Starting phenix.real_space_refine
on Mon May 19 10:00:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smx_40605/05_2025/8smx_40605.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smx_40605/05_2025/8smx_40605.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8smx_40605/05_2025/8smx_40605.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smx_40605/05_2025/8smx_40605.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smx_40605/05_2025/8smx_40605.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smx_40605/05_2025/8smx_40605.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.123
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 5925 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: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     294      5.49       5
     S      32      5.16       5
     C    7891      2.51       5
     N    2608      2.21       5
     O    3171      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 13998
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 691
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
      Conformer: "B"
        Number of residues, atoms: 85, 687
          Classifications: {'peptide': 85}
          Link IDs: {'PTRANS': 6, 'TRANS': 78}
          bond proxies already assigned to first conformer: 698
    Chain: "L"
      Number of atoms: 1188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 148, 1188
          Classifications: {'peptide': 148}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  12296  SG  CYS K  31      32.756  69.086  46.490  1.00 27.36           S
  ATOM  12446  SG  CYS K  51      31.674  65.517  46.031  1.00 24.79           S
  ATOM  12470  SG  CYS K  54      32.868  67.529  43.025  1.00 27.29           S
  ATOM  12187  SG  CYS K  16      23.703  62.014  53.077  1.00 58.61           S
  ATOM  12205  SG  CYS K  19      21.687  59.882  55.391  1.00 62.50           S
  ATOM  12335  SG  CYS K  36      23.658  62.811  56.830  1.00 42.90           S
  ATOM  12357  SG  CYS K  39      25.492  59.705  55.463  1.00 39.01           S

  Time building chain proxies: 8.13, per 1000 atoms: 0.58
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 130.144, 126.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      32     16.00
     P     294     15.00
     O    3171      8.00
     N    2608      7.00
     C    7891      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 3.15
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 301 "
        pdb="ZN    ZN K 301 " - pdb=" ND1 HIS K  33 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  31 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 301 " - pdb=" SG  CYS K  54 "
      pdb="  ZN K 302 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
      Number of angles added : 9


  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1888

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 12 sheets defined
      64.1% alpha, 4.5% beta
      136 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 5.78
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.611A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.565A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.844A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.593A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.740A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 89
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.508A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.640A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.764A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.538A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 123
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.761A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.579A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.588A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
      removed outlier: 3.585A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.819A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.684A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.559A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
      removed outlier: 3.641A  pdb=" N   ASN G  94 " --> pdb=" O   ASP G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.574A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 122
    Processing helix  chain 'K' and resid 37 through 46
    Processing helix  chain 'K' and resid 58 through 67
      removed outlier: 3.858A  pdb=" N   ARG K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 74 through 84
      removed outlier: 4.158A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   TYR K  84 " --> pdb=" O   ILE K  80 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.917A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 86 through 91
      removed outlier: 3.538A  pdb=" N   ARG L  90 " --> pdb=" O   LEU L  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 98 through 112
      removed outlier: 3.860A  pdb=" N   LEU L 110 " --> pdb=" O   ILE L 106 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   ASP L 111 " --> pdb=" O   ALA L 107 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP L 112 " --> pdb=" O   SER L 108 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 120 through 130
    Processing helix  chain 'L' and resid 130 through 143
      removed outlier: 3.639A  pdb=" N   TYR L 134 " --> pdb=" O   ASP L 130 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.155A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.444A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.800A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.010A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.606A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28
    Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25

    462 hydrogen bonds defined for protein.
    1368 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 4.75

  Time building geometry restraints manager: 3.71 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2974
        1.33 -     1.45: 4495
        1.45 -     1.57: 6762
        1.57 -     1.69: 586
        1.69 -     1.81: 47
  Bond restraints: 14864
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.460 -0.038 3.00e-02 1.11e+03 1.60e+00
  bond pdb=" CG  PRO L  61 "
       pdb=" CD  PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.512  1.478  0.034 2.70e-02 1.37e+03 1.57e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.457 -0.035 3.00e-02 1.11e+03 1.39e+00
  bond pdb=" CB  ARG A 129 "
       pdb=" CG  ARG A 129 "
    ideal  model  delta    sigma   weight residual
    1.520  1.550 -0.030 3.00e-02 1.11e+03 1.01e+00
  bond pdb=" CB  THR K  66 "
       pdb=" CG2 THR K  66 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.17e-01
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 20929
        1.77 -     3.54: 395
        3.54 -     5.31: 22
        5.31 -     7.08: 5
        7.08 -     8.85: 2
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" CB  MET B  84 "
        pdb=" CG  MET B  84 "
        pdb=" SD  MET B  84 "
      ideal   model   delta    sigma   weight residual
     112.70  121.55   -8.85 3.00e+00 1.11e-01 8.71e+00
  angle pdb=" C3'  DG J -70 "
        pdb=" C2'  DG J -70 "
        pdb=" C1'  DG J -70 "
      ideal   model   delta    sigma   weight residual
     101.60  105.56   -3.96 1.50e+00 4.44e-01 6.98e+00
  angle pdb=" C   LEU L  89 "
        pdb=" N   ARG L  90 "
        pdb=" CA  ARG L  90 "
      ideal   model   delta    sigma   weight residual
     122.58  117.16    5.42 2.07e+00 2.33e-01 6.85e+00
  angle pdb=" N   GLY D 104 "
        pdb=" CA  GLY D 104 "
        pdb=" C   GLY D 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.96   -5.78 2.37e+00 1.78e-01 5.94e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  118.62   -5.44 2.37e+00 1.78e-01 5.26e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.13: 6796
       35.13 -    70.26: 1411
       70.26 -   105.39: 21
      105.39 -   140.51: 0
      140.51 -   175.64: 2
  Dihedral angle restraints: 8230
    sinusoidal: 5306
      harmonic: 2924
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.36  175.64     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   66.14  153.86     1      3.50e+01 8.16e-04 1.49e+01
  dihedral pdb=" CA  PHE E  84 "
           pdb=" C   PHE E  84 "
           pdb=" N   GLN E  85 "
           pdb=" CA  GLN E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.10   16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1636
       0.030 -    0.061: 556
       0.061 -    0.091: 160
       0.091 -    0.121: 60
       0.121 -    0.151: 7
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CG  LEU L 103 "
            pdb=" CB  LEU L 103 "
            pdb=" CD1 LEU L 103 "
            pdb=" CD2 LEU L 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.74    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" CA  LEU E  65 "
            pdb=" N   LEU E  65 "
            pdb=" C   LEU E  65 "
            pdb=" CB  LEU E  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.56e-01
  chirality pdb=" CA  ILE L  54 "
            pdb=" N   ILE L  54 "
            pdb=" C   ILE L  54 "
            pdb=" CB  ILE L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.026 2.00e-02 2.50e+03   1.14e-02 3.60e+00
        pdb=" N9   DA I -35 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.024 2.00e-02 2.50e+03   1.03e-02 3.20e+00
        pdb=" N9   DG I  47 "    0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  17 "    0.024 2.00e-02 2.50e+03   1.06e-02 3.07e+00
        pdb=" N9   DA I  17 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8   DA I  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  17 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  17 "    0.006 2.00e-02 2.50e+03
        pdb=" N1   DA I  17 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  17 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  17 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  17 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2062
        2.77 -     3.30: 11830
        3.30 -     3.83: 25259
        3.83 -     4.37: 31139
        4.37 -     4.90: 45796
  Nonbonded interactions: 116086
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.236 2.496
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" NZ  LYS D 116 "
            pdb=" O   ALA K  47 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.294 2.560
  ... (remaining 116081 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.17 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.960
  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:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.140
  Process input model:                     37.200
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.147
  Angle     :  0.567   8.854  21368  Z= 0.333
  Chirality :  0.036   0.151   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 26.376 175.642   6336
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.43 (0.27), residues: 983
  helix:  1.97 (0.21), residues: 628
  sheet: -0.51 (0.92), residues: 24
  loop : -0.96 (0.31), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K  77 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.010   0.001   TYR D 121 
 ARG   0.004   0.000   ARG B  45 

Details of bonding type rmsd
  link_TRANS           : bond        0.00193 (    2)
  link_TRANS           : angle       0.44603 (    6)
  hydrogen bonds       : bond        0.11293 (  811)
  hydrogen bonds       : angle       3.76124 ( 2062)
  metal coordination   : bond        0.00466 (    8)
  metal coordination   : angle       1.84038 (    9)
  covalent geometry    : bond        0.00314 (14864)
  covalent geometry    : angle       0.56577 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.997 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7865 (pttm) cc_final: 0.7286 (ptpp)
REVERT: D   35 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8128 (mt-10)
REVERT: D  116 LYS cc_start: 0.7954 (ttmt) cc_final: 0.7592 (mtmm)
REVERT: E   53 ARG cc_start: 0.8258 (ttm170) cc_final: 0.8015 (ttm170)
REVERT: H   54 ILE cc_start: 0.9102 (tt) cc_final: 0.8879 (tt)
REVERT: H  112 SER cc_start: 0.9103 (t) cc_final: 0.8481 (m)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.3800
  time to fit residues: 49.9428
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 37 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 110 optimal weight:   40.0000
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.165257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.115751 restraints weight = 18520.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.17
r_work: 0.2775 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2775
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2725
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2725 r_free = 0.2725    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2725
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.0514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14874  Z= 0.193
  Angle     :  0.577   7.021  21368  Z= 0.338
  Chirality :  0.037   0.148   2419
  Planarity :  0.005   0.040   1688
  Dihedral  : 29.348 176.256   4332
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 3.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  4.21 %
    Favored  : 95.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.45 (0.26), residues: 983
  helix:  2.00 (0.21), residues: 634
  sheet: -0.83 (0.88), residues: 24
  loop : -1.03 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  93 
 HIS   0.005   0.001   HIS A 113 
 PHE   0.011   0.002   PHE F  61 
 TYR   0.018   0.001   TYR G  50 
 ARG   0.005   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00158 (    2)
  link_TRANS           : angle       0.54567 (    6)
  hydrogen bonds       : bond        0.05702 (  811)
  hydrogen bonds       : angle       3.03448 ( 2062)
  metal coordination   : bond        0.00533 (    8)
  metal coordination   : angle       2.00395 (    9)
  covalent geometry    : bond        0.00443 (14864)
  covalent geometry    : angle       0.57610 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 1.260 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7839 (mt-10)
REVERT: C  118 LYS cc_start: 0.7887 (pttm) cc_final: 0.7127 (ptpp)
REVERT: D   35 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7881 (mt-10)
REVERT: H   54 ILE cc_start: 0.9263 (tt) cc_final: 0.9033 (tt)
REVERT: H  112 SER cc_start: 0.9109 (t) cc_final: 0.8453 (m)
REVERT: L   78 ILE cc_start: 0.6188 (mp) cc_final: 0.5761 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.3660
  time to fit residues: 47.4952
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 1.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9990
   chunk 101 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 106 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 29 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.168109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.119515 restraints weight = 19529.081|
|-----------------------------------------------------------------------------|
r_work (start): 0.3197 rms_B_bonded: 1.03
r_work: 0.2922 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.2922
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2717
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2717 r_free = 0.2717    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2717
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.0549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14874  Z= 0.181
  Angle     :  0.567   7.169  21368  Z= 0.333
  Chirality :  0.036   0.142   2419
  Planarity :  0.004   0.041   1688
  Dihedral  : 29.332 176.329   4332
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  5.84 %
    Favored  : 93.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.51 (0.26), residues: 983
  helix:  2.06 (0.21), residues: 634
  sheet: -0.77 (0.88), residues: 24
  loop : -1.03 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.002   PHE F  61 
 TYR   0.011   0.001   TYR G  50 
 ARG   0.003   0.000   ARG A 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00087 (    2)
  link_TRANS           : angle       0.43330 (    6)
  hydrogen bonds       : bond        0.05511 (  811)
  hydrogen bonds       : angle       3.00563 ( 2062)
  metal coordination   : bond        0.00501 (    8)
  metal coordination   : angle       1.95689 (    9)
  covalent geometry    : bond        0.00412 (14864)
  covalent geometry    : angle       0.56559 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 1.022 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7825 (mt-10)
REVERT: C  118 LYS cc_start: 0.7840 (pttm) cc_final: 0.7133 (ptpp)
REVERT: D   35 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7792 (mt-10)
REVERT: H   54 ILE cc_start: 0.9289 (tt) cc_final: 0.9047 (tt)
REVERT: H  112 SER cc_start: 0.9140 (t) cc_final: 0.8475 (m)
REVERT: L   42 ASP cc_start: 0.7434 (m-30) cc_final: 0.7094 (m-30)
REVERT: L   59 ASP cc_start: 0.6543 (p0) cc_final: 0.6100 (p0)
REVERT: L   78 ILE cc_start: 0.5996 (mp) cc_final: 0.5639 (tp)
REVERT: L  132 ASP cc_start: 0.5306 (m-30) cc_final: 0.4912 (p0)
  outliers start: 4
  outliers final: 3
  residues processed: 102
  average time/residue: 0.3633
  time to fit residues: 49.6544
Evaluate side-chains
  95 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain D residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0020
   chunk 58 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    0.7980
   chunk 120 optimal weight:    6.9990
   overall best weight:    0.6790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.168803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.122686 restraints weight = 24502.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3238 rms_B_bonded: 1.48
r_work: 0.2850 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.0565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14874  Z= 0.155
  Angle     :  0.554   7.268  21368  Z= 0.328
  Chirality :  0.035   0.137   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.313 176.196   4332
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  6.89 %
    Favored  : 92.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.62 (0.27), residues: 983
  helix:  2.15 (0.21), residues: 634
  sheet: -0.79 (0.89), residues: 24
  loop : -1.01 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K  61 
 HIS   0.002   0.001   HIS A 113 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.002   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00059 (    2)
  link_TRANS           : angle       0.51570 (    6)
  hydrogen bonds       : bond        0.05252 (  811)
  hydrogen bonds       : angle       2.99212 ( 2062)
  metal coordination   : bond        0.00489 (    8)
  metal coordination   : angle       1.84316 (    9)
  covalent geometry    : bond        0.00335 (14864)
  covalent geometry    : angle       0.55289 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 94
  time to evaluate  : 1.135 
Fit side-chains
REVERT: B   74 GLU cc_start: 0.8242 (mt-10) cc_final: 0.8004 (mt-10)
REVERT: C  118 LYS cc_start: 0.7787 (pttm) cc_final: 0.7096 (ptpp)
REVERT: D   35 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7842 (mt-10)
REVERT: H   54 ILE cc_start: 0.9299 (tt) cc_final: 0.9048 (tt)
REVERT: H  112 SER cc_start: 0.9128 (t) cc_final: 0.8475 (m)
REVERT: K   60 SER cc_start: 0.8583 (t) cc_final: 0.8297 (m)
REVERT: L   78 ILE cc_start: 0.5973 (mp) cc_final: 0.5586 (tp)
  outliers start: 4
  outliers final: 2
  residues processed: 97
  average time/residue: 0.3679
  time to fit residues: 47.3162
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 37 optimal weight:    0.2980
   chunk 116 optimal weight:    8.9990
   chunk 109 optimal weight:    0.0770
   chunk 115 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   overall best weight:    0.5338

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.160043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.113289 restraints weight = 23873.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 1.51
r_work: 0.2874 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.0588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14874  Z= 0.148
  Angle     :  0.547   6.923  21368  Z= 0.324
  Chirality :  0.035   0.132   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.278 176.357   4332
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.35 %
    Allowed  :  7.24 %
    Favored  : 92.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.71 (0.27), residues: 983
  helix:  2.23 (0.21), residues: 634
  sheet: -0.70 (0.90), residues: 24
  loop : -0.98 (0.31), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K  61 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.009   0.001   PHE F  61 
 TYR   0.008   0.001   TYR B  51 
 ARG   0.004   0.000   ARG A 129 

Details of bonding type rmsd
  link_TRANS           : bond        0.00152 (    2)
  link_TRANS           : angle       0.86080 (    6)
  hydrogen bonds       : bond        0.05072 (  811)
  hydrogen bonds       : angle       2.94205 ( 2062)
  metal coordination   : bond        0.00501 (    8)
  metal coordination   : angle       1.80303 (    9)
  covalent geometry    : bond        0.00316 (14864)
  covalent geometry    : angle       0.54541 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 93
  time to evaluate  : 0.969 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7774 (pttm) cc_final: 0.7085 (ptpp)
REVERT: D   35 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7878 (mt-10)
REVERT: H   54 ILE cc_start: 0.9293 (tt) cc_final: 0.9052 (tt)
REVERT: H  112 SER cc_start: 0.9139 (t) cc_final: 0.8470 (m)
REVERT: K   60 SER cc_start: 0.8581 (t) cc_final: 0.8300 (m)
REVERT: L   78 ILE cc_start: 0.5959 (mp) cc_final: 0.5608 (tp)
  outliers start: 3
  outliers final: 1
  residues processed: 95
  average time/residue: 0.3712
  time to fit residues: 47.0509
Evaluate side-chains
  92 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 91
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 120 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D 109 HIS
H  47 GLN
L  77 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.149707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.112442 restraints weight = 24652.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 1.99
r_work: 0.2578 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.2578
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2542
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2542 r_free = 0.2542    target_work(ls_wunit_k1) = 0.072         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2542
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.0895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  14874  Z= 0.297
  Angle     :  0.647   7.560  21368  Z= 0.373
  Chirality :  0.042   0.161   2419
  Planarity :  0.005   0.048   1688
  Dihedral  : 29.654 176.710   4332
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  8.64 %
    Favored  : 90.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.06 (0.26), residues: 983
  helix:  1.72 (0.20), residues: 636
  sheet: -0.71 (0.88), residues: 24
  loop : -1.29 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.007   0.002   HIS A 113 
 PHE   0.018   0.003   PHE D  65 
 TYR   0.017   0.002   TYR D 121 
 ARG   0.006   0.001   ARG B  45 

Details of bonding type rmsd
  link_TRANS           : bond        0.00017 (    2)
  link_TRANS           : angle       0.79914 (    6)
  hydrogen bonds       : bond        0.07096 (  811)
  hydrogen bonds       : angle       3.17160 ( 2062)
  metal coordination   : bond        0.00743 (    8)
  metal coordination   : angle       2.30544 (    9)
  covalent geometry    : bond        0.00709 (14864)
  covalent geometry    : angle       0.64583 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 1.027 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7932 (pttm) cc_final: 0.7100 (ptpp)
REVERT: D   35 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: E  133 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8343 (mt-10)
REVERT: G   95 LYS cc_start: 0.9071 (ttmt) cc_final: 0.8712 (ttpt)
REVERT: H   54 ILE cc_start: 0.9270 (tt) cc_final: 0.9027 (tt)
REVERT: H  112 SER cc_start: 0.9149 (t) cc_final: 0.8502 (m)
  outliers start: 4
  outliers final: 3
  residues processed: 100
  average time/residue: 0.3546
  time to fit residues: 47.4437
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 4 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 71 optimal weight:    0.7980
   chunk 44 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 88 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.163394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.122776 restraints weight = 24812.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 1.91
r_work: 0.2639 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2587
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.0788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14874  Z= 0.154
  Angle     :  0.586   8.174  21368  Z= 0.345
  Chirality :  0.037   0.138   2419
  Planarity :  0.005   0.041   1688
  Dihedral  : 29.549 175.409   4332
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.46 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.40 (0.26), residues: 983
  helix:  2.00 (0.21), residues: 636
  sheet: -0.67 (0.89), residues: 24
  loop : -1.18 (0.30), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.004   0.001   HIS A 113 
 PHE   0.010   0.001   PHE F  61 
 TYR   0.009   0.001   TYR B  51 
 ARG   0.004   0.000   ARG A 131 

Details of bonding type rmsd
  link_TRANS           : bond        0.00213 (    2)
  link_TRANS           : angle       0.76741 (    6)
  hydrogen bonds       : bond        0.05609 (  811)
  hydrogen bonds       : angle       3.06710 ( 2062)
  metal coordination   : bond        0.00411 (    8)
  metal coordination   : angle       1.87735 (    9)
  covalent geometry    : bond        0.00331 (14864)
  covalent geometry    : angle       0.58493 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 1.164 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7890 (pttm) cc_final: 0.7061 (ptpp)
REVERT: D   35 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7909 (mt-10)
REVERT: H   54 ILE cc_start: 0.9259 (tt) cc_final: 0.9007 (tt)
REVERT: H  112 SER cc_start: 0.9097 (t) cc_final: 0.8454 (m)
REVERT: L   78 ILE cc_start: 0.5841 (mp) cc_final: 0.5582 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 99
  average time/residue: 0.3686
  time to fit residues: 48.7974
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 87 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.151751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.114939 restraints weight = 24232.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 2.50
r_work (final): 0.3143
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3154
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3154 r_free = 0.3154    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3154
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.0904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  14874  Z= 0.254
  Angle     :  0.616   7.924  21368  Z= 0.357
  Chirality :  0.040   0.156   2419
  Planarity :  0.005   0.041   1688
  Dihedral  : 29.601 175.435   4332
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.51 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.12 (0.26), residues: 983
  helix:  1.80 (0.20), residues: 638
  sheet: -0.79 (0.88), residues: 24
  loop : -1.34 (0.30), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.007   0.001   HIS A 113 
 PHE   0.015   0.002   PHE D  65 
 TYR   0.014   0.002   TYR D 121 
 ARG   0.005   0.001   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00016 (    2)
  link_TRANS           : angle       0.79430 (    6)
  hydrogen bonds       : bond        0.06542 (  811)
  hydrogen bonds       : angle       3.11041 ( 2062)
  metal coordination   : bond        0.00623 (    8)
  metal coordination   : angle       2.25883 (    9)
  covalent geometry    : bond        0.00601 (14864)
  covalent geometry    : angle       0.61459 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 1.009 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8255 (tmt170) cc_final: 0.8027 (tmt170)
REVERT: C  118 LYS cc_start: 0.7945 (pttm) cc_final: 0.7244 (ptpp)
REVERT: D   35 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7851 (mt-10)
REVERT: H   54 ILE cc_start: 0.9100 (tt) cc_final: 0.8868 (tt)
REVERT: H  112 SER cc_start: 0.9035 (t) cc_final: 0.8443 (m)
  outliers start: 5
  outliers final: 4
  residues processed: 98
  average time/residue: 0.3694
  time to fit residues: 48.2971
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    0.2980
   chunk 101 optimal weight:    0.8980
   chunk 116 optimal weight:    9.9990
   chunk 86 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0770
   chunk 78 optimal weight:    2.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.165971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.124296 restraints weight = 30152.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 2.46
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3155
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3155 r_free = 0.3155    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3155
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.0777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14874  Z= 0.150
  Angle     :  0.559   7.191  21368  Z= 0.331
  Chirality :  0.036   0.134   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.464 175.718   4332
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.05 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.52 (0.27), residues: 983
  helix:  2.10 (0.21), residues: 638
  sheet: -0.80 (0.90), residues: 24
  loop : -1.16 (0.30), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.003   0.001   HIS L  75 
 PHE   0.008   0.001   PHE L  62 
 TYR   0.010   0.001   TYR F  51 
 ARG   0.003   0.000   ARG K  68 

Details of bonding type rmsd
  link_TRANS           : bond        0.00085 (    2)
  link_TRANS           : angle       0.68020 (    6)
  hydrogen bonds       : bond        0.05266 (  811)
  hydrogen bonds       : angle       2.92302 ( 2062)
  metal coordination   : bond        0.00545 (    8)
  metal coordination   : angle       1.82173 (    9)
  covalent geometry    : bond        0.00320 (14864)
  covalent geometry    : angle       0.55769 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 1.121 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8138 (tmt170) cc_final: 0.7932 (tmt170)
REVERT: C  118 LYS cc_start: 0.7913 (pttm) cc_final: 0.7206 (ptpp)
REVERT: D   35 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7883 (mt-10)
REVERT: H   54 ILE cc_start: 0.9096 (tt) cc_final: 0.8834 (tt)
REVERT: H  112 SER cc_start: 0.9116 (t) cc_final: 0.8472 (m)
  outliers start: 5
  outliers final: 5
  residues processed: 101
  average time/residue: 0.3765
  time to fit residues: 50.9270
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 117 optimal weight:    0.4980
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 99 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.154405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.117910 restraints weight = 34549.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3183 rms_B_bonded: 2.65
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3186
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3186 r_free = 0.3186    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3186
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.0826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14874  Z= 0.191
  Angle     :  0.570   7.174  21368  Z= 0.334
  Chirality :  0.037   0.144   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.428 175.554   4332
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 10.40 %
    Favored  : 89.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.48 (0.26), residues: 983
  helix:  2.08 (0.21), residues: 638
  sheet: -0.66 (0.91), residues: 24
  loop : -1.22 (0.30), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K  61 
 HIS   0.004   0.001   HIS L  75 
 PHE   0.011   0.002   PHE F  61 
 TYR   0.010   0.001   TYR D 121 
 ARG   0.003   0.000   ARG C  35 

Details of bonding type rmsd
  link_TRANS           : bond        0.00061 (    2)
  link_TRANS           : angle       0.67307 (    6)
  hydrogen bonds       : bond        0.05560 (  811)
  hydrogen bonds       : angle       2.95800 ( 2062)
  metal coordination   : bond        0.00481 (    8)
  metal coordination   : angle       1.87137 (    9)
  covalent geometry    : bond        0.00438 (14864)
  covalent geometry    : angle       0.56846 (21353)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 1.097 
Fit side-chains
REVERT: C  118 LYS cc_start: 0.7968 (pttm) cc_final: 0.7251 (ptpp)
REVERT: H   54 ILE cc_start: 0.9093 (tt) cc_final: 0.8864 (tt)
REVERT: H  112 SER cc_start: 0.9055 (t) cc_final: 0.8429 (m)
  outliers start: 5
  outliers final: 5
  residues processed: 99
  average time/residue: 0.3674
  time to fit residues: 48.3697
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   71 VAL
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain L residue   52 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 55 optimal weight:    0.8980
   chunk 43 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0470
   chunk 22 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.7280

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.159921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.115981 restraints weight = 19508.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 1.26
r_work: 0.2739 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2658
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2658 r_free = 0.2658    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2658
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.0817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14874  Z= 0.156
  Angle     :  0.574  16.250  21368  Z= 0.333
  Chirality :  0.036   0.176   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.410 175.351   4332
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  : 11.10 %
    Favored  : 88.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  1.56 (0.26), residues: 983
  helix:  2.16 (0.21), residues: 638
  sheet: -0.66 (0.91), residues: 24
  loop : -1.21 (0.30), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K  61 
 HIS   0.015   0.001   HIS L  75 
 PHE   0.010   0.001   PHE F  61 
 TYR   0.011   0.001   TYR L  74 
 ARG   0.003   0.000   ARG C  32 

Details of bonding type rmsd
  link_TRANS           : bond        0.00085 (    2)
  link_TRANS           : angle       0.71714 (    6)
  hydrogen bonds       : bond        0.05255 (  811)
  hydrogen bonds       : angle       2.95044 ( 2062)
  metal coordination   : bond        0.00480 (    8)
  metal coordination   : angle       1.81598 (    9)
  covalent geometry    : bond        0.00340 (14864)
  covalent geometry    : angle       0.57246 (21353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5881.77 seconds
wall clock time: 102 minutes 24.49 seconds (6144.49 seconds total)