Starting phenix.real_space_refine (version: 1.21rc1)
on Sat Apr 22 08:33:32 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/04_2023/6o1d_0586.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/04_2023/6o1d_0586.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.395
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/04_2023/6o1d_0586.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/04_2023/6o1d_0586.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/04_2023/6o1d_0586.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/04_2023/6o1d_0586.pdb"
  }
  resolution = 3.395
  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
-------------------------------------------------------------------------------
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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S       8      5.16       5
     C    6664      2.51       5
     N    2229      2.21       5
     O    2791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   42": "NH1" <-> "NH2"
    Residue "A ARG   43": "NH1" <-> "NH2"
    Residue "A ARG   44": "NH1" <-> "NH2"
    Residue "A ARG   80": "NH1" <-> "NH2"
    Residue "C TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ARG   31": "NH1" <-> "NH2"
    Residue "E ARG   42": "NH1" <-> "NH2"
    Residue "E ARG   43": "NH1" <-> "NH2"
    Residue "E ARG   44": "NH1" <-> "NH2"
    Residue "E ARG   80": "NH1" <-> "NH2"
    Residue "G TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H ARG   31": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 11982
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "B"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "C"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 4, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 2, 'TRANS': 96}
    Chain: "F"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "G"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 833
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 4, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2957
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2988
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 6.41, per 1000 atoms: 0.53
  Number of scatterers: 11982
  At special positions: 0
  Unit cell: (91.665, 117.127, 119.674, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S       8     16.00
     P     290     15.00
     O    2791      8.00
     N    2229      7.00
     C    6664      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  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 5.91
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1406

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 9 sheets defined
      67.4% alpha, 2.9% beta
      120 base pairs and 258 stacking pairs defined.
    Time for finding SS restraints: 4.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 3.707A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 69
      removed outlier: 3.571A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 75
    Processing helix  chain 'A' and resid 94 through 101
      removed outlier: 3.582A  pdb=" N   ALA A 100 " --> pdb=" O   GLU A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 116
      removed outlier: 3.878A  pdb=" N   LEU A 111 " --> pdb=" O   GLU A 107 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LEU A 112 " --> pdb=" O   ASP A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 134
      removed outlier: 3.712A  pdb=" N   VAL A 126 " --> pdb=" O   PHE A 122 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   LEU A 128 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ARG A 131 " --> pdb=" O   GLN A 127 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   GLY A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.761A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.830A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 46 through 72
      removed outlier: 3.514A  pdb=" N   ALA C  53 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   GLU C  64 " --> pdb=" O   ALA C  60 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   GLY C  67 " --> pdb=" O   LEU C  63 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.642A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.696A  pdb=" N   TYR D  42 " --> pdb=" O   SER D  38 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LYS D  43 " --> pdb=" O   ILE D  39 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 56 through 84
      removed outlier: 3.960A  pdb=" N   MET D  62 " --> pdb=" O   ALA D  58 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLU D  71 " --> pdb=" O   ASN D  67 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLY D  75 " --> pdb=" O   GLU D  71 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.728A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LEU D 100 " --> pdb=" O   THR D  96 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.875A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ALA D 117 " --> pdb=" O   GLU D 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 56
      removed outlier: 3.525A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 69
      removed outlier: 3.708A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 69 through 75
    Processing helix  chain 'E' and resid 76 through 79
    Processing helix  chain 'E' and resid 89 through 116
      removed outlier: 3.882A  pdb=" N   GLN E  95 " --> pdb=" O   LEU E  91 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   ALA E  97 " --> pdb=" O   ALA E  93 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   HIS E 104 " --> pdb=" O   ALA E 100 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU E 111 " --> pdb=" O   GLU E 107 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LEU E 112 " --> pdb=" O   ASP E 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 122 through 133
      removed outlier: 3.856A  pdb=" N   VAL E 126 " --> pdb=" O   PHE E 122 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU E 128 " --> pdb=" O   LYS E 124 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   ARG E 131 " --> pdb=" O   GLN E 127 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ARG E 133 " --> pdb=" O   ALA E 129 " (cutoff:3.500A)
    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: 3.703A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.137A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.732A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.749A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 80 through 89
      removed outlier: 3.759A  pdb=" N   ALA G  86 " --> pdb=" O   HIS G  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
      removed outlier: 3.548A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.694A  pdb=" N   TYR H  42 " --> pdb=" O   SER H  38 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LYS H  43 " --> pdb=" O   ILE H  39 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.524A  pdb=" N   VAL H  66 " --> pdb=" O   MET H  62 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG H  79 " --> pdb=" O   GLY H  75 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA H  81 " --> pdb=" O   ALA H  77 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   HIS H  82 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.788A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 108 through 122
      removed outlier: 3.932A  pdb=" N   SER H 112 " --> pdb=" O   LYS H 108 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ALA H 117 " --> pdb=" O   GLU H 113 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LYS H 120 " --> pdb=" O   LYS H 116 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86
      removed outlier: 7.325A  pdb=" N   ASN A  85 " --> 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 120 through 121
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.371A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.699A  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 100 through 102
      removed outlier: 6.921A  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 85 through 86
      removed outlier: 7.290A  pdb=" N   ASN E  85 " --> 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 120 through 121
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.754A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    299 hydrogen bonds defined for protein.
    879 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      288 hydrogen bonds
      576 hydrogen bond angles
      0 basepair planarities
      120 basepair parallelities
      258 stacking parallelities
  Total time for adding SS restraints: 3.76

  Time building geometry restraints manager: 6.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1944
        1.33 -     1.44: 4321
        1.44 -     1.56: 5932
        1.56 -     1.68: 578
        1.68 -     1.80: 14
  Bond restraints: 12789
  Sorted by residual:
  bond pdb=" CG  LEU E 112 "
       pdb=" CD2 LEU E 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.425  0.096 3.30e-02 9.18e+02 8.38e+00
  bond pdb=" CB  ILE F  46 "
       pdb=" CG2 ILE F  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.428  0.093 3.30e-02 9.18e+02 7.88e+00
  bond pdb=" CG  LEU A 112 "
       pdb=" CD2 LEU A 112 "
    ideal  model  delta    sigma   weight residual
    1.521  1.434  0.087 3.30e-02 9.18e+02 6.94e+00
  bond pdb=" CG1 ILE A 132 "
       pdb=" CD1 ILE A 132 "
    ideal  model  delta    sigma   weight residual
    1.513  1.413  0.100 3.90e-02 6.57e+02 6.57e+00
  bond pdb=" CB  THR H  96 "
       pdb=" CG2 THR H  96 "
    ideal  model  delta    sigma   weight residual
    1.521  1.445  0.076 3.30e-02 9.18e+02 5.35e+00
  ... (remaining 12784 not shown)

  Histogram of bond angle deviations from ideal:
       97.65 -   104.93: 1237
      104.93 -   112.20: 6816
      112.20 -   119.48: 4445
      119.48 -   126.76: 5132
      126.76 -   134.03: 882
  Bond angle restraints: 18512
  Sorted by residual:
  angle pdb=" N   ALA D 107 "
        pdb=" CA  ALA D 107 "
        pdb=" C   ALA D 107 "
      ideal   model   delta    sigma   weight residual
     111.36  116.40   -5.04 1.09e+00 8.42e-01 2.14e+01
  angle pdb=" C   SER H  32 "
        pdb=" CA  SER H  32 "
        pdb=" CB  SER H  32 "
      ideal   model   delta    sigma   weight residual
     110.02  100.12    9.90 2.30e+00 1.89e-01 1.85e+01
  angle pdb=" N   GLN G  24 "
        pdb=" CA  GLN G  24 "
        pdb=" C   GLN G  24 "
      ideal   model   delta    sigma   weight residual
     114.31  109.21    5.10 1.29e+00 6.01e-01 1.56e+01
  angle pdb=" N   ARG H  33 "
        pdb=" CA  ARG H  33 "
        pdb=" C   ARG H  33 "
      ideal   model   delta    sigma   weight residual
     111.69  116.30   -4.61 1.23e+00 6.61e-01 1.40e+01
  angle pdb=" N   HIS D 109 "
        pdb=" CA  HIS D 109 "
        pdb=" CB  HIS D 109 "
      ideal   model   delta    sigma   weight residual
     110.20  115.64   -5.44 1.49e+00 4.50e-01 1.33e+01
  ... (remaining 18507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.47: 5207
       35.47 -    70.94: 1419
       70.94 -   106.42: 19
      106.42 -   141.89: 1
      141.89 -   177.36: 1
  Dihedral angle restraints: 6647
    sinusoidal: 4462
      harmonic: 2185
  Sorted by residual:
  dihedral pdb=" C   SER H  32 "
           pdb=" N   SER H  32 "
           pdb=" CA  SER H  32 "
           pdb=" CB  SER H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.17  -13.43     0      2.50e+00 1.60e-01 2.89e+01
  dihedral pdb=" CA  LYS H  46 "
           pdb=" C   LYS H  46 "
           pdb=" N   GLN H  47 "
           pdb=" CA  GLN H  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.93   25.07     0      5.00e+00 4.00e-02 2.51e+01
  dihedral pdb=" CA  ARG G  17 "
           pdb=" C   ARG G  17 "
           pdb=" N   SER G  18 "
           pdb=" CA  SER G  18 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.50   24.50     0      5.00e+00 4.00e-02 2.40e+01
  ... (remaining 6644 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1686
       0.066 -    0.131: 376
       0.131 -    0.197: 35
       0.197 -    0.263: 3
       0.263 -    0.328: 1
  Chirality restraints: 2101
  Sorted by residual:
  chirality pdb=" CA  SER H  32 "
            pdb=" N   SER H  32 "
            pdb=" C   SER H  32 "
            pdb=" CB  SER H  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.70e+00
  chirality pdb=" CB  ILE D  54 "
            pdb=" CA  ILE D  54 "
            pdb=" CG1 ILE D  54 "
            pdb=" CG2 ILE D  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.66e+00
  chirality pdb=" CG  LEU B  62 "
            pdb=" CB  LEU B  62 "
            pdb=" CD1 LEU B  62 "
            pdb=" CD2 LEU B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 2098 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  78 "   -0.036 2.00e-02 2.50e+03   1.84e-02 7.61e+00
        pdb=" N1   DC J  78 "    0.038 2.00e-02 2.50e+03
        pdb=" C2   DC J  78 "    0.005 2.00e-02 2.50e+03
        pdb=" O2   DC J  78 "    0.005 2.00e-02 2.50e+03
        pdb=" N3   DC J  78 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DC J  78 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  78 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5   DC J  78 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DC J  78 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE G  25 "   -0.016 2.00e-02 2.50e+03   1.87e-02 6.14e+00
        pdb=" CG  PHE G  25 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 PHE G  25 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 PHE G  25 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE G  25 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE G  25 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE G  25 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J 130 "    0.032 2.00e-02 2.50e+03   1.37e-02 5.64e+00
        pdb=" N9   DG J 130 "   -0.032 2.00e-02 2.50e+03
        pdb=" C8   DG J 130 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG J 130 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DG J 130 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DG J 130 "    0.005 2.00e-02 2.50e+03
        pdb=" O6   DG J 130 "    0.010 2.00e-02 2.50e+03
        pdb=" N1   DG J 130 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DG J 130 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2   DG J 130 "   -0.006 2.00e-02 2.50e+03
        pdb=" N3   DG J 130 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG J 130 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 3196
        2.83 -     3.35: 9746
        3.35 -     3.87: 23087
        3.87 -     4.38: 27368
        4.38 -     4.90: 37961
  Nonbonded interactions: 101358
  Sorted by model distance:
  nonbonded pdb=" O   TYR C  39 "
            pdb=" OG  SER D  78 "
     model   vdw
     2.317 2.440
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" OD2 ASP E 125 "
     model   vdw
     2.324 2.440
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.356 2.440
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.361 2.440
  nonbonded pdb=" O   HIS B  75 "
            pdb=" NH1 ARG D  92 "
     model   vdw
     2.371 2.520
  ... (remaining 101353 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 10 through 116)
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:                  0.010
  Normalize map: mean=0, sd=1:             0.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.680
  Check model and map are aligned:         0.170
  Set scattering table:                    0.110
  Process input model:                     35.970
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.040
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
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      :  0.010   0.104  12789  Z= 0.622
  Angle     :  0.951   9.905  18512  Z= 0.552
  Chirality :  0.053   0.328   2101
  Planarity :  0.007   0.059   1335
  Dihedral  : 28.083 177.359   5241
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.72 (0.21), residues: 745
  helix: -3.19 (0.15), residues: 510
  sheet:  None (None), residues: 0
  loop : -2.48 (0.30), residues: 235

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.934 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.4292
  time to fit residues: 82.1939
Evaluate side-chains
  121 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.986 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1922
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
D  49 HIS
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8312
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12789  Z= 0.207
  Angle     :  0.623   6.346  18512  Z= 0.371
  Chirality :  0.036   0.134   2101
  Planarity :  0.005   0.046   1335
  Dihedral  : 31.865 179.528   3759
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer Outliers :  1.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.73 (0.26), residues: 745
  helix: -1.63 (0.20), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.80 (0.34), residues: 225

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 118
  time to evaluate  : 0.941 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 119
  average time/residue: 0.3940
  time to fit residues: 60.3524
Evaluate side-chains
  116 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.1631
  time to fit residues: 2.6771
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 90 optimal weight:   10.0000
   chunk 98 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 72 optimal weight:   10.0000
   chunk 89 optimal weight:    8.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  84 ASN
F  75 HIS
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.063  12789  Z= 0.402
  Angle     :  0.650   6.057  18512  Z= 0.380
  Chirality :  0.038   0.133   2101
  Planarity :  0.005   0.048   1335
  Dihedral  : 31.906 177.839   3759
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  1.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.08 (0.28), residues: 745
  helix: -1.03 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.88 (0.33), residues: 226

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.859 
Fit side-chains
  outliers start: 11
  outliers final: 9
  residues processed: 125
  average time/residue: 0.3429
  time to fit residues: 55.3849
Evaluate side-chains
  119 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.846 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1075
  time to fit residues: 2.8174
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    0.3980
   chunk 91 optimal weight:   10.0000
   chunk 96 optimal weight:    8.9990
   chunk 86 optimal weight:   20.0000
   chunk 26 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 54 optimal weight:    0.0170
   overall best weight:    0.8420

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

Flipped N/Q/H residues before XYZ refinement:
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12789  Z= 0.179
  Angle     :  0.544   5.744  18512  Z= 0.333
  Chirality :  0.032   0.128   2101
  Planarity :  0.003   0.040   1335
  Dihedral  : 31.259 178.137   3759
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer Outliers :  1.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.04 (0.29), residues: 745
  helix: -0.28 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.42 (0.36), residues: 224

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.861 
Fit side-chains
  outliers start: 9
  outliers final: 2
  residues processed: 127
  average time/residue: 0.3712
  time to fit residues: 60.0114
Evaluate side-chains
  119 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 0.888 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1219
  time to fit residues: 1.4906
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 71 optimal weight:    0.2980
   chunk 39 optimal weight:    0.4980
   chunk 82 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 86 optimal weight:   20.0000
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12789  Z= 0.166
  Angle     :  0.528   6.276  18512  Z= 0.324
  Chirality :  0.032   0.131   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 31.097 179.353   3759
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer Outliers :  1.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.30), residues: 745
  helix:  0.31 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.25 (0.36), residues: 222

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.930 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 122
  average time/residue: 0.3849
  time to fit residues: 59.8731
Evaluate side-chains
  117 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.956 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1251
  time to fit residues: 2.0397
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 96 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 50 optimal weight:    5.9990
   chunk 93 optimal weight:    8.9990
   chunk 10 optimal weight:    0.9990
   overall best weight:    2.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.051  12789  Z= 0.311
  Angle     :  0.585   6.350  18512  Z= 0.347
  Chirality :  0.035   0.131   2101
  Planarity :  0.004   0.038   1335
  Dihedral  : 31.369 179.159   3759
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer Outliers :  1.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.29), residues: 745
  helix:  0.10 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -1.42 (0.35), residues: 223

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 0.955 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 117
  average time/residue: 0.3798
  time to fit residues: 56.7864
Evaluate side-chains
  119 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.853 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.2402
  time to fit residues: 2.9640
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    0.8980
   chunk 58 optimal weight:    0.7980
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0470
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12789  Z= 0.168
  Angle     :  0.530   6.720  18512  Z= 0.323
  Chirality :  0.031   0.137   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 30.906 178.344   3759
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.30), residues: 745
  helix:  0.57 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.04 (0.37), residues: 216

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.923 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.3718
  time to fit residues: 54.7060
Evaluate side-chains
  109 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.829 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0626
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 61 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 84 optimal weight:    8.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12789  Z= 0.351
  Angle     :  0.603   6.215  18512  Z= 0.354
  Chirality :  0.036   0.166   2101
  Planarity :  0.004   0.038   1335
  Dihedral  : 31.392 179.790   3759
  Min Nonbonded Distance : 2.132

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer Outliers :  0.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.30), residues: 745
  helix:  0.28 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.34 (0.35), residues: 222

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.881 
Fit side-chains
  outliers start: 5
  outliers final: 5
  residues processed: 118
  average time/residue: 0.3415
  time to fit residues: 52.6893
Evaluate side-chains
  119 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.819 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1191
  time to fit residues: 2.0467
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 27 optimal weight:    0.1980
   chunk 81 optimal weight:   10.0000
   chunk 84 optimal weight:    7.9990
   chunk 89 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:    8.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12789  Z= 0.230
  Angle     :  0.560   6.365  18512  Z= 0.335
  Chirality :  0.033   0.142   2101
  Planarity :  0.004   0.038   1335
  Dihedral  : 31.169 179.208   3759
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.30), residues: 745
  helix:  0.51 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.21 (0.36), residues: 222

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.905 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 115
  average time/residue: 0.3576
  time to fit residues: 53.3683
Evaluate side-chains
  114 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.933 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.1222
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 79 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 48 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12789  Z= 0.203
  Angle     :  0.556   8.287  18512  Z= 0.333
  Chirality :  0.033   0.146   2101
  Planarity :  0.003   0.038   1335
  Dihedral  : 31.127 179.339   3759
  Min Nonbonded Distance : 2.180

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer Outliers :  0.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.30), residues: 745
  helix:  0.66 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.12 (0.36), residues: 222

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

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

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1490 Ramachandran restraints generated.
    745 Oldfield, 0 Emsley, 745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.852 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 112
  average time/residue: 0.3624
  time to fit residues: 52.3071
Evaluate side-chains
  113 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.805 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0982
  time to fit residues: 1.1660
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 73 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 79 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 10 optimal weight:    0.5980
   chunk 14 optimal weight:    4.9990
   chunk 69 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** D  67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.175925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.111515 restraints weight = 15618.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 1.66
r_work: 0.3025 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12789  Z= 0.188
  Angle     :  0.538   6.549  18512  Z= 0.326
  Chirality :  0.032   0.142   2101
  Planarity :  0.003   0.039   1335
  Dihedral  : 31.027 179.572   3759
  Min Nonbonded Distance : 2.189

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer Outliers :  0.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.30), residues: 745
  helix:  0.78 (0.23), residues: 531
  sheet:  None (None), residues: 0
  loop : -1.05 (0.37), residues: 214

===============================================================================
Job complete
usr+sys time: 2016.98 seconds
wall clock time: 37 minutes 25.13 seconds (2245.13 seconds total)