Starting phenix.real_space_refine
on Thu Sep 18 03:21:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8smz_40607/09_2025/8smz_40607.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8smz_40607/09_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_40607/09_2025/8smz_40607.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8smz_40607/09_2025/8smz_40607.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8smz_40607/09_2025/8smz_40607.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8smz_40607/09_2025/8smz_40607.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.21, per 1000 atoms: 0.23
  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: 1.03
  Conformation dependent library (CDL) restraints added in 417.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  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: 2.00
  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: 2.22

  Time building geometry restraints manager: 1.43 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:             1.120
  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:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     15.540
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.350
-------------------------------------------------------------------------------
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 : 5.39
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.007   0.000   ARG G  99 
 TYR   0.014   0.001   TYR G  50 
 PHE   0.012   0.002   PHE L  69 
 TRP   0.010   0.002   TRP L 141 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (14864)
  covalent geometry    : angle       0.57224 (21353)
  hydrogen bonds       : bond        0.10275 (  810)
  hydrogen bonds       : angle       3.97434 ( 2059)
  metal coordination   : bond        0.02492 (    8)
  metal coordination   : angle       3.18961 (    9)
  link_TRANS           : bond        0.00115 (    2)
  link_TRANS           : angle       0.60516 (    6)

*********************** 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  : 0.298 
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: 0.1679
  time to fit residues: 25.0654
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  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    7.9990
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.3915 r_free = 0.3915 target = 0.173749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.118770 restraints weight = 28300.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.82
r_work: 0.2901 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2692
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2692 r_free = 0.2692    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2692
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.0493

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     :  0.567   7.253  21368  Z= 0.332
  Chirality :  0.036   0.160   2419
  Planarity :  0.004   0.046   1688
  Dihedral  : 29.481 172.844   4332
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.79 %
    Favored  : 94.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.27), residues: 983
  helix:  2.18 (0.21), residues: 623
  sheet: -0.05 (1.01), residues: 23
  loop : -1.49 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  99 
 TYR   0.013   0.001   TYR G  50 
 PHE   0.009   0.001   PHE A  78 
 TRP   0.008   0.001   TRP L 141 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (14864)
  covalent geometry    : angle       0.56409 (21353)
  hydrogen bonds       : bond        0.05670 (  810)
  hydrogen bonds       : angle       3.28536 ( 2059)
  metal coordination   : bond        0.01443 (    8)
  metal coordination   : angle       2.97735 (    9)
  link_TRANS           : bond        0.00044 (    2)
  link_TRANS           : angle       0.58007 (    6)

*********************** 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  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7836 (t0) cc_final: 0.7350 (t0)
REVERT: B   84 MET cc_start: 0.8569 (mmt) cc_final: 0.8311 (mmt)
  outliers start: 5
  outliers final: 3
  residues processed: 103
  average time/residue: 0.1757
  time to fit residues: 24.2080
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  : 0.380 
-------------------------------------------------------------------------------
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 103 optimal weight:    9.9990
   chunk 117 optimal weight:    6.9990
   chunk 82 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 85 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.170547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.119751 restraints weight = 24624.071|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 1.85
r_work: 0.2879 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2608
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2608 r_free = 0.2608    target_work(ls_wunit_k1) = 0.074         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2608
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.0631

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= 0.190
  Angle     :  0.559   6.544  21368  Z= 0.328
  Chirality :  0.036   0.164   2419
  Planarity :  0.004   0.044   1688
  Dihedral  : 29.473 173.085   4332
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.01 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.27), residues: 983
  helix:  2.20 (0.21), residues: 624
  sheet:  0.33 (1.08), residues: 21
  loop : -1.52 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  99 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.009   0.001   PHE A  78 
 TRP   0.008   0.001   TRP L 141 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 (14864)
  covalent geometry    : angle       0.55549 (21353)
  hydrogen bonds       : bond        0.05562 (  810)
  hydrogen bonds       : angle       3.20654 ( 2059)
  metal coordination   : bond        0.01196 (    8)
  metal coordination   : angle       2.95512 (    9)
  link_TRANS           : bond        0.00041 (    2)
  link_TRANS           : angle       0.40026 (    6)

*********************** 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: 6
    poor density    : 95
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7984 (t0) cc_final: 0.7520 (t0)
  outliers start: 6
  outliers final: 5
  residues processed: 99
  average time/residue: 0.1812
  time to fit residues: 24.0032
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  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain G residue   11 SER
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 75 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0270
   chunk 106 optimal weight:    0.5980
   chunk 112 optimal weight:   20.0000
   overall best weight:    0.9242

-------------------------------------------------------------------------------
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 = 0.3871 r_free = 0.3871 target = 0.170662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.114763 restraints weight = 19744.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.45
r_work: 0.2764 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2618 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  14874  Z= 0.164
  Angle     :  0.545   6.310  21368  Z= 0.323
  Chirality :  0.036   0.129   2419
  Planarity :  0.004   0.042   1688
  Dihedral  : 29.438 173.156   4332
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  8.29 %
    Favored  : 91.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.27), residues: 983
  helix:  2.31 (0.21), residues: 624
  sheet:  0.35 (1.07), residues: 21
  loop : -1.51 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  99 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 (14864)
  covalent geometry    : angle       0.54219 (21353)
  hydrogen bonds       : bond        0.05242 (  810)
  hydrogen bonds       : angle       3.15980 ( 2059)
  metal coordination   : bond        0.00962 (    8)
  metal coordination   : angle       2.88731 (    9)
  link_TRANS           : bond        0.00070 (    2)
  link_TRANS           : angle       0.37570 (    6)

*********************** 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
  99 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7928 (t0) cc_final: 0.7479 (t0)
  outliers start: 5
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1824
  time to fit residues: 23.5388
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  : 0.381 
-------------------------------------------------------------------------------
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 17 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0980
   chunk 6 optimal weight:    0.5980
   chunk 26 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.6584

-------------------------------------------------------------------------------
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 = 0.3911 r_free = 0.3911 target = 0.173787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.125937 restraints weight = 27888.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.20
r_work: 0.2912 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2912
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2664
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2664 r_free = 0.2664    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2664
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.0717

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= 0.152
  Angle     :  0.540   6.052  21368  Z= 0.319
  Chirality :  0.035   0.128   2419
  Planarity :  0.004   0.040   1688
  Dihedral  : 29.400 173.337   4332
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  8.76 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.27), residues: 983
  helix:  2.39 (0.21), residues: 624
  sheet:  0.34 (1.07), residues: 21
  loop : -1.47 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 129 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.007   0.001   PHE E  67 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (14864)
  covalent geometry    : angle       0.53662 (21353)
  hydrogen bonds       : bond        0.05027 (  810)
  hydrogen bonds       : angle       3.11546 ( 2059)
  metal coordination   : bond        0.00849 (    8)
  metal coordination   : angle       2.81616 (    9)
  link_TRANS           : bond        0.00087 (    2)
  link_TRANS           : angle       0.38958 (    6)

*********************** 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: 6
    poor density    : 94
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7958 (t0) cc_final: 0.7518 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 98
  average time/residue: 0.1774
  time to fit residues: 23.4201
Evaluate side-chains
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 99 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.2184

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.174729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.120813 restraints weight = 20114.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 1.46
r_work: 0.2846 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2580 r_free = 0.2580    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.0802

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= 0.183
  Angle     :  0.547   6.212  21368  Z= 0.323
  Chirality :  0.036   0.132   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.399 172.714   4332
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  9.35 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.27), residues: 983
  helix:  2.33 (0.21), residues: 624
  sheet:  0.41 (1.07), residues: 21
  loop : -1.54 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  92 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.010   0.001   PHE A  78 
 TRP   0.006   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (14864)
  covalent geometry    : angle       0.54374 (21353)
  hydrogen bonds       : bond        0.05375 (  810)
  hydrogen bonds       : angle       3.10372 ( 2059)
  metal coordination   : bond        0.01060 (    8)
  metal coordination   : angle       2.85546 (    9)
  link_TRANS           : bond        0.00041 (    2)
  link_TRANS           : angle       0.35478 (    6)

*********************** 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: 8
    poor density    : 94
  time to evaluate  : 0.324 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7983 (t0) cc_final: 0.7535 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1655
  time to fit residues: 22.0951
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 12 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.174955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.121104 restraints weight = 19644.005|
|-----------------------------------------------------------------------------|
r_work (start): 0.3129 rms_B_bonded: 1.44
r_work: 0.2853 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.0810

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= 0.180
  Angle     :  0.547   8.766  21368  Z= 0.322
  Chirality :  0.036   0.161   2419
  Planarity :  0.004   0.039   1688
  Dihedral  : 29.396 172.901   4332
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.51 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.27), residues: 983
  helix:  2.33 (0.21), residues: 625
  sheet:  0.43 (1.06), residues: 21
  loop : -1.53 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.010   0.001   PHE A  78 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 (14864)
  covalent geometry    : angle       0.54420 (21353)
  hydrogen bonds       : bond        0.05320 (  810)
  hydrogen bonds       : angle       3.09737 ( 2059)
  metal coordination   : bond        0.01028 (    8)
  metal coordination   : angle       2.86906 (    9)
  link_TRANS           : bond        0.00025 (    2)
  link_TRANS           : angle       0.38894 (    6)

*********************** 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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.435 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7975 (t0) cc_final: 0.7523 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1746
  time to fit residues: 22.2471
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  : 0.383 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 100 optimal weight:    8.9990
   chunk 95 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 15 optimal weight:    0.5980
   chunk 107 optimal weight:    6.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3924 r_free = 0.3924 target = 0.174523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.118127 restraints weight = 24901.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3240 rms_B_bonded: 1.78
r_work: 0.2914 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
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      :  0.004   0.040  14874  Z= 0.161
  Angle     :  0.541   7.706  21368  Z= 0.319
  Chirality :  0.035   0.145   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.392 172.912   4332
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.59 (0.27), residues: 983
  helix:  2.35 (0.21), residues: 625
  sheet:  0.43 (1.06), residues: 21
  loop : -1.52 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  99 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (14864)
  covalent geometry    : angle       0.53757 (21353)
  hydrogen bonds       : bond        0.05227 (  810)
  hydrogen bonds       : angle       3.09131 ( 2059)
  metal coordination   : bond        0.00970 (    8)
  metal coordination   : angle       2.85811 (    9)
  link_TRANS           : bond        0.00031 (    2)
  link_TRANS           : angle       0.37590 (    6)

*********************** 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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.337 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7966 (t0) cc_final: 0.7519 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1655
  time to fit residues: 21.1434
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 92 optimal weight:    3.9990
   chunk 113 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 116 optimal weight:    6.9990
   chunk 66 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3920 r_free = 0.3920 target = 0.174174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.119333 restraints weight = 27485.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.78
r_work: 0.2935 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.0816

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= 0.162
  Angle     :  0.539   7.737  21368  Z= 0.319
  Chirality :  0.035   0.128   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.390 172.925   4332
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.27), residues: 983
  helix:  2.37 (0.21), residues: 625
  sheet:  0.43 (1.06), residues: 21
  loop : -1.52 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  92 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.009   0.001   PHE E  67 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (14864)
  covalent geometry    : angle       0.53614 (21353)
  hydrogen bonds       : bond        0.05181 (  810)
  hydrogen bonds       : angle       3.08496 ( 2059)
  metal coordination   : bond        0.00953 (    8)
  metal coordination   : angle       2.84868 (    9)
  link_TRANS           : bond        0.00055 (    2)
  link_TRANS           : angle       0.37815 (    6)

*********************** 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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7954 (t0) cc_final: 0.7508 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1712
  time to fit residues: 21.8485
Evaluate side-chains
  97 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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 42 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0010
   chunk 119 optimal weight:    0.0470
   chunk 43 optimal weight:    0.5980
   chunk 114 optimal weight:    0.0470
   chunk 19 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 50 optimal weight:    3.9990
   chunk 96 optimal weight:    3.9990
   chunk 72 optimal weight:    8.9990
   overall best weight:    0.5384

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.175063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.119168 restraints weight = 25409.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.84
r_work: 0.2924 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2924
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
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   0.039  14874  Z= 0.145
  Angle     :  0.533   7.516  21368  Z= 0.316
  Chirality :  0.034   0.178   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.373 173.003   4332
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.86 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.27), residues: 983
  helix:  2.42 (0.21), residues: 625
  sheet:  0.45 (1.07), residues: 21
  loop : -1.49 (0.30), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  99 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.010   0.001   PHE E  67 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (14864)
  covalent geometry    : angle       0.53053 (21353)
  hydrogen bonds       : bond        0.05006 (  810)
  hydrogen bonds       : angle       3.07035 ( 2059)
  metal coordination   : bond        0.00864 (    8)
  metal coordination   : angle       2.80896 (    9)
  link_TRANS           : bond        0.00053 (    2)
  link_TRANS           : angle       0.35675 (    6)

********************** 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
  98 residues out of total 850 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: A   77 ASP cc_start: 0.7947 (t0) cc_final: 0.7509 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 95
  average time/residue: 0.1650
  time to fit residues: 21.0519
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  : 0.391 
-------------------------------------------------------------------------------
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 54 optimal weight:    2.9990
   chunk 109 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 98 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 115 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.173574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119943 restraints weight = 19827.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.48
r_work: 0.2772 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2627 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2656
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2656 r_free = 0.2656    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2656
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.0854

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= 0.167
  Angle     :  0.538   7.510  21368  Z= 0.317
  Chirality :  0.035   0.184   2419
  Planarity :  0.004   0.038   1688
  Dihedral  : 29.362 173.381   4332
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.27), residues: 983
  helix:  2.38 (0.21), residues: 626
  sheet:  0.47 (1.07), residues: 21
  loop : -1.55 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  99 
 TYR   0.010   0.001   TYR D 121 
 PHE   0.008   0.001   PHE A  78 
 TRP   0.005   0.001   TRP L  33 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (14864)
  covalent geometry    : angle       0.53502 (21353)
  hydrogen bonds       : bond        0.05125 (  810)
  hydrogen bonds       : angle       3.05894 ( 2059)
  metal coordination   : bond        0.00957 (    8)
  metal coordination   : angle       2.80699 (    9)
  link_TRANS           : bond        0.00037 (    2)
  link_TRANS           : angle       0.31742 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3574.19 seconds
wall clock time: 61 minutes 40.79 seconds (3700.79 seconds total)