Starting phenix.real_space_refine
on Thu Jul 31 16:33:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smz_40607/07_2025/8smz_40607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smz_40607/07_2025/8smz_40607.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/8smz_40607/07_2025/8smz_40607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2025/8smz_40607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2025/8smz_40607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smz_40607/07_2025/8smz_40607.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=   0.105
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 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 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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      34.493  67.206  42.369  1.00 54.60           S
  ATOM  12446  SG  CYS K  51      32.878  63.788  42.788  1.00 53.45           S
  ATOM  12470  SG  CYS K  54      34.673  64.732  39.472  1.00 59.59           S
  ATOM  12187  SG  CYS K  16      22.650  64.083  47.853  1.00 61.09           S
  ATOM  12205  SG  CYS K  19      20.144  62.240  49.932  1.00 66.08           S
  ATOM  12335  SG  CYS K  36      22.147  65.128  51.321  1.00 55.44           S
  ATOM  12357  SG  CYS K  39      23.894  61.698  50.708  1.00 56.03           S

  Time building chain proxies: 9.16, per 1000 atoms: 0.65
  Number of scatterers: 13998
  At special positions: 0
  Unit cell: (108.896, 128.816, 127.488, 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: 3.24
  Conformation dependent library (CDL) restraints added in 1.4 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  16 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 302 " - pdb=" SG  CYS K  39 "
      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:
      42 helices and 11 sheets defined
      64.8% alpha, 4.2% beta
      136 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 6.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.502A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.714A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.588A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.967A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.906A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.597A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
      removed outlier: 3.560A  pdb=" N   ARG C  20 " --> pdb=" O   THR C  16 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.608A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.545A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.795A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.564A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.563A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.894A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS D 109 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.508A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.512A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.863A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.526A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.610A  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
      removed outlier: 3.625A  pdb=" N   ALA G  86 " --> pdb=" O   HIS G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.541A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.592A  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 47
    Processing helix  chain 'K' and resid 58 through 69
      removed outlier: 4.088A  pdb=" N   THR K  62 " --> pdb=" O   VAL K  58 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ARG K  63 " --> pdb=" O   SER K  59 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG K  68 " --> pdb=" O   TYR K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.899A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 91
      removed outlier: 3.961A  pdb=" N   CYS K  88 " --> pdb=" O   TYR K  84 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LYS K  89 " --> pdb=" O   PRO K  85 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU K  90 " --> pdb=" O   ARG K  86 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 1 through 16
    Processing helix  chain 'L' and resid 98 through 112
    Processing helix  chain 'L' and resid 120 through 130
      removed outlier: 4.444A  pdb=" N   ALA L 124 " --> pdb=" O   VAL L 120 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG L 125 " --> pdb=" O   PRO L 121 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 130 through 146
      removed outlier: 3.728A  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: 6.952A  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: 7.328A  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: 6.767A  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: 7.302A  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: 7.899A  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 'K' and resid 26 through 28
    Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24

    461 hydrogen bonds defined for protein.
    1365 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      349 hydrogen bonds
      694 hydrogen bond angles
      0 basepair planarities
      136 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 4.90

  Time building geometry restraints manager: 3.92 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3294
        1.34 -     1.46: 4482
        1.46 -     1.58: 6455
        1.58 -     1.70: 586
        1.70 -     1.82: 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  1.462 -0.040 3.00e-02 1.11e+03 1.76e+00
  bond pdb=" C3'  DG J  20 "
       pdb=" O3'  DG J  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.456 -0.034 3.00e-02 1.11e+03 1.27e+00
  bond pdb=" C3'  DA J -73 "
       pdb=" C2'  DA J -73 "
    ideal  model  delta    sigma   weight residual
    1.525  1.546 -0.021 2.00e-02 2.50e+03 1.12e+00
  bond pdb=" CB  MET B  84 "
       pdb=" CG  MET B  84 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 3.00e-02 1.11e+03 1.10e+00
  bond pdb=" CG  PRO L  61 "
       pdb=" CD  PRO L  61 "
    ideal  model  delta    sigma   weight residual
    1.512  1.485  0.027 2.70e-02 1.37e+03 1.02e+00
  ... (remaining 14859 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 20605
        1.37 -     2.74: 681
        2.74 -     4.10: 48
        4.10 -     5.47: 13
        5.47 -     6.84: 6
  Bond angle restraints: 21353
  Sorted by residual:
  angle pdb=" C   ASN L   7 "
        pdb=" N   LYS L   8 "
        pdb=" CA  LYS L   8 "
      ideal   model   delta    sigma   weight residual
     120.44  117.21    3.23 1.30e+00 5.92e-01 6.17e+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  118.89   -5.71 2.37e+00 1.78e-01 5.81e+00
  angle pdb=" CB  LYS L   8 "
        pdb=" CG  LYS L   8 "
        pdb=" CD  LYS L   8 "
      ideal   model   delta    sigma   weight residual
     111.30  116.82   -5.52 2.30e+00 1.89e-01 5.76e+00
  angle pdb=" CB  LEU L  86 "
        pdb=" CG  LEU L  86 "
        pdb=" CD2 LEU L  86 "
      ideal   model   delta    sigma   weight residual
     110.70  103.86    6.84 3.00e+00 1.11e-01 5.20e+00
  angle pdb=" C3'  DA J -73 "
        pdb=" C2'  DA J -73 "
        pdb=" C1'  DA J -73 "
      ideal   model   delta    sigma   weight residual
     101.60  104.69   -3.09 1.50e+00 4.44e-01 4.23e+00
  ... (remaining 21348 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.50: 6746
       34.50 -    69.00: 1457
       69.00 -   103.50: 25
      103.50 -   138.00: 0
      138.00 -   172.50: 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   47.50  172.50     1      3.50e+01 8.16e-04 1.56e+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   68.78  151.22     1      3.50e+01 8.16e-04 1.47e+01
  dihedral pdb=" CA  ILE L  78 "
           pdb=" C   ILE L  78 "
           pdb=" N   ASN L  79 "
           pdb=" CA  ASN L  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.83   17.17     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 8227 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1868
       0.042 -    0.083: 463
       0.083 -    0.125: 79
       0.125 -    0.167: 7
       0.167 -    0.208: 2
  Chirality restraints: 2419
  Sorted by residual:
  chirality pdb=" CG  LEU L  86 "
            pdb=" CB  LEU L  86 "
            pdb=" CD1 LEU L  86 "
            pdb=" CD2 LEU L  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.80    0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CB  ILE L 123 "
            pdb=" CA  ILE L 123 "
            pdb=" CG1 ILE L 123 "
            pdb=" CG2 ILE L 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  ILE L  84 "
            pdb=" N   ILE L  84 "
            pdb=" C   ILE L  84 "
            pdb=" CB  ILE L  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.83e-01
  ... (remaining 2416 not shown)

  Planarity restraints: 1690
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS L  75 "   -0.033 5.00e-02 4.00e+02   5.01e-02 4.02e+00
        pdb=" N   PRO L  76 "    0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO L  76 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO L  76 "   -0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "   -0.028 2.00e-02 2.50e+03   1.15e-02 3.97e+00
        pdb=" N9   DG I  47 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "   -0.009 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 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "   -0.027 2.00e-02 2.50e+03   1.17e-02 3.78e+00
        pdb=" N9   DA I -35 "    0.025 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "   -0.010 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
  ... (remaining 1687 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1902
        2.76 -     3.30: 11924
        3.30 -     3.83: 25122
        3.83 -     4.37: 31196
        4.37 -     4.90: 45644
  Nonbonded interactions: 115788
  Sorted by model distance:
  nonbonded pdb=" N4   DC I  21 "
            pdb=" O6   DG J -21 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR L  45 "
            pdb=" O   TYR L  74 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OE2 GLU C  61 "
            pdb=" NH2 ARG K  63 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.294 2.496
  ... (remaining 115783 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:             1.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.610
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     41.230
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.070
  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:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  14874  Z= 0.168
  Angle     :  0.576   6.842  21368  Z= 0.339
  Chirality :  0.037   0.208   2419
  Planarity :  0.005   0.050   1688
  Dihedral  : 26.569 172.502   6336
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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:  1.15 (0.27), residues: 983
  helix:  1.95 (0.21), residues: 621
  sheet: -0.29 (0.99), residues: 23
  loop : -1.48 (0.30), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP L 141 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.012   0.002   PHE L  69 
 TYR   0.014   0.001   TYR G  50 
 ARG   0.007   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00115 (    2)
  link_TRANS           : angle       0.60516 (    6)
  hydrogen bonds       : bond        0.10275 (  810)
  hydrogen bonds       : angle       3.97434 ( 2059)
  metal coordination   : bond        0.02492 (    8)
  metal coordination   : angle       3.18961 (    9)
  covalent geometry    : bond        0.00373 (14864)
  covalent geometry    : angle       0.57224 (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
  112 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 1.105 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7661 (t0) cc_final: 0.7141 (t0)
REVERT: C   36 LYS cc_start: 0.8450 (mttm) cc_final: 0.8169 (mmmm)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.3688
  time to fit residues: 55.0935
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 95 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9990
   chunk 110 optimal weight:    8.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.175710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118462 restraints weight = 18947.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.51
r_work: 0.3031 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2742
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2742 r_free = 0.2742    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2742
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.0617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14874  Z= 0.161
  Angle     :  0.549   7.534  21368  Z= 0.323
  Chirality :  0.035   0.150   2419
  Planarity :  0.004   0.045   1688
  Dihedral  : 29.331 173.529   4332
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.44 %
    Favored  : 94.98 %
  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:  1.58 (0.27), residues: 983
  helix:  2.30 (0.21), residues: 624
  sheet: -0.02 (1.02), residues: 23
  loop : -1.41 (0.30), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 141 
 HIS   0.005   0.001   HIS K  65 
 PHE   0.007   0.001   PHE F  61 
 TYR   0.012   0.001   TYR G  50 
 ARG   0.005   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00042 (    2)
  link_TRANS           : angle       0.49238 (    6)
  hydrogen bonds       : bond        0.05130 (  810)
  hydrogen bonds       : angle       3.19663 ( 2059)
  metal coordination   : bond        0.01208 (    8)
  metal coordination   : angle       2.86573 (    9)
  covalent geometry    : bond        0.00357 (14864)
  covalent geometry    : angle       0.54593 (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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7838 (t0) cc_final: 0.7363 (t0)
  outliers start: 5
  outliers final: 3
  residues processed: 102
  average time/residue: 0.3622
  time to fit residues: 49.5077
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 97
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   11 SER
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 101 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   chunk 120 optimal weight:   10.0000
   chunk 106 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    0.4980
   chunk 75 optimal weight:    4.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.173996 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.115652 restraints weight = 20245.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3017 rms_B_bonded: 1.53
r_work: 0.2757 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.0800

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= 0.162
  Angle     :  0.535   6.310  21368  Z= 0.317
  Chirality :  0.035   0.128   2419
  Planarity :  0.004   0.046   1688
  Dihedral  : 29.286 173.455   4332
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  6.78 %
    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:  1.64 (0.27), residues: 983
  helix:  2.38 (0.21), residues: 625
  sheet:  0.11 (1.03), residues: 23
  loop : -1.45 (0.29), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP L 141 
 HIS   0.016   0.001   HIS L  75 
 PHE   0.008   0.001   PHE F  61 
 TYR   0.010   0.001   TYR D 121 
 ARG   0.005   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00076 (    2)
  link_TRANS           : angle       0.29239 (    6)
  hydrogen bonds       : bond        0.04963 (  810)
  hydrogen bonds       : angle       3.10576 ( 2059)
  metal coordination   : bond        0.00972 (    8)
  metal coordination   : angle       2.77710 (    9)
  covalent geometry    : bond        0.00363 (14864)
  covalent geometry    : angle       0.53244 (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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7906 (t0) cc_final: 0.7471 (t0)
  outliers start: 5
  outliers final: 4
  residues processed: 99
  average time/residue: 0.3493
  time to fit residues: 46.9993
Evaluate side-chains
  96 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 92
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 76 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 16 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 120 optimal weight:    0.3980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
K  65 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.176382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.119687 restraints weight = 25289.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 1.77
r_work: 0.2959 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2716
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2716 r_free = 0.2716    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 = 0.2716 r_free = 0.2716    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2716
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.0838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14874  Z= 0.149
  Angle     :  0.528   7.696  21368  Z= 0.314
  Chirality :  0.034   0.124   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.263 173.496   4332
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.53 %
    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:  1.72 (0.27), residues: 983
  helix:  2.45 (0.21), residues: 625
  sheet:  0.11 (1.02), residues: 23
  loop : -1.45 (0.29), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  33 
 HIS   0.003   0.001   HIS K  65 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.009   0.001   TYR D 121 
 ARG   0.004   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00085 (    2)
  link_TRANS           : angle       0.32984 (    6)
  hydrogen bonds       : bond        0.04789 (  810)
  hydrogen bonds       : angle       3.06938 ( 2059)
  metal coordination   : bond        0.00798 (    8)
  metal coordination   : angle       2.73317 (    9)
  covalent geometry    : bond        0.00327 (14864)
  covalent geometry    : angle       0.52555 (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: 5
    poor density    : 93
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7930 (t0) cc_final: 0.7516 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 96
  average time/residue: 0.3607
  time to fit residues: 46.9503
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 116 optimal weight:    5.9990
   chunk 109 optimal weight:   20.0000
   chunk 115 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 88 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3895 r_free = 0.3895 target = 0.172346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.115091 restraints weight = 24407.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.74
r_work: 0.2914 rms_B_bonded: 3.79 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.0851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  14874  Z= 0.188
  Angle     :  0.547   6.612  21368  Z= 0.322
  Chirality :  0.036   0.132   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.341 172.901   4332
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.11 %
    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:  1.58 (0.27), residues: 983
  helix:  2.35 (0.21), residues: 626
  sheet:  0.20 (1.03), residues: 23
  loop : -1.54 (0.29), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 
 PHE   0.011   0.002   PHE A  78 
 TYR   0.010   0.001   TYR D 121 
 ARG   0.004   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00034 (    2)
  link_TRANS           : angle       0.34542 (    6)
  hydrogen bonds       : bond        0.05364 (  810)
  hydrogen bonds       : angle       3.08690 ( 2059)
  metal coordination   : bond        0.01091 (    8)
  metal coordination   : angle       2.80807 (    9)
  covalent geometry    : bond        0.00432 (14864)
  covalent geometry    : angle       0.54438 (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
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7983 (t0) cc_final: 0.7544 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 97
  average time/residue: 0.3534
  time to fit residues: 46.3208
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 120 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3909 r_free = 0.3909 target = 0.173072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.116305 restraints weight = 24466.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.69
r_work: 0.2683 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.23   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.0872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  14874  Z= 0.211
  Angle     :  0.566   6.306  21368  Z= 0.331
  Chirality :  0.037   0.133   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.489 172.955   4332
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  9.58 %
    Favored  : 89.25 %
  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:  1.49 (0.27), residues: 983
  helix:  2.27 (0.21), residues: 625
  sheet:  0.14 (1.01), residues: 23
  loop : -1.55 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP L 141 
 HIS   0.005   0.001   HIS H  49 
 PHE   0.012   0.002   PHE A  78 
 TYR   0.011   0.002   TYR D 121 
 ARG   0.004   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00029 (    2)
  link_TRANS           : angle       0.44085 (    6)
  hydrogen bonds       : bond        0.05826 (  810)
  hydrogen bonds       : angle       3.13472 ( 2059)
  metal coordination   : bond        0.01197 (    8)
  metal coordination   : angle       2.95097 (    9)
  covalent geometry    : bond        0.00495 (14864)
  covalent geometry    : angle       0.56247 (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: 10
    poor density    : 92
  time to evaluate  : 1.177 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7912 (t0) cc_final: 0.7452 (t0)
  outliers start: 10
  outliers final: 8
  residues processed: 98
  average time/residue: 0.3725
  time to fit residues: 48.7598
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 37 optimal weight:    0.2980
   chunk 88 optimal weight:    4.9990
   chunk 17 optimal weight:    0.0980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3904 r_free = 0.3904 target = 0.173213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117520 restraints weight = 25370.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.81
r_work: 0.2699 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.0908

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= 0.146
  Angle     :  0.540   6.399  21368  Z= 0.320
  Chirality :  0.035   0.138   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.427 173.125   4332
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.28 %
    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:  1.70 (0.27), residues: 983
  helix:  2.45 (0.21), residues: 626
  sheet:  0.11 (1.01), residues: 23
  loop : -1.51 (0.30), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L  33 
 HIS   0.003   0.001   HIS A  39 
 PHE   0.008   0.001   PHE D  65 
 TYR   0.011   0.001   TYR D 121 
 ARG   0.003   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00088 (    2)
  link_TRANS           : angle       0.29132 (    6)
  hydrogen bonds       : bond        0.05034 (  810)
  hydrogen bonds       : angle       3.05183 ( 2059)
  metal coordination   : bond        0.00830 (    8)
  metal coordination   : angle       2.77146 (    9)
  covalent geometry    : bond        0.00316 (14864)
  covalent geometry    : angle       0.53697 (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
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.225 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7905 (t0) cc_final: 0.7474 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 95
  average time/residue: 0.4112
  time to fit residues: 53.4788
Evaluate side-chains
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   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:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 93 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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 = 0.3923 r_free = 0.3923 target = 0.174568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.117920 restraints weight = 24410.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 1.71
r_work: 0.2893 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2663
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2663 r_free = 0.2663    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2663
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.0999

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= 0.172
  Angle     :  0.538   6.430  21368  Z= 0.318
  Chirality :  0.035   0.128   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.366 173.444   4332
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.63 %
    Favored  : 88.32 %
  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:  1.69 (0.27), residues: 983
  helix:  2.44 (0.21), residues: 626
  sheet:  0.42 (0.93), residues: 21
  loop : -1.52 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP L  33 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.008   0.001   PHE A  78 
 TYR   0.011   0.001   TYR D 121 
 ARG   0.007   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00040 (    2)
  link_TRANS           : angle       0.33213 (    6)
  hydrogen bonds       : bond        0.05164 (  810)
  hydrogen bonds       : angle       3.01664 ( 2059)
  metal coordination   : bond        0.00954 (    8)
  metal coordination   : angle       2.78878 (    9)
  covalent geometry    : bond        0.00391 (14864)
  covalent geometry    : angle       0.53538 (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
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 1.060 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7975 (t0) cc_final: 0.7536 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 97
  average time/residue: 0.3563
  time to fit residues: 46.7830
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 63 optimal weight:    0.0570
   chunk 5 optimal weight:    0.7980
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    9.9990
   chunk 101 optimal weight:    0.0060
   chunk 116 optimal weight:   10.0000
   chunk 86 optimal weight:    7.9990
   chunk 92 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 18 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.4314

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.175676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.122978 restraints weight = 30883.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3252 rms_B_bonded: 2.02
r_work: 0.2891 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.1035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14874  Z= 0.143
  Angle     :  0.530   6.621  21368  Z= 0.315
  Chirality :  0.034   0.127   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.347 173.314   4332
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 10.86 %
    Favored  : 88.08 %
  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:  1.83 (0.27), residues: 983
  helix:  2.57 (0.21), residues: 625
  sheet:  0.27 (0.95), residues: 21
  loop : -1.47 (0.29), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  33 
 HIS   0.003   0.001   HIS L  32 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.009   0.001   TYR D 121 
 ARG   0.007   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00105 (    2)
  link_TRANS           : angle       0.28412 (    6)
  hydrogen bonds       : bond        0.04813 (  810)
  hydrogen bonds       : angle       2.99198 ( 2059)
  metal coordination   : bond        0.00769 (    8)
  metal coordination   : angle       2.72828 (    9)
  covalent geometry    : bond        0.00306 (14864)
  covalent geometry    : angle       0.52715 (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: 9
    poor density    : 94
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7953 (t0) cc_final: 0.7527 (t0)
  outliers start: 9
  outliers final: 8
  residues processed: 98
  average time/residue: 0.3550
  time to fit residues: 47.0207
Evaluate side-chains
  101 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Chi-restraints excluded: chain L residue  109 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 90 optimal weight:    4.9990
   chunk 53 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 27 optimal weight:    4.9990
   chunk 117 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9990
   chunk 99 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.175631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.123505 restraints weight = 34443.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.18
r_work: 0.2812 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2803
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2803 r_free = 0.2803    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2803
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1073

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= 0.158
  Angle     :  0.532   8.047  21368  Z= 0.314
  Chirality :  0.035   0.127   2419
  Planarity :  0.004   0.037   1688
  Dihedral  : 29.310 173.710   4332
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.75 %
    Favored  : 88.08 %
  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:  1.78 (0.27), residues: 983
  helix:  2.53 (0.21), residues: 625
  sheet: -0.35 (0.98), residues: 23
  loop : -1.47 (0.29), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP L  33 
 HIS   0.003   0.001   HIS H  49 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.009   0.001   TYR D 121 
 ARG   0.007   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00051 (    2)
  link_TRANS           : angle       0.26219 (    6)
  hydrogen bonds       : bond        0.04922 (  810)
  hydrogen bonds       : angle       2.97817 ( 2059)
  metal coordination   : bond        0.00888 (    8)
  metal coordination   : angle       2.71573 (    9)
  covalent geometry    : bond        0.00355 (14864)
  covalent geometry    : angle       0.52972 (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
  104 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 1.138 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7972 (t0) cc_final: 0.7552 (t0)
  outliers start: 10
  outliers final: 7
  residues processed: 100
  average time/residue: 0.3511
  time to fit residues: 47.7204
Evaluate side-chains
  100 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  118 THR
Chi-restraints excluded: chain K residue   35 LEU
Chi-restraints excluded: chain L residue    3 LEU
Chi-restraints excluded: chain L residue   49 VAL
Chi-restraints excluded: chain L residue   84 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 55 optimal weight:    0.0070
   chunk 43 optimal weight:    0.6980
   chunk 101 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 15 optimal weight:    0.8980
   chunk 104 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 103 optimal weight:    9.9990
   overall best weight:    0.6400

-------------------------------------------------------------------------------
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 = 0.3913 r_free = 0.3913 target = 0.174137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.116699 restraints weight = 19635.967|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 1.55
r_work: 0.2758 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.1101

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= 0.149
  Angle     :  0.529   8.032  21368  Z= 0.313
  Chirality :  0.034   0.126   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.299 173.671   4332
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 11.33 %
    Favored  : 87.85 %
  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:  1.78 (0.27), residues: 983
  helix:  2.53 (0.21), residues: 625
  sheet: -0.42 (0.99), residues: 23
  loop : -1.46 (0.30), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP L  33 
 HIS   0.003   0.001   HIS L  75 
 PHE   0.008   0.001   PHE E  67 
 TYR   0.009   0.001   TYR D 121 
 ARG   0.007   0.000   ARG G  99 

Details of bonding type rmsd
  link_TRANS           : bond        0.00076 (    2)
  link_TRANS           : angle       0.24884 (    6)
  hydrogen bonds       : bond        0.04814 (  810)
  hydrogen bonds       : angle       2.98712 ( 2059)
  metal coordination   : bond        0.00808 (    8)
  metal coordination   : angle       2.68619 (    9)
  covalent geometry    : bond        0.00327 (14864)
  covalent geometry    : angle       0.52607 (21353)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6911.48 seconds
wall clock time: 118 minutes 37.94 seconds (7117.94 seconds total)