Starting phenix.real_space_refine
on Wed Mar 12 19:38:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6v0v_21003/03_2025/6v0v_21003.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6v0v_21003/03_2025/6v0v_21003.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.61
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2025/6v0v_21003.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2025/6v0v_21003.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2025/6v0v_21003.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6v0v_21003/03_2025/6v0v_21003.cif"
  }
  resolution = 3.61
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Ca      2      9.91       5
     Zn      1      6.06       5
     P      60      5.49       5
     S      51      5.16       5
     C    5002      2.51       5
     N    1428      2.21       5
     O    1648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8192
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 541, 4286
          Classifications: {'peptide': 541}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 516}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 77
          Unresolved non-hydrogen angles: 89
          Unresolved non-hydrogen dihedrals: 67
          Planarities with less than four sites: {'GLU:plan': 7, 'HIS:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 46
    Chain: "B"
      Number of atoms: 2673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 346, 2673
          Classifications: {'peptide': 346}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 19, 'TRANS': 326}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "F"
      Number of atoms: 617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 617
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "I"
      Number of atoms: 613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 613
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 2, ' ZN': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2016  SG  CYS A 727      70.241  55.803  61.715  1.00 82.81           S
  ATOM   2037  SG  CYS A 730      72.316  58.531  60.217  1.00 86.87           S

  Time building chain proxies: 5.73, per 1000 atoms: 0.70
  Number of scatterers: 8192
  At special positions: 0
  Unit cell: (107.06, 95.4, 118.72, 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)
     Zn      1     29.99
     Ca      2     19.99
     S      51     16.00
     P      60     15.00
     O    1648      8.00
     N    1428      7.00
     C    5002      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=0, symmetry=0
  Time building additional restraints: 2.35
  Conformation dependent library (CDL) restraints added in 897.3 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1103 "
        pdb="ZN    ZN A1103 " - pdb=" NE2 HIS A 937 "
        pdb="ZN    ZN A1103 " - pdb=" NE2 HIS A 942 "
        pdb="ZN    ZN A1103 " - pdb=" SG  CYS A 730 "
        pdb="ZN    ZN A1103 " - pdb=" SG  CYS A 727 "
      Number of angles added : 2


  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1662

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      33.8% alpha, 25.0% beta
      28 base pairs and 50 stacking pairs defined.
    Time for finding SS restraints: 2.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 463 through 474
      removed outlier: 3.849A  pdb=" N   CYS A 467 " --> pdb=" O   GLN A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 493
    Processing helix  chain 'A' and resid 499 through 511
      removed outlier: 3.670A  pdb=" N   ALA A 506 " --> pdb=" O   ALA A 502 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A 508 " --> pdb=" O   ARG A 504 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   VAL A 509 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   LEU A 510 " --> pdb=" O   ALA A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 570
      removed outlier: 3.603A  pdb=" N   SER A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   MET A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 581
    Processing helix  chain 'A' and resid 664 through 682
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 708 through 716
      removed outlier: 3.579A  pdb=" N   GLU A 716 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 738
    Processing helix  chain 'A' and resid 750 through 763
    Processing helix  chain 'A' and resid 768 through 776
    Processing helix  chain 'A' and resid 793 through 814
      removed outlier: 3.964A  pdb=" N   GLY A 813 " --> pdb=" O   GLN A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 824 through 841
    Processing helix  chain 'A' and resid 850 through 858
      removed outlier: 4.005A  pdb=" N   MET A 858 " --> pdb=" O   ALA A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 870
      removed outlier: 3.548A  pdb=" N   VAL A 863 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 873 through 890
      removed outlier: 3.769A  pdb=" N   GLU A 877 " --> pdb=" O   GLU A 873 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 882 " --> pdb=" O   ALA A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 890 through 895
    Processing helix  chain 'A' and resid 897 through 902
      removed outlier: 3.843A  pdb=" N   CYS A 902 " --> pdb=" O   PRO A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 924
      removed outlier: 5.330A  pdb=" N   SER A 910 " --> pdb=" O   LEU A 906 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   PHE A 911 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   PHE A 916 " --> pdb=" O   ASN A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 942
      removed outlier: 3.904A  pdb=" N   HIS A 937 " --> pdb=" O   THR A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 942 through 950
      removed outlier: 3.787A  pdb=" N   GLU A 948 " --> pdb=" O   PRO A 944 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 964
    Processing helix  chain 'A' and resid 964 through 975
      removed outlier: 3.567A  pdb=" N   PHE A 968 " --> pdb=" O   GLY A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 995
      removed outlier: 3.815A  pdb=" N   VAL A 987 " --> pdb=" O   GLU A 983 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU A 988 " --> pdb=" O   MET A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 996 through 1001
    Processing helix  chain 'A' and resid 1002 through 1005
    Processing helix  chain 'B' and resid 11 through 15
      removed outlier: 4.008A  pdb=" N   LEU B  14 " --> pdb=" O   ASN B  11 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 518 through 520
      removed outlier: 10.087A  pdb=" N   PHE A 591 " --> pdb=" O   PHE A 700 " (cutoff:3.500A)
      removed outlier: 10.936A  pdb=" N   PHE A 702 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLY A 704 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 10.350A  pdb=" N   VAL A 595 " --> pdb=" O   GLY A 704 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY A 706 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A 631 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 621 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   PHE A 624 " --> pdb=" O   PRO A 654 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520
      removed outlier: 10.087A  pdb=" N   PHE A 591 " --> pdb=" O   PHE A 700 " (cutoff:3.500A)
      removed outlier: 10.936A  pdb=" N   PHE A 702 " --> pdb=" O   PHE A 591 " (cutoff:3.500A)
      removed outlier: 10.265A  pdb=" N   VAL A 593 " --> pdb=" O   PHE A 702 " (cutoff:3.500A)
      removed outlier: 10.586A  pdb=" N   GLY A 704 " --> pdb=" O   VAL A 593 " (cutoff:3.500A)
      removed outlier: 10.350A  pdb=" N   VAL A 595 " --> pdb=" O   GLY A 704 " (cutoff:3.500A)
      removed outlier: 8.502A  pdb=" N   GLY A 706 " --> pdb=" O   VAL A 595 " (cutoff:3.500A)
      removed outlier: 7.197A  pdb=" N   GLU A 597 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
      removed outlier: 5.412A  pdb=" N   ILE A 631 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ARG A 621 " --> pdb=" O   ASP A 600 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   ILE A 631 " --> pdb=" O   LYS A 639 " (cutoff:3.500A)
      removed outlier: 5.846A  pdb=" N   LYS A 639 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   HIS A 633 " --> pdb=" O   ASN A 637 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ASN A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 6
      removed outlier: 4.650A  pdb=" N   PHE B 345 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 20 through 24
      removed outlier: 4.147A  pdb=" N   VAL B  28 " --> pdb=" O   PHE B  48 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   ASP B  49 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62
      removed outlier: 7.102A  pdb=" N   ILE B  61 " --> pdb=" O   PHE B 122 " (cutoff:3.500A)
      removed outlier: 7.955A  pdb=" N   CYS B 124 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
      removed outlier: 5.575A  pdb=" N   LYS B 119 " --> pdb=" O   LYS B 115 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   LYS B 115 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
      removed outlier: 6.740A  pdb=" N   THR B 121 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 130 through 131
      removed outlier: 6.722A  pdb=" N   VAL B 130 " --> pdb=" O   ALA B 192 " (cutoff:3.500A)
      removed outlier: 8.527A  pdb=" N   SER B 194 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 212
      removed outlier: 4.540A  pdb=" N   LEU B 233 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 262 through 267
      removed outlier: 3.809A  pdb=" N   ILE B 262 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   THR B 266 " --> pdb=" O   GLU B 270 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLU B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)

    303 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      70 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      28 basepair parallelities
      50 stacking parallelities
  Total time for adding SS restraints: 3.05

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2196
        1.33 -     1.45: 2147
        1.45 -     1.58: 3960
        1.58 -     1.70: 117
        1.70 -     1.82: 78
  Bond restraints: 8498
  Sorted by residual:
  bond pdb=" O3'  DT F  29 "
       pdb=" P    DG F  30 "
    ideal  model  delta    sigma   weight residual
    1.607  1.562  0.045 1.50e-02 4.44e+03 9.15e+00
  bond pdb=" CA  LEU A 735 "
       pdb=" C   LEU A 735 "
    ideal  model  delta    sigma   weight residual
    1.522  1.484  0.038 1.37e-02 5.33e+03 7.83e+00
  bond pdb=" N   MET A 847 "
       pdb=" CA  MET A 847 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.24e-02 6.50e+03 6.22e+00
  bond pdb=" C   PRO A 654 "
       pdb=" N   LEU A 655 "
    ideal  model  delta    sigma   weight residual
    1.331  1.299  0.033 1.40e-02 5.10e+03 5.47e+00
  bond pdb=" C3'  DG I   6 "
       pdb=" O3'  DG I   6 "
    ideal  model  delta    sigma   weight residual
    1.422  1.491 -0.069 3.00e-02 1.11e+03 5.34e+00
  ... (remaining 8493 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.76: 11497
        2.76 -     5.53: 234
        5.53 -     8.29: 22
        8.29 -    11.06: 4
       11.06 -    13.82: 1
  Bond angle restraints: 11758
  Sorted by residual:
  angle pdb=" C4'  DT F  29 "
        pdb=" C3'  DT F  29 "
        pdb=" O3'  DT F  29 "
      ideal   model   delta    sigma   weight residual
     110.00   96.18   13.82 1.50e+00 4.44e-01 8.49e+01
  angle pdb=" C2'  DC F  26 "
        pdb=" C1'  DC F  26 "
        pdb=" N1   DC F  26 "
      ideal   model   delta    sigma   weight residual
     113.50  120.36   -6.86 1.50e+00 4.44e-01 2.09e+01
  angle pdb=" C   ARG B 212 "
        pdb=" N   ASN B 213 "
        pdb=" CA  ASN B 213 "
      ideal   model   delta    sigma   weight residual
     121.54  130.19   -8.65 1.91e+00 2.74e-01 2.05e+01
  angle pdb=" C4'  DT F  27 "
        pdb=" C3'  DT F  27 "
        pdb=" O3'  DT F  27 "
      ideal   model   delta    sigma   weight residual
     110.00  103.31    6.69 1.50e+00 4.44e-01 1.99e+01
  angle pdb=" C3'  DG I   6 "
        pdb=" O3'  DG I   6 "
        pdb=" P    DG I   7 "
      ideal   model   delta    sigma   weight residual
     120.20  125.96   -5.76 1.50e+00 4.44e-01 1.47e+01
  ... (remaining 11753 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.36: 4578
       35.36 -    70.72: 347
       70.72 -   106.09: 9
      106.09 -   141.45: 1
      141.45 -   176.81: 2
  Dihedral angle restraints: 4937
    sinusoidal: 2358
      harmonic: 2579
  Sorted by residual:
  dihedral pdb=" CA  ARG B 212 "
           pdb=" C   ARG B 212 "
           pdb=" N   ASN B 213 "
           pdb=" CA  ASN B 213 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.68   25.32     0      5.00e+00 4.00e-02 2.57e+01
  dihedral pdb=" CA  CYS B  41 "
           pdb=" C   CYS B  41 "
           pdb=" N   PRO B  42 "
           pdb=" CA  PRO B  42 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.91  -22.09     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  PRO A 871 "
           pdb=" C   PRO A 871 "
           pdb=" N   SER A 872 "
           pdb=" CA  SER A 872 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.23  -21.77     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 4934 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1013
       0.065 -    0.129: 244
       0.129 -    0.194: 33
       0.194 -    0.259: 6
       0.259 -    0.323: 2
  Chirality restraints: 1298
  Sorted by residual:
  chirality pdb=" C1'  DC F  26 "
            pdb=" O4'  DC F  26 "
            pdb=" C2'  DC F  26 "
            pdb=" N1   DC F  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.15    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CB  VAL A 943 "
            pdb=" CA  VAL A 943 "
            pdb=" CG1 VAL A 943 "
            pdb=" CG2 VAL A 943 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" CB  VAL B   8 "
            pdb=" CA  VAL B   8 "
            pdb=" CG1 VAL B   8 "
            pdb=" CG2 VAL B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.23 2.00e-01 2.50e+01 1.38e+00
  ... (remaining 1295 not shown)

  Planarity restraints: 1303
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC F  26 "    0.095 2.00e-02 2.50e+03   4.30e-02 4.17e+01
        pdb=" N1   DC F  26 "   -0.043 2.00e-02 2.50e+03
        pdb=" C2   DC F  26 "   -0.021 2.00e-02 2.50e+03
        pdb=" O2   DC F  26 "   -0.030 2.00e-02 2.50e+03
        pdb=" N3   DC F  26 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DC F  26 "    0.009 2.00e-02 2.50e+03
        pdb=" N4   DC F  26 "    0.044 2.00e-02 2.50e+03
        pdb=" C5   DC F  26 "   -0.018 2.00e-02 2.50e+03
        pdb=" C6   DC F  26 "   -0.046 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 212 "    0.015 2.00e-02 2.50e+03   3.09e-02 9.57e+00
        pdb=" C   ARG B 212 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   ARG B 212 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ASN B 213 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  98 "   -0.050 5.00e-02 4.00e+02   7.49e-02 8.98e+00
        pdb=" N   PRO B  99 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.042 5.00e-02 4.00e+02
  ... (remaining 1300 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.53: 83
        2.53 -     3.12: 5775
        3.12 -     3.71: 13865
        3.71 -     4.31: 18150
        4.31 -     4.90: 28488
  Nonbonded interactions: 66361
  Sorted by model distance:
  nonbonded pdb=" OP1  DC I  17 "
            pdb="CA    CA A1102 "
     model   vdw
     1.932 2.510
  nonbonded pdb=" OE1 GLU A 962 "
            pdb="CA    CA A1102 "
     model   vdw
     2.026 2.510
  nonbonded pdb=" OD1 ASP A 600 "
            pdb="CA    CA A1101 "
     model   vdw
     2.193 2.510
  nonbonded pdb=" OE2 GLU A 803 "
            pdb=" OH  TYR A 928 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" O   SER A 958 "
            pdb=" OG  SER A 958 "
     model   vdw
     2.266 3.040
  ... (remaining 66356 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=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:             2.090
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.600
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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      :  0.008   0.087   8498  Z= 0.479
  Angle     :  1.005  13.822  11758  Z= 0.577
  Chirality :  0.057   0.323   1298
  Planarity :  0.007   0.075   1303
  Dihedral  : 21.033 176.809   3275
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  7.28 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.88 %
    Favored  : 92.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -3.85 (0.23), residues: 879
  helix: -2.89 (0.22), residues: 271
  sheet: -1.77 (0.40), residues: 158
  loop : -2.63 (0.23), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 893 
 HIS   0.008   0.002   HIS B  47 
 PHE   0.035   0.003   PHE A 804 
 TYR   0.016   0.002   TYR A 805 
 ARG   0.006   0.001   ARG A 696 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8011 (tm-30)
REVERT: A  753 ASN cc_start: 0.8184 (t0) cc_final: 0.6963 (t0)
REVERT: A  857 LEU cc_start: 0.9194 (mt) cc_final: 0.8898 (tt)
REVERT: B   24 PHE cc_start: 0.6579 (m-10) cc_final: 0.6234 (m-80)
REVERT: B   80 TYR cc_start: 0.7482 (t80) cc_final: 0.6994 (t80)
REVERT: B   90 GLN cc_start: 0.8212 (pt0) cc_final: 0.7827 (pt0)
REVERT: B  269 ASP cc_start: 0.6285 (t0) cc_final: 0.6067 (t0)
REVERT: B  281 ASN cc_start: 0.7903 (p0) cc_final: 0.7451 (p0)
REVERT: B  313 HIS cc_start: 0.8340 (t70) cc_final: 0.7986 (t-90)
  outliers start: 3
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2342
  time to fit residues: 44.2221
Evaluate side-chains
  80 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    0.2980
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    8.9990
   chunk 28 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0010
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 515 HIS
A 800 ASN
A 820 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
B 267 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.087579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.066308 restraints weight = 24792.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.068125 restraints weight = 13663.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.069306 restraints weight = 9493.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8498  Z= 0.197
  Angle     :  0.639   8.066  11758  Z= 0.348
  Chirality :  0.042   0.164   1298
  Planarity :  0.005   0.058   1303
  Dihedral  : 23.607 176.020   1618
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.62 %
    Favored  : 84.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -2.32 (0.26), residues: 879
  helix: -1.12 (0.29), residues: 272
  sheet: -0.77 (0.41), residues: 164
  loop : -2.12 (0.25), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 937 
 PHE   0.032   0.002   PHE A 804 
 TYR   0.012   0.001   TYR A 757 
 ARG   0.006   0.001   ARG A 838 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.888 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8161 (tm-30)
REVERT: A  841 MET cc_start: 0.8194 (OUTLIER) cc_final: 0.7943 (mmp)
REVERT: A  919 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8193 (tt)
REVERT: B   80 TYR cc_start: 0.7645 (t80) cc_final: 0.7368 (t80)
REVERT: B   90 GLN cc_start: 0.8161 (pt0) cc_final: 0.7783 (pt0)
REVERT: B  313 HIS cc_start: 0.8480 (t70) cc_final: 0.8180 (t-90)
  outliers start: 14
  outliers final: 6
  residues processed: 112
  average time/residue: 0.1782
  time to fit residues: 28.7387
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  518 GLU
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  812 ILE
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue  272 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 60 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0770
   chunk 83 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 89 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
A 842 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 934 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.087362 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065650 restraints weight = 24731.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.067498 restraints weight = 13649.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.068687 restraints weight = 9465.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8498  Z= 0.179
  Angle     :  0.611   9.235  11758  Z= 0.327
  Chirality :  0.041   0.163   1298
  Planarity :  0.004   0.055   1303
  Dihedral  : 23.324 175.414   1618
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.74 %
    Favored  : 81.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -1.55 (0.27), residues: 879
  helix: -0.29 (0.31), residues: 273
  sheet: -0.45 (0.41), residues: 173
  loop : -1.75 (0.27), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 317 
 HIS   0.002   0.001   HIS A 937 
 PHE   0.037   0.002   PHE A 804 
 TYR   0.011   0.001   TYR A 757 
 ARG   0.006   0.000   ARG A 838 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8015 (ttm) cc_final: 0.7593 (ttm)
REVERT: A  576 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: A  760 TRP cc_start: 0.8828 (OUTLIER) cc_final: 0.8437 (t-100)
REVERT: A  887 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9072 (mp)
REVERT: A  919 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8158 (tt)
REVERT: A  961 ASN cc_start: 0.6861 (t0) cc_final: 0.6577 (t0)
REVERT: A  965 ASN cc_start: 0.8070 (m-40) cc_final: 0.7764 (m110)
REVERT: B   80 TYR cc_start: 0.7712 (t80) cc_final: 0.7414 (t80)
  outliers start: 21
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1765
  time to fit residues: 24.7909
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.902 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  662 GLU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  887 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0170
   chunk 54 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    6.9990
   chunk 59 optimal weight:    0.0970
   chunk 83 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 2 optimal weight:    0.2980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** 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 = 0.3715 r_free = 0.3715 target = 0.088115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.066162 restraints weight = 24687.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.068039 restraints weight = 13642.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.069227 restraints weight = 9483.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8498  Z= 0.166
  Angle     :  0.585   8.287  11758  Z= 0.317
  Chirality :  0.041   0.159   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.176 176.148   1618
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 17.86 %
    Favored  : 79.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.97 (0.28), residues: 879
  helix:  0.28 (0.32), residues: 269
  sheet:  0.04 (0.42), residues: 171
  loop : -1.53 (0.28), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 317 
 HIS   0.002   0.000   HIS A 937 
 PHE   0.038   0.001   PHE A 804 
 TYR   0.010   0.001   TYR A 757 
 ARG   0.004   0.000   ARG A 848 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.818 
Fit side-chains
REVERT: A  568 MET cc_start: 0.8019 (ttm) cc_final: 0.7711 (ttm)
REVERT: A  576 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8124 (tm-30)
REVERT: A  760 TRP cc_start: 0.8776 (OUTLIER) cc_final: 0.8372 (t-100)
REVERT: A  849 MET cc_start: 0.6985 (OUTLIER) cc_final: 0.6552 (mtm)
REVERT: A  919 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8195 (tt)
REVERT: B   80 TYR cc_start: 0.7751 (t80) cc_final: 0.7479 (t80)
  outliers start: 21
  outliers final: 7
  residues processed: 96
  average time/residue: 0.1523
  time to fit residues: 22.1407
Evaluate side-chains
  84 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.832 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  849 MET
Chi-restraints excluded: chain A residue  884 ASP
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 750 HIS
A 852 ASN
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 961 ASN
B  33 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.084450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.062503 restraints weight = 24374.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.064223 restraints weight = 13816.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.065335 restraints weight = 9759.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8498  Z= 0.240
  Angle     :  0.649   9.965  11758  Z= 0.339
  Chirality :  0.042   0.183   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.189 175.957   1618
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 18.39 %
    Favored  : 78.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.78 (0.28), residues: 879
  helix:  0.32 (0.33), residues: 270
  sheet:  0.35 (0.43), residues: 155
  loop : -1.36 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 317 
 HIS   0.004   0.001   HIS A 515 
 PHE   0.038   0.002   PHE A 804 
 TYR   0.010   0.001   TYR A 805 
 ARG   0.005   0.000   ARG A 848 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 78
  time to evaluate  : 0.879 
Fit side-chains
REVERT: A  505 ASN cc_start: 0.8481 (m-40) cc_final: 0.8114 (m-40)
REVERT: A  568 MET cc_start: 0.8387 (ttm) cc_final: 0.7946 (ttm)
REVERT: A  576 GLU cc_start: 0.8484 (tm-30) cc_final: 0.8115 (tm-30)
REVERT: A  760 TRP cc_start: 0.8953 (OUTLIER) cc_final: 0.8659 (t-100)
REVERT: A  844 LYS cc_start: 0.6549 (mmtt) cc_final: 0.5892 (tttp)
REVERT: A  883 MET cc_start: 0.8172 (tpp) cc_final: 0.7901 (tpt)
REVERT: A  919 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8254 (tt)
REVERT: A  961 ASN cc_start: 0.6894 (t0) cc_final: 0.6535 (t0)
REVERT: B   80 TYR cc_start: 0.7831 (t80) cc_final: 0.7581 (t80)
REVERT: B  280 GLU cc_start: 0.7982 (pm20) cc_final: 0.7753 (pm20)
REVERT: B  302 MET cc_start: 0.7553 (mmm) cc_final: 0.7282 (mmm)
  outliers start: 21
  outliers final: 15
  residues processed: 93
  average time/residue: 0.1723
  time to fit residues: 24.0961
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  760 TRP
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  879 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  200 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  263 LEU
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 75 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 975 ASN
B  89 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.081815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.060029 restraints weight = 24782.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.061701 restraints weight = 13973.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.062777 restraints weight = 9856.273|
|-----------------------------------------------------------------------------|
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.4218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   8498  Z= 0.332
  Angle     :  0.696   9.816  11758  Z= 0.364
  Chirality :  0.044   0.203   1298
  Planarity :  0.004   0.055   1303
  Dihedral  : 23.399 176.745   1618
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.97 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.73 (0.28), residues: 879
  helix:  0.29 (0.33), residues: 269
  sheet:  0.44 (0.43), residues: 153
  loop : -1.29 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 317 
 HIS   0.004   0.001   HIS A 515 
 PHE   0.035   0.002   PHE A 804 
 TYR   0.014   0.002   TYR A 805 
 ARG   0.005   0.001   ARG A 734 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.849 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: A  838 ARG cc_start: 0.7458 (ttp-110) cc_final: 0.7244 (mtm110)
REVERT: A  843 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.7922 (tt)
REVERT: A  844 LYS cc_start: 0.6652 (mmtt) cc_final: 0.6277 (tttp)
REVERT: A  858 MET cc_start: 0.7359 (tmm) cc_final: 0.7059 (tmm)
REVERT: A  883 MET cc_start: 0.8191 (tpp) cc_final: 0.7969 (tpt)
REVERT: A  919 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8231 (tt)
REVERT: B  280 GLU cc_start: 0.7971 (pm20) cc_final: 0.7655 (pm20)
REVERT: B  302 MET cc_start: 0.8059 (mmm) cc_final: 0.7771 (mmm)
  outliers start: 21
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1787
  time to fit residues: 21.6983
Evaluate side-chains
  78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0870
   chunk 90 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
A 836 HIS
** A 912 ASN ** 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 = 0.3626 r_free = 0.3626 target = 0.083954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.062182 restraints weight = 24618.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.063909 restraints weight = 13773.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.065028 restraints weight = 9657.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.4396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8498  Z= 0.202
  Angle     :  0.621   9.197  11758  Z= 0.328
  Chirality :  0.042   0.179   1298
  Planarity :  0.004   0.054   1303
  Dihedral  : 23.281 178.830   1618
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 10.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 20.24 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.49 (0.28), residues: 879
  helix:  0.52 (0.33), residues: 269
  sheet:  0.47 (0.42), residues: 167
  loop : -1.18 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.035   0.002   PHE A 804 
 TYR   0.018   0.001   TYR A 485 
 ARG   0.004   0.000   ARG A 734 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8491 (tm-30) cc_final: 0.8119 (tm-30)
REVERT: A  843 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7899 (tt)
REVERT: A  844 LYS cc_start: 0.6620 (mmtt) cc_final: 0.6124 (tttp)
REVERT: A  919 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8210 (tt)
REVERT: B  280 GLU cc_start: 0.7942 (pm20) cc_final: 0.7672 (pm20)
REVERT: B  302 MET cc_start: 0.8007 (mmm) cc_final: 0.7710 (mmm)
REVERT: B  322 MET cc_start: 0.8679 (mtm) cc_final: 0.8082 (mpp)
  outliers start: 18
  outliers final: 11
  residues processed: 85
  average time/residue: 0.1809
  time to fit residues: 22.8088
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  843 LEU
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 56 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.084211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.062107 restraints weight = 24974.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.063894 restraints weight = 13643.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.065055 restraints weight = 9462.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8498  Z= 0.204
  Angle     :  0.624  12.702  11758  Z= 0.329
  Chirality :  0.042   0.180   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.204 178.277   1618
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 21.69 %
    Favored  : 76.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.46 (0.29), residues: 879
  helix:  0.60 (0.33), residues: 269
  sheet:  0.26 (0.41), residues: 168
  loop : -1.09 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.034   0.002   PHE A 804 
 TYR   0.019   0.001   TYR A 485 
 ARG   0.007   0.000   ARG A 838 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 68
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A  568 MET cc_start: 0.8664 (ttm) cc_final: 0.8432 (ttm)
REVERT: A  576 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8141 (tm-30)
REVERT: A  627 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7116 (ttp)
REVERT: A  844 LYS cc_start: 0.6641 (mmtt) cc_final: 0.5987 (tttp)
REVERT: A  883 MET cc_start: 0.8097 (tpt) cc_final: 0.7711 (tpp)
REVERT: A  919 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8303 (tt)
REVERT: B  263 LEU cc_start: 0.8360 (tp) cc_final: 0.8145 (tp)
REVERT: B  280 GLU cc_start: 0.7964 (pm20) cc_final: 0.7745 (pm20)
REVERT: B  302 MET cc_start: 0.8027 (mmm) cc_final: 0.7728 (mmm)
REVERT: B  322 MET cc_start: 0.8671 (mtm) cc_final: 0.8056 (mpp)
  outliers start: 17
  outliers final: 11
  residues processed: 81
  average time/residue: 0.1809
  time to fit residues: 21.3372
Evaluate side-chains
  77 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 92 optimal weight:    5.9990
   chunk 78 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** 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 = 0.3625 r_free = 0.3625 target = 0.083874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.061745 restraints weight = 25219.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.063544 restraints weight = 13833.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.064691 restraints weight = 9602.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8498  Z= 0.219
  Angle     :  0.637  12.078  11758  Z= 0.332
  Chirality :  0.042   0.178   1298
  Planarity :  0.004   0.053   1303
  Dihedral  : 23.199 178.264   1618
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 21.69 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.44 (0.29), residues: 879
  helix:  0.57 (0.33), residues: 269
  sheet:  0.32 (0.42), residues: 168
  loop : -1.06 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.001   HIS A 501 
 PHE   0.033   0.002   PHE A 804 
 TYR   0.019   0.001   TYR A 485 
 ARG   0.005   0.000   ARG A 838 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 62
  time to evaluate  : 0.895 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: A  627 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7152 (ttp)
REVERT: A  844 LYS cc_start: 0.6972 (mmtt) cc_final: 0.5779 (tptt)
REVERT: A  919 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8361 (tt)
REVERT: B  263 LEU cc_start: 0.8414 (tp) cc_final: 0.8120 (tp)
REVERT: B  280 GLU cc_start: 0.7964 (pm20) cc_final: 0.7737 (pm20)
REVERT: B  322 MET cc_start: 0.8710 (mtm) cc_final: 0.8043 (mpp)
  outliers start: 16
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1856
  time to fit residues: 19.9585
Evaluate side-chains
  75 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 73 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 54 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 11 optimal weight:    0.2980
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A 912 ASN ** 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 = 0.3597 r_free = 0.3597 target = 0.082457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.060504 restraints weight = 24915.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.062174 restraints weight = 13999.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.063277 restraints weight = 9903.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.4866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8498  Z= 0.278
  Angle     :  0.679  11.379  11758  Z= 0.353
  Chirality :  0.043   0.179   1298
  Planarity :  0.004   0.052   1303
  Dihedral  : 23.286 178.099   1618
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.30 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.49 (0.28), residues: 879
  helix:  0.43 (0.33), residues: 269
  sheet:  0.52 (0.42), residues: 161
  loop : -1.12 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 317 
 HIS   0.003   0.001   HIS A 795 
 PHE   0.042   0.002   PHE A 804 
 TYR   0.021   0.001   TYR A 485 
 ARG   0.005   0.000   ARG A 838 

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  576 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8195 (tm-30)
REVERT: A  627 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7241 (ttm)
REVERT: A  844 LYS cc_start: 0.7071 (mmtt) cc_final: 0.6005 (tttp)
REVERT: A  919 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8379 (tt)
REVERT: B  263 LEU cc_start: 0.8456 (tp) cc_final: 0.8147 (tp)
REVERT: B  280 GLU cc_start: 0.7920 (pm20) cc_final: 0.7665 (pm20)
REVERT: B  322 MET cc_start: 0.8709 (mtm) cc_final: 0.8071 (mpp)
  outliers start: 19
  outliers final: 15
  residues processed: 76
  average time/residue: 0.1735
  time to fit residues: 19.7351
Evaluate side-chains
  79 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  627 MET
Chi-restraints excluded: chain A residue  686 GLU
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  723 SER
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  788 VAL
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  987 VAL
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue   91 TYR
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  289 LEU
Chi-restraints excluded: chain B residue  350 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 83 optimal weight:   10.0000
   chunk 84 optimal weight:    0.0030
   chunk 45 optimal weight:    0.0870
   chunk 52 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 92 optimal weight:    6.9990
   chunk 81 optimal weight:    6.9990
   chunk 74 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0980
   overall best weight:    0.3368

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

Flipped N/Q/H residues before XYZ refinement:
A 501 HIS
** A 912 ASN ** 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 = 0.3659 r_free = 0.3659 target = 0.085423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.063374 restraints weight = 25027.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.065210 restraints weight = 13560.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.066343 restraints weight = 9364.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8498  Z= 0.170
  Angle     :  0.620  11.255  11758  Z= 0.322
  Chirality :  0.041   0.185   1298
  Planarity :  0.004   0.055   1303
  Dihedral  : 23.123 179.948   1618
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 21.56 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.38 %
    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: -0.27 (0.29), residues: 879
  helix:  0.70 (0.33), residues: 270
  sheet:  0.47 (0.42), residues: 163
  loop : -0.97 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 317 
 HIS   0.003   0.000   HIS A 876 
 PHE   0.018   0.001   PHE A 853 
 TYR   0.020   0.001   TYR A 485 
 ARG   0.005   0.000   ARG A 838 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2572.43 seconds
wall clock time: 45 minutes 44.08 seconds (2744.08 seconds total)