLU A 721 " --> pdb=" O   THR A 717 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   THR A 722 " --> pdb=" O   ASN A 718 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 717 through 722'
    Processing helix  chain 'A' and resid 758 through 769
      removed outlier: 3.897A  pdb=" N   ALA A 769 " --> pdb=" O   ARG A 765 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 789
    Processing helix  chain 'A' and resid 802 through 812
    Processing helix  chain 'A' and resid 816 through 823
    Processing helix  chain 'A' and resid 829 through 843
      removed outlier: 3.891A  pdb=" N   VAL A 833 " --> pdb=" O   PRO A 829 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 862
      removed outlier: 3.619A  pdb=" N   ARG A 861 " --> pdb=" O   ARG A 857 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 862 " --> pdb=" O   LEU A 858 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 878
      removed outlier: 4.405A  pdb=" N   MET A 871 " --> pdb=" O   ARG A 867 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 874 " --> pdb=" O   LYS A 870 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ALA A 876 " --> pdb=" O   MET A 872 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   VAL A 877 " --> pdb=" O   VAL A 873 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 893
    Processing helix  chain 'A' and resid 908 through 914
    Processing helix  chain 'A' and resid 920 through 937
    Processing helix  chain 'A' and resid 939 through 950
      removed outlier: 3.668A  pdb=" N   GLU A 943 " --> pdb=" O   GLY A 939 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   ARG A 945 " --> pdb=" O   HIS A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 975
    Processing helix  chain 'A' and resid 994 through 1008
    Processing helix  chain 'A' and resid 1101 through 1110
    Processing helix  chain 'A' and resid 1110 through 1125
      removed outlier: 4.235A  pdb=" N   ALA A1114 " --> pdb=" O   ALA A1110 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU A1116 " --> pdb=" O   LYS A1112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1129
      removed outlier: 3.713A  pdb=" N   ILE A1129 " --> pdb=" O   PRO A1126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1126 through 1129'
    Processing helix  chain 'A' and resid 1133 through 1147
    Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192
    Processing sheet with id=AA2, first strand: chain 'A' and resid 335 through 336
      removed outlier: 3.604A  pdb=" N   CYS A 341 " --> pdb=" O   ASN A 336 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 405
      removed outlier: 6.545A  pdb=" N   VAL A 403 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   THR A 486 " --> pdb=" O   SER A 468 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 569
      removed outlier: 6.339A  pdb=" N   GLN A 567 " --> pdb=" O   CYS A 777 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL A 730 " --> pdb=" O   PHE A 776 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   PHE A 778 " --> pdb=" O   VAL A 730 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   VAL A 732 " --> pdb=" O   PHE A 778 " (cutoff:3.500A)
      removed outlier: 6.499A  pdb=" N   ALA A 655 " --> pdb=" O   PHE A 731 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   ILE A 733 " --> pdb=" O   ALA A 655 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LEU A 657 " --> pdb=" O   ILE A 733 " (cutoff:3.500A)
      removed outlier: 6.415A  pdb=" N   GLN A 686 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   LEU A 715 " --> pdb=" O   GLN A 686 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   LEU A 688 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 737 through 743
      removed outlier: 4.192A  pdb=" N   ALA A 753 " --> pdb=" O   MET A 740 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1054 through 1056
      removed outlier: 8.220A  pdb=" N   CYS A1063 " --> pdb=" O   ALA A1028 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   LEU A1030 " --> pdb=" O   CYS A1063 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   LYS A1020 " --> pdb=" O   LYS A1016 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1082 through 1085
      removed outlier: 3.619A  pdb=" N   ILE A1089 " --> pdb=" O   ALA A1085 " (cutoff:3.500A)

    337 hydrogen bonds defined for protein.
    966 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      39 hydrogen bonds
      74 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      29 stacking parallelities
  Total time for adding SS restraints: 3.60

  Time building geometry restraints manager: 2.63 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2569
        1.34 -     1.46: 1381
        1.46 -     1.57: 4529
        1.57 -     1.69: 82
        1.69 -     1.81: 75
  Bond restraints: 8636
  Sorted by residual:
  bond pdb=" F1  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.684  1.784 -0.100 2.00e-02 2.50e+03 2.52e+01
  bond pdb=" N   ASP A 603 "
       pdb=" CA  ASP A 603 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.032 6.40e-03 2.44e+04 2.48e+01
  bond pdb=" F3  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.784 -0.099 2.00e-02 2.50e+03 2.43e+01
  bond pdb=" F2  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.685  1.783 -0.098 2.00e-02 2.50e+03 2.42e+01
  bond pdb=" F4  ALF A1202 "
       pdb="AL   ALF A1202 "
    ideal  model  delta    sigma   weight residual
    1.686  1.783 -0.097 2.00e-02 2.50e+03 2.33e+01
  ... (remaining 8631 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.19: 11891
       14.19 -    28.38: 4
       28.38 -    42.57: 0
       42.57 -    56.76: 0
       56.76 -    70.95: 2
  Bond angle restraints: 11897
  Sorted by residual:
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F2  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     108.68  179.63  -70.95 3.00e+00 1.11e-01 5.59e+02
  angle pdb=" F3  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.63  179.62  -69.99 3.00e+00 1.11e-01 5.44e+02
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F3  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.59   89.38   20.21 3.00e+00 1.11e-01 4.54e+01
  angle pdb=" F2  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     110.21   90.36   19.85 3.00e+00 1.11e-01 4.38e+01
  angle pdb=" F1  ALF A1202 "
        pdb="AL   ALF A1202 "
        pdb=" F4  ALF A1202 "
      ideal   model   delta    sigma   weight residual
     109.02   89.66   19.36 3.00e+00 1.11e-01 4.16e+01
  ... (remaining 11892 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.48: 4870
       20.48 -    40.95: 315
       40.95 -    61.43: 100
       61.43 -    81.91: 33
       81.91 -   102.38: 6
  Dihedral angle restraints: 5324
    sinusoidal: 2531
      harmonic: 2793
  Sorted by residual:
  dihedral pdb=" O1B ADP A1201 "
           pdb=" O3A ADP A1201 "
           pdb=" PB  ADP A1201 "
           pdb=" PA  ADP A1201 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -162.38  102.38     1      2.00e+01 2.50e-03 2.91e+01
  dihedral pdb=" CA  TYR A 263 "
           pdb=" C   TYR A 263 "
           pdb=" N   PRO A 264 "
           pdb=" CA  PRO A 264 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.69  -24.31     0      5.00e+00 4.00e-02 2.36e+01
  dihedral pdb=" CA  MET A 629 "
           pdb=" C   MET A 629 "
           pdb=" N   LEU A 630 "
           pdb=" CA  LEU A 630 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.42   23.58     0      5.00e+00 4.00e-02 2.22e+01
  ... (remaining 5321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 868
       0.027 -    0.054: 328
       0.054 -    0.081: 103
       0.081 -    0.108: 74
       0.108 -    0.135: 22
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CA  VAL A 559 "
            pdb=" N   VAL A 559 "
            pdb=" C   VAL A 559 "
            pdb=" CB  VAL A 559 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  PRO A 385 "
            pdb=" N   PRO A 385 "
            pdb=" C   PRO A 385 "
            pdb=" CB  PRO A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.36e-01
  chirality pdb=" CA  ILE A 542 "
            pdb=" N   ILE A 542 "
            pdb=" C   ILE A 542 "
            pdb=" CB  ILE A 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  ... (remaining 1392 not shown)

  Planarity restraints: 1381
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 440 "   -0.038 5.00e-02 4.00e+02   5.83e-02 5.44e+00
        pdb=" N   PRO A 441 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 441 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 441 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 390 "   -0.010 2.00e-02 2.50e+03   2.00e-02 3.98e+00
        pdb=" C   ARG A 390 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ARG A 390 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER A 391 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A1009 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A1010 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A1010 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A1010 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1378 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 376
        2.71 -     3.26: 9101
        3.26 -     3.80: 14735
        3.80 -     4.35: 17695
        4.35 -     4.90: 27573
  Nonbonded interactions: 69480
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 332 "
            pdb=" OH  TYR A 479 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OG BSER A1070 "
            pdb=" OE1 GLN A1073 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" OD2 ASP A 993 "
            pdb=" OG  SER A1150 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O3B ADP A1201 "
            pdb=" F1  ALF A1202 "
     model   vdw
     2.201 2.990
  nonbonded pdb=" OE1 GLU A 459 "
            pdb=" OG1 THR A 464 "
     model   vdw
     2.209 3.040
  ... (remaining 69475 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             1.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.110
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     30.610
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5385
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      :  0.004   0.100   8636  Z= 0.213
  Angle     :  1.152  70.945  11897  Z= 0.460
  Chirality :  0.039   0.135   1395
  Planarity :  0.004   0.058   1381
  Dihedral  : 15.724 102.381   3506
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.63 %
    Allowed  : 10.48 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 10.79 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.29), residues: 947
  helix:  0.99 (0.26), residues: 413
  sheet: -1.34 (0.42), residues: 157
  loop : -2.06 (0.34), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 328 
 HIS   0.002   0.000   HIS A 691 
 PHE   0.007   0.001   PHE A 475 
 TYR   0.008   0.001   TYR A 467 
 ARG   0.003   0.000   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 107
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  492 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7344 (mmp80)
REVERT: A  602 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6464 (pm20)
REVERT: A  643 LEU cc_start: 0.8885 (tp) cc_final: 0.8664 (tt)
  outliers start: 40
  outliers final: 9
  residues processed: 141
  average time/residue: 0.2148
  time to fit residues: 42.9529
Evaluate side-chains
  79 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 75 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0270
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0470
   chunk 40 optimal weight:    0.9990
   chunk 77 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 89 optimal weight:    0.2980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 922 HIS
A 958 ASN
A1037 ASN
A1073 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.064892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.044037 restraints weight = 109119.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.045580 restraints weight = 70358.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.046690 restraints weight = 52152.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3284
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3284 r_free = 0.3284    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3283 r_free = 0.3283    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3283
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8636  Z= 0.211
  Angle     :  0.754  11.259  11897  Z= 0.363
  Chirality :  0.046   0.388   1395
  Planarity :  0.005   0.042   1381
  Dihedral  : 15.302  90.639   1654
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 18.05
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.84 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.32 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.28), residues: 947
  helix:  0.54 (0.25), residues: 420
  sheet: -1.13 (0.45), residues: 140
  loop : -1.99 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 328 
 HIS   0.011   0.001   HIS A 534 
 PHE   0.016   0.002   PHE A1045 
 TYR   0.009   0.001   TYR A 752 
 ARG   0.008   0.001   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.914 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8837 (pmm) cc_final: 0.8540 (pmm)
REVERT: A  483 LEU cc_start: 0.8906 (tp) cc_final: 0.8678 (tp)
REVERT: A  543 ASP cc_start: 0.8943 (p0) cc_final: 0.8220 (p0)
REVERT: A  756 TRP cc_start: 0.8372 (m100) cc_final: 0.8050 (m100)
REVERT: A  871 MET cc_start: 0.8971 (mmp) cc_final: 0.8554 (mmt)
REVERT: A  898 PHE cc_start: 0.8916 (m-80) cc_final: 0.8517 (m-80)
REVERT: A  922 HIS cc_start: 0.8518 (m90) cc_final: 0.8243 (m-70)
REVERT: A 1037 ASN cc_start: 0.8404 (m110) cc_final: 0.8047 (m-40)
REVERT: A 1047 TYR cc_start: 0.8512 (m-80) cc_final: 0.8156 (m-80)
REVERT: A 1153 ASP cc_start: 0.9067 (m-30) cc_final: 0.8376 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1974
  time to fit residues: 28.2648
Evaluate side-chains
  73 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 57 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 80 optimal weight:    0.5980
   chunk 83 optimal weight:    8.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A 440 GLN
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 966 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 = 0.3744 r_free = 0.3744 target = 0.063741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.041958 restraints weight = 162906.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.043787 restraints weight = 90725.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.045181 restraints weight = 63105.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3248
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3248 r_free = 0.3248    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3248
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8636  Z= 0.189
  Angle     :  0.697  11.095  11897  Z= 0.337
  Chirality :  0.043   0.332   1395
  Planarity :  0.004   0.037   1381
  Dihedral  : 15.128  91.179   1654
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  9.31 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.44 %
    Favored  : 98.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.28), residues: 947
  helix:  0.42 (0.25), residues: 425
  sheet: -1.17 (0.43), residues: 150
  loop : -2.09 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 328 
 HIS   0.005   0.001   HIS A 534 
 PHE   0.012   0.001   PHE A 518 
 TYR   0.021   0.001   TYR A 420 
 ARG   0.006   0.001   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.909 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8908 (pmm) cc_final: 0.8626 (pmm)
REVERT: A  543 ASP cc_start: 0.9041 (p0) cc_final: 0.8411 (p0)
REVERT: A  756 TRP cc_start: 0.8421 (m100) cc_final: 0.8000 (m100)
REVERT: A  871 MET cc_start: 0.9021 (mmp) cc_final: 0.8661 (mmt)
REVERT: A  898 PHE cc_start: 0.8857 (m-80) cc_final: 0.8426 (m-80)
REVERT: A  922 HIS cc_start: 0.8749 (m90) cc_final: 0.8401 (m-70)
REVERT: A  957 MET cc_start: 0.9584 (ttt) cc_final: 0.9229 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1878
  time to fit residues: 24.8427
Evaluate side-chains
  70 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 98 optimal weight:   10.0000
   chunk 24 optimal weight:    7.9990
   chunk 4 optimal weight:   30.0000
   chunk 69 optimal weight:    0.0050
   chunk 36 optimal weight:    3.9990
   chunk 90 optimal weight:    1.9990
   chunk 13 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 50 optimal weight:    2.9990
   chunk 96 optimal weight:   10.0000
   overall best weight:    2.0002

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.062381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.041209 restraints weight = 160660.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.042985 restraints weight = 92117.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.044188 restraints weight = 64465.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3215
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3215 r_free = 0.3215    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3215
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8636  Z= 0.205
  Angle     :  0.690  11.433  11897  Z= 0.335
  Chirality :  0.044   0.396   1395
  Planarity :  0.004   0.035   1381
  Dihedral  : 15.115  91.251   1654
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 18.11
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.74 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.92 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.28), residues: 947
  helix:  0.49 (0.25), residues: 425
  sheet: -1.28 (0.42), residues: 143
  loop : -1.99 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 328 
 HIS   0.004   0.001   HIS A 803 
 PHE   0.012   0.001   PHE A 731 
 TYR   0.010   0.001   TYR A 420 
 ARG   0.004   0.000   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8961 (pmm) cc_final: 0.8691 (pmm)
REVERT: A  543 ASP cc_start: 0.9090 (p0) cc_final: 0.8397 (p0)
REVERT: A  756 TRP cc_start: 0.8507 (m100) cc_final: 0.8160 (m100)
REVERT: A  871 MET cc_start: 0.9139 (mmp) cc_final: 0.8798 (mmt)
REVERT: A  898 PHE cc_start: 0.8913 (m-80) cc_final: 0.8234 (m-80)
REVERT: A  922 HIS cc_start: 0.8785 (m90) cc_final: 0.8408 (m-70)
REVERT: A  957 MET cc_start: 0.9551 (ttt) cc_final: 0.9194 (ptt)
REVERT: A 1063 CYS cc_start: 0.7875 (p) cc_final: 0.7134 (m)
REVERT: A 1153 ASP cc_start: 0.9198 (m-30) cc_final: 0.8608 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1858
  time to fit residues: 21.0488
Evaluate side-chains
  63 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 0 optimal weight:   40.0000
   chunk 75 optimal weight:    1.9990
   chunk 73 optimal weight:    9.9990
   chunk 77 optimal weight:    0.2980
   chunk 95 optimal weight:   20.0000
   chunk 46 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 646 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.061746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.040050 restraints weight = 223537.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.042167 restraints weight = 109313.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.043649 restraints weight = 70870.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3202
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3202 r_free = 0.3202    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3202
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8636  Z= 0.196
  Angle     :  0.691  10.858  11897  Z= 0.335
  Chirality :  0.044   0.341   1395
  Planarity :  0.004   0.035   1381
  Dihedral  : 15.068  91.434   1654
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.31 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.80 %
    Favored  : 97.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.28), residues: 947
  helix:  0.46 (0.25), residues: 425
  sheet: -1.30 (0.42), residues: 142
  loop : -2.01 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 961 
 HIS   0.004   0.001   HIS A 984 
 PHE   0.013   0.001   PHE A 976 
 TYR   0.009   0.001   TYR A 420 
 ARG   0.005   0.000   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.953 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 MET cc_start: 0.8986 (pmm) cc_final: 0.8714 (pmm)
REVERT: A  543 ASP cc_start: 0.9112 (p0) cc_final: 0.8428 (p0)
REVERT: A  756 TRP cc_start: 0.8480 (m100) cc_final: 0.8199 (m100)
REVERT: A  871 MET cc_start: 0.9146 (mmp) cc_final: 0.8835 (mmt)
REVERT: A  898 PHE cc_start: 0.8800 (m-80) cc_final: 0.8354 (m-80)
REVERT: A  922 HIS cc_start: 0.8856 (m90) cc_final: 0.8478 (m-70)
REVERT: A  957 MET cc_start: 0.9580 (ttt) cc_final: 0.9293 (tmm)
REVERT: A 1063 CYS cc_start: 0.7912 (p) cc_final: 0.7126 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1874
  time to fit residues: 20.9062
Evaluate side-chains
  62 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 81 optimal weight:    8.9990
   chunk 26 optimal weight:    0.9980
   chunk 92 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 966 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 = 0.3681 r_free = 0.3681 target = 0.060495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.039421 restraints weight = 198340.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.041312 restraints weight = 104028.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.042646 restraints weight = 70090.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3174
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3174 r_free = 0.3174    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3174
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8115
moved from start:          0.3218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8636  Z= 0.235
  Angle     :  0.714  13.126  11897  Z= 0.347
  Chirality :  0.044   0.346   1395
  Planarity :  0.004   0.037   1381
  Dihedral  : 15.129  91.377   1654
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 20.49
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  9.74 %
    Favored  : 89.84 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.32 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.28), residues: 947
  helix:  0.39 (0.24), residues: 428
  sheet: -1.57 (0.42), residues: 135
  loop : -1.99 (0.34), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP A 165 
 HIS   0.004   0.001   HIS A 803 
 PHE   0.027   0.002   PHE A 778 
 TYR   0.012   0.001   TYR A 437 
 ARG   0.006   0.000   ARG A 237 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.016 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  543 ASP cc_start: 0.9159 (p0) cc_final: 0.8441 (p0)
REVERT: A  756 TRP cc_start: 0.8457 (m100) cc_final: 0.8245 (m100)
REVERT: A  871 MET cc_start: 0.9125 (mmp) cc_final: 0.8820 (mmt)
REVERT: A  898 PHE cc_start: 0.8738 (m-80) cc_final: 0.8085 (m-80)
REVERT: A  922 HIS cc_start: 0.8872 (m90) cc_final: 0.8494 (m-70)
REVERT: A  957 MET cc_start: 0.9571 (ttt) cc_final: 0.9297 (tmm)
REVERT: A 1063 CYS cc_start: 0.7804 (p) cc_final: 0.7069 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1905
  time to fit residues: 21.3921
Evaluate side-chains
  63 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0770
   chunk 10 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 85 optimal weight:   20.0000
   chunk 95 optimal weight:   20.0000
   chunk 93 optimal weight:    0.9990
   chunk 92 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.9344

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

Flipped N/Q/H residues before XYZ refinement:
** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 966 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 = 0.3714 r_free = 0.3714 target = 0.062271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.041709 restraints weight = 149580.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.043431 restraints weight = 86967.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.044640 restraints weight = 61277.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8636  Z= 0.173
  Angle     :  0.679  10.160  11897  Z= 0.327
  Chirality :  0.044   0.354   1395
  Planarity :  0.004   0.036   1381
  Dihedral  : 14.958  91.692   1654
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.42 %
    Allowed  :  8.47 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.60 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.27), residues: 947
  helix:  0.46 (0.25), residues: 424
  sheet: -1.50 (0.42), residues: 136
  loop : -1.93 (0.33), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 165 
 HIS   0.003   0.001   HIS A 503 
 PHE   0.013   0.001   PHE A 898 
 TYR   0.013   0.001   TYR A 890 
 ARG   0.004   0.000   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  543 ASP cc_start: 0.9114 (p0) cc_final: 0.8439 (p0)
REVERT: A  756 TRP cc_start: 0.8380 (m100) cc_final: 0.7906 (m100)
REVERT: A  807 LEU cc_start: 0.9470 (mt) cc_final: 0.9119 (tp)
REVERT: A  871 MET cc_start: 0.9103 (mmp) cc_final: 0.8764 (mmt)
REVERT: A  898 PHE cc_start: 0.8703 (m-80) cc_final: 0.8226 (m-80)
REVERT: A  922 HIS cc_start: 0.8821 (m90) cc_final: 0.8546 (m-70)
REVERT: A  957 MET cc_start: 0.9524 (ttt) cc_final: 0.9273 (tmm)
REVERT: A  981 MET cc_start: 0.8583 (ppp) cc_final: 0.8351 (ppp)
REVERT: A 1063 CYS cc_start: 0.7763 (p) cc_final: 0.6789 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1985
  time to fit residues: 22.1468
Evaluate side-chains
  64 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0470
   chunk 83 optimal weight:    0.1980
   chunk 49 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0770
   chunk 84 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.4638

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

Flipped N/Q/H residues before XYZ refinement:
A 534 HIS
** A 966 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 = 0.3771 r_free = 0.3771 target = 0.063189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.042557 restraints weight = 154814.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.044534 restraints weight = 83728.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.045925 restraints weight = 56631.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3267
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3267 r_free = 0.3267    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3267
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   8636  Z= 0.163
  Angle     :  0.677   9.972  11897  Z= 0.327
  Chirality :  0.044   0.363   1395
  Planarity :  0.004   0.037   1381
  Dihedral  : 14.726  90.646   1654
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 15.06
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.99 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.84 %
    Favored  : 98.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.08 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.27), residues: 947
  helix:  0.46 (0.25), residues: 425
  sheet: -1.32 (0.42), residues: 146
  loop : -1.87 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 961 
 HIS   0.003   0.001   HIS A 503 
 PHE   0.014   0.001   PHE A 518 
 TYR   0.014   0.001   TYR A 890 
 ARG   0.004   0.000   ARG A 492 

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

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

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1894 Ramachandran restraints generated.
    947 Oldfield, 0 Emsley, 947 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
REVERT: A  543 ASP cc_start: 0.9104 (p0) cc_final: 0.8442 (p0)
REVERT: A  756 TRP cc_start: 0.8374 (m100) cc_final: 0.7784 (m100)
REVERT: A  807 LEU cc_start: 0.9458 (mt) cc_final: 0.9102 (tp)
REVERT: A  871 MET cc_start: 0.9095 (mmp) cc_final: 0.8745 (mmt)
REVERT: A  898 PHE cc_start: 0.8599 (m-80) cc_final: 0.8172 (m-80)
REVERT: A  922 HIS cc_start: 0.8861 (m90) cc_final: 0.8563 (m-70)
REVERT: A  957 MET cc_start: 0.9532 (ttt) cc_final: 0.9154 (tmm)
REVERT: A  981 MET cc_start: 0.8736 (ppp) cc_final: 0.8473 (ppp)
REVERT: A 1063 CYS cc_start: 0.7581 (p) cc_final: 0.6546 (m)
REVERT: A 1153 ASP cc_start: 0.9133 (m-30) cc_final: 0.8776 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1814
  time to fit residues: 20.9346
Evaluate side-chains
  62 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 64.2233 > 50:
  distance: 61 - 66:  17.651
  distance: 66 - 67:  11.910
  distance: 67 - 68:  31.916
  distance: 67 - 70:  38.830
  distance: 68 - 69:  22.598
  distance: 68 - 74:  22.790
  distance: 70 - 71:  22.898
  distance: 70 - 72:  42.046
  distance: 71 - 73:  45.104
  distance: 74 - 75:  28.331
  distance: 75 - 76:  48.811
  distance: 76 - 77:  44.754
  distance: 76 - 82:  12.718
  distance: 78 - 79:  41.013
  distance: 79 - 80:  37.302
  distance: 82 - 83:  13.696
  distance: 83 - 84:  38.666
  distance: 83 - 86:  11.806
  distance: 84 - 85:  22.291
  distance: 84 - 89:  32.888
  distance: 85 - 116:  37.048
  distance: 86 - 87:  28.275
  distance: 86 - 88:  34.317
  distance: 89 - 90:  20.291
  distance: 90 - 91:  25.610
  distance: 90 - 93:  40.167
  distance: 91 - 92:  13.788
  distance: 91 - 96:  27.318
  distance: 92 - 122:  22.402
  distance: 93 - 94:   7.642
  distance: 93 - 95:  28.560
  distance: 96 - 97:   8.143
  distance: 97 - 98:  35.164
  distance: 97 - 100:  16.800
  distance: 98 - 99:  28.193
  distance: 98 - 105:  31.273
  distance: 99 - 131:  53.473
  distance: 100 - 101:  17.260
  distance: 101 - 102:  23.549
  distance: 102 - 103:  28.045
  distance: 103 - 104:  21.509
  distance: 105 - 106:  10.239
  distance: 106 - 107:  21.851
  distance: 106 - 109:  45.808
  distance: 107 - 108:  30.099
  distance: 107 - 116:  11.251
  distance: 109 - 110:   8.901
  distance: 110 - 111:  26.322
  distance: 110 - 112:  10.416
  distance: 111 - 113:  29.254
  distance: 112 - 114:  25.553
  distance: 113 - 115:  23.044
  distance: 114 - 115:  21.723
  distance: 116 - 117:   6.579
  distance: 117 - 118:  22.239
  distance: 117 - 120:  17.142
  distance: 118 - 119:  13.923
  distance: 118 - 122:  17.837
  distance: 120 - 121:  36.775
  distance: 122 - 123:  22.180
  distance: 123 - 124:  16.075
  distance: 123 - 126:  12.376
  distance: 124 - 125:  19.496
  distance: 124 - 131:  34.208
  distance: 126 - 127:  21.557
  distance: 127 - 128:  16.029
  distance: 128 - 129:  12.256
  distance: 129 - 130:  19.721
  distance: 131 - 132:  24.314
  distance: 132 - 133:  21.617
  distance: 132 - 135:  24.572
  distance: 133 - 134:  20.184
  distance: 133 - 143:  10.106
  distance: 135 - 136:  34.716
  distance: 136 - 137:  18.436
  distance: 136 - 138:   9.700
  distance: 137 - 139:  16.453
  distance: 138 - 140:  18.453
  distance: 139 - 141:  10.008
  distance: 140 - 141:  14.924
  distance: 141 - 142:  12.220
  distance: 143 - 144:   8.098
  distance: 144 - 145:   8.293
  distance: 144 - 147:  10.725
  distance: 145 - 146:  23.885
  distance: 145 - 154:  28.625
  distance: 147 - 148:  32.946
  distance: 148 - 149:  29.872
  distance: 148 - 150:  31.344
  distance: 149 - 151:  19.093
  distance: 150 - 152:  28.877
  distance: 151 - 153:   8.002
  distance: 152 - 153:  41.781