Starting phenix.real_space_refine
on Wed Sep 25 23:22:27 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/09_2024/6o1d_0586.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/09_2024/6o1d_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_0586/09_2024/6o1d_0586.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/09_2024/6o1d_0586.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/09_2024/6o1d_0586.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o1d_0586/09_2024/6o1d_0586.cif"
  }
  resolution = 3.395
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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. Time to flip 12 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 7.01, per 1000 atoms: 0.59
  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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.79
  Conformation dependent library (CDL) restraints added in 880.1 milliseconds
  

  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: 5.27
  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: 3.31 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:
        0.00 -     1.98: 17518
        1.98 -     3.96: 918
        3.96 -     5.94: 56
        5.94 -     7.92: 16
        7.92 -     9.90: 4
  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: 5509
       35.47 -    70.94: 1473
       70.94 -   106.42: 19
      106.42 -   141.89: 1
      141.89 -   177.36: 1
  Dihedral angle restraints: 7003
    sinusoidal: 4818
      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 7000 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 3.040
  nonbonded pdb=" OG1 THR E 113 "
            pdb=" OD2 ASP E 125 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OG1 THR A 113 "
            pdb=" OD2 ASP A 125 "
     model   vdw
     2.356 3.040
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.361 3.040
  nonbonded pdb=" O   HIS B  75 "
            pdb=" NH1 ARG D  92 "
     model   vdw
     2.371 3.120
  ... (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
Time spend for trying shortcut: 0.00
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:                  0.000
  Normalize map: mean=0, sd=1:             0.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.650
  Find NCS groups from input model:        0.250
  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:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.900
-------------------------------------------------------------------------------
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  : 28.016 177.359   5597
  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 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP E  86 
 HIS   0.018   0.003   HIS F  75 
 PHE   0.043   0.005   PHE G  25 
 TYR   0.023   0.003   TYR G  50 
 ARG   0.017   0.002   ARG E 118 

*********************** 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  : 0.929 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8923 (ptmm) cc_final: 0.8625 (pttp)
REVERT: D  113 GLU cc_start: 0.8391 (tp30) cc_final: 0.7952 (tp30)
REVERT: D  120 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8660 (tttp)
REVERT: E   96 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7837 (mm-30)
REVERT: G   15 LYS cc_start: 0.8496 (mtmp) cc_final: 0.8253 (mttt)
REVERT: G   61 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tp30)
REVERT: G   72 ASP cc_start: 0.8337 (m-30) cc_final: 0.7915 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.4256
  time to fit residues: 81.6967
Evaluate side-chains
  122 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.1980
   chunk 40 optimal weight:    0.9980
   chunk 78 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 90 optimal weight:    8.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
D  49 HIS
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8301
moved from start:          0.1506

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= 0.199
  Angle     :  0.603   6.597  18512  Z= 0.364
  Chirality :  0.034   0.151   2101
  Planarity :  0.005   0.042   1335
  Dihedral  : 31.163 179.665   4115
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  7.22 %
    Favored  : 91.81 %
  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: -2.66 (0.26), residues: 745
  helix: -1.61 (0.20), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.69 (0.35), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.013   0.001   PHE A  84 
 TYR   0.015   0.002   TYR H  83 
 ARG   0.006   0.001   ARG A  80 

*********************** 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
  130 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8858 (ptmm) cc_final: 0.8524 (pttp)
REVERT: C   36 LYS cc_start: 0.8495 (mmtm) cc_final: 0.8268 (ttmm)
REVERT: C   41 GLU cc_start: 0.7943 (tt0) cc_final: 0.7679 (tt0)
REVERT: D  113 GLU cc_start: 0.8272 (tp30) cc_final: 0.7976 (tp30)
REVERT: D  120 LYS cc_start: 0.8805 (ttmt) cc_final: 0.8449 (tttp)
REVERT: G   72 ASP cc_start: 0.8326 (m-30) cc_final: 0.7870 (m-30)
REVERT: H  105 GLU cc_start: 0.7699 (tp30) cc_final: 0.7462 (mm-30)
  outliers start: 6
  outliers final: 6
  residues processed: 124
  average time/residue: 0.3497
  time to fit residues: 55.7609
Evaluate side-chains
  119 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 113
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain C residue   56 GLU
Chi-restraints excluded: chain E residue   53 LYS
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue   47 GLN
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:    0.8980
   chunk 75 optimal weight:    8.9990
   chunk 61 optimal weight:    0.0030
   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:    2.9990
   chunk 72 optimal weight:   20.0000
   chunk 89 optimal weight:    8.9990
   overall best weight:    2.5796

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1868

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= 0.332
  Angle     :  0.631   5.939  18512  Z= 0.374
  Chirality :  0.037   0.133   2101
  Planarity :  0.006   0.046   1335
  Dihedral  : 31.128 177.694   4115
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  :  8.67 %
    Favored  : 89.41 %
  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: -1.78 (0.28), residues: 745
  helix: -0.95 (0.22), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.36 (0.37), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.016   0.002   PHE C  25 
 TYR   0.026   0.002   TYR H  40 
 ARG   0.005   0.001   ARG C  99 

*********************** 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
  127 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 115
  time to evaluate  : 0.882 
Fit side-chains
REVERT: A   53 LYS cc_start: 0.8944 (ptmm) cc_final: 0.8558 (pttp)
REVERT: C   41 GLU cc_start: 0.7990 (tt0) cc_final: 0.7640 (tt0)
REVERT: D  120 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8425 (tttp)
REVERT: E  139 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6932 (mp)
REVERT: G   72 ASP cc_start: 0.8339 (m-30) cc_final: 0.7869 (m-30)
REVERT: H   52 THR cc_start: 0.9041 (m) cc_final: 0.8787 (t)
  outliers start: 12
  outliers final: 9
  residues processed: 120
  average time/residue: 0.3603
  time to fit residues: 57.6309
Evaluate side-chains
  120 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   73 GLU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue   47 GLN
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 91 optimal weight:   10.0000
   chunk 96 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12789  Z= 0.187
  Angle     :  0.547   5.623  18512  Z= 0.333
  Chirality :  0.032   0.131   2101
  Planarity :  0.004   0.038   1335
  Dihedral  : 30.465 178.857   4115
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 11.24 %
    Favored  : 87.64 %
  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: -0.73 (0.30), residues: 745
  helix: -0.13 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.06 (0.38), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.009   0.001   PHE H  65 
 TYR   0.023   0.001   TYR H  40 
 ARG   0.004   0.000   ARG C  71 

*********************** 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
  132 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6511 (ptp90) cc_final: 0.6269 (ptt-90)
REVERT: B   84 MET cc_start: 0.7942 (mmm) cc_final: 0.7691 (mmm)
REVERT: C   41 GLU cc_start: 0.7935 (tt0) cc_final: 0.7608 (tt0)
REVERT: D  120 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8427 (tttp)
REVERT: E  139 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6820 (mp)
REVERT: G   72 ASP cc_start: 0.8257 (m-30) cc_final: 0.7798 (m-30)
REVERT: H   52 THR cc_start: 0.9010 (m) cc_final: 0.8697 (t)
  outliers start: 7
  outliers final: 3
  residues processed: 128
  average time/residue: 0.3607
  time to fit residues: 58.8024
Evaluate side-chains
  118 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 114
  time to evaluate  : 0.922 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   82 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 82 optimal weight:    8.9990
   chunk 66 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 86 optimal weight:   20.0000
   chunk 24 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12789  Z= 0.212
  Angle     :  0.549   5.685  18512  Z= 0.333
  Chirality :  0.033   0.139   2101
  Planarity :  0.004   0.037   1335
  Dihedral  : 30.526 179.546   4115
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.04 %
    Favored  : 86.68 %
  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: -0.44 (0.30), residues: 745
  helix:  0.12 (0.23), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.06 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.013   0.001   PHE G  25 
 TYR   0.025   0.001   TYR H  40 
 ARG   0.005   0.000   ARG F  36 

*********************** 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
  128 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.804 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6586 (ptp90) cc_final: 0.6277 (ptt-90)
REVERT: D   34 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8707 (mmmt)
REVERT: D  120 LYS cc_start: 0.8774 (ttmt) cc_final: 0.8446 (tttp)
REVERT: E   52 ARG cc_start: 0.8358 (mtt180) cc_final: 0.8152 (mtt180)
REVERT: E  139 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6862 (mp)
REVERT: G   72 ASP cc_start: 0.8239 (m-30) cc_final: 0.7778 (m-30)
REVERT: H   33 ARG cc_start: 0.7326 (ttp80) cc_final: 0.7119 (ttp80)
REVERT: H   52 THR cc_start: 0.8952 (m) cc_final: 0.8645 (t)
  outliers start: 8
  outliers final: 4
  residues processed: 123
  average time/residue: 0.3644
  time to fit residues: 57.3511
Evaluate side-chains
  122 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 GLU
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:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    0.1980
   chunk 32 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 10 optimal weight:    0.8980
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.2801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12789  Z= 0.213
  Angle     :  0.545   5.681  18512  Z= 0.330
  Chirality :  0.033   0.135   2101
  Planarity :  0.004   0.037   1335
  Dihedral  : 30.427 179.463   4115
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 11.88 %
    Favored  : 86.36 %
  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: -0.19 (0.30), residues: 745
  helix:  0.32 (0.23), residues: 530
  sheet:  None (None), residues: 0
  loop : -1.02 (0.38), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  47 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.008   0.001   PHE G  25 
 TYR   0.021   0.001   TYR H  40 
 ARG   0.004   0.000   ARG F  36 

*********************** 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
  128 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.839 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6560 (ptp90) cc_final: 0.6269 (ptt-90)
REVERT: A   99 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6897 (mt-10)
REVERT: B   84 MET cc_start: 0.7942 (mmm) cc_final: 0.7673 (mmm)
REVERT: C   41 GLU cc_start: 0.7963 (tt0) cc_final: 0.7659 (tt0)
REVERT: D  120 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8451 (tttp)
REVERT: E  139 LEU cc_start: 0.7227 (OUTLIER) cc_final: 0.6894 (mp)
REVERT: G   72 ASP cc_start: 0.8238 (m-30) cc_final: 0.7794 (m-30)
REVERT: H   52 THR cc_start: 0.8983 (m) cc_final: 0.8665 (t)
  outliers start: 11
  outliers final: 7
  residues processed: 123
  average time/residue: 0.3654
  time to fit residues: 57.6004
Evaluate side-chains
  122 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 54 optimal weight:    0.1980
   chunk 81 optimal weight:   10.0000
   chunk 96 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   overall best weight:    0.7582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12789  Z= 0.169
  Angle     :  0.531   7.029  18512  Z= 0.323
  Chirality :  0.032   0.134   2101
  Planarity :  0.003   0.037   1335
  Dihedral  : 30.273 178.830   4115
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 11.72 %
    Favored  : 86.20 %
  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 (0.31), residues: 745
  helix:  0.71 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.82 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  47 
 HIS   0.006   0.000   HIS F  75 
 PHE   0.006   0.001   PHE E  84 
 TYR   0.023   0.001   TYR H  40 
 ARG   0.005   0.000   ARG F  36 

*********************** 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
  128 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.890 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6539 (ptp90) cc_final: 0.6275 (ptt-90)
REVERT: D  120 LYS cc_start: 0.8784 (ttmt) cc_final: 0.8462 (tttp)
REVERT: E  139 LEU cc_start: 0.7197 (OUTLIER) cc_final: 0.6864 (mp)
REVERT: G   72 ASP cc_start: 0.8224 (m-30) cc_final: 0.7788 (m-30)
  outliers start: 13
  outliers final: 9
  residues processed: 120
  average time/residue: 0.3528
  time to fit residues: 54.7132
Evaluate side-chains
  121 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain B residue   64 ASN
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   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:    4.5788

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

Flipped N/Q/H residues before XYZ refinement:
A  95 GLN
F  25 ASN
G  84 GLN
** H  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.068  12789  Z= 0.507
  Angle     :  0.688   8.764  18512  Z= 0.393
  Chirality :  0.041   0.226   2101
  Planarity :  0.006   0.057   1335
  Dihedral  : 31.045 179.215   4115
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.52 %
    Favored  : 85.55 %
  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: -0.63 (0.30), residues: 745
  helix:  0.03 (0.23), residues: 516
  sheet:  None (None), residues: 0
  loop : -1.23 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP E  86 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.019   0.002   PHE G  25 
 TYR   0.036   0.002   TYR H  40 
 ARG   0.006   0.001   ARG E  52 

*********************** 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
  134 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.882 
Fit side-chains
REVERT: D  120 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8416 (tttp)
REVERT: E  139 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.6933 (mp)
REVERT: G   56 GLU cc_start: 0.8133 (tt0) cc_final: 0.7933 (tt0)
REVERT: G   72 ASP cc_start: 0.8370 (m-30) cc_final: 0.7881 (m-30)
REVERT: H   33 ARG cc_start: 0.7282 (ttp80) cc_final: 0.7081 (ttp80)
REVERT: H   52 THR cc_start: 0.8898 (m) cc_final: 0.8516 (t)
  outliers start: 12
  outliers final: 7
  residues processed: 128
  average time/residue: 0.3542
  time to fit residues: 58.3018
Evaluate side-chains
  127 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain B residue   50 ILE
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain H residue  113 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 92 optimal weight:    6.9990
   chunk 54 optimal weight:    0.0170
   chunk 39 optimal weight:    5.9990
   chunk 70 optimal weight:    0.2980
   chunk 27 optimal weight:    0.9980
   chunk 81 optimal weight:    8.9990
   chunk 84 optimal weight:    7.9990
   chunk 89 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 94 optimal weight:    7.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
D  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.3217

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= 0.169
  Angle     :  0.547   7.552  18512  Z= 0.331
  Chirality :  0.032   0.141   2101
  Planarity :  0.004   0.038   1335
  Dihedral  : 30.196 177.996   4115
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.45 %
    Favored  : 84.59 %
  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:  0.10 (0.30), residues: 745
  helix:  0.56 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -0.96 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP E  86 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.020   0.001   TYR H  40 
 ARG   0.004   0.000   ARG F  36 

*********************** 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
  120 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 1.006 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6481 (ptp90) cc_final: 0.6250 (ptt-90)
REVERT: D  120 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8401 (tttp)
REVERT: H   52 THR cc_start: 0.8888 (m) cc_final: 0.8517 (t)
  outliers start: 6
  outliers final: 4
  residues processed: 117
  average time/residue: 0.3762
  time to fit residues: 56.6879
Evaluate side-chains
  117 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   80 THR
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:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 84 optimal weight:    8.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    1.6184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12789  Z= 0.232
  Angle     :  0.559   7.145  18512  Z= 0.334
  Chirality :  0.033   0.143   2101
  Planarity :  0.004   0.038   1335
  Dihedral  : 30.338 179.856   4115
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.13 %
    Favored  : 84.75 %
  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:  0.31 (0.31), residues: 745
  helix:  0.70 (0.23), residues: 522
  sheet:  None (None), residues: 0
  loop : -0.79 (0.39), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  86 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.010   0.001   PHE G  25 
 TYR   0.031   0.001   TYR H  40 
 ARG   0.004   0.000   ARG F  36 

********************** 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
  123 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.798 
Fit side-chains
REVERT: A   44 ARG cc_start: 0.6610 (ptp90) cc_final: 0.6377 (ptt-90)
REVERT: D  120 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8458 (tttp)
REVERT: E  139 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6893 (mp)
REVERT: H   52 THR cc_start: 0.8896 (m) cc_final: 0.8529 (t)
REVERT: H   68 ASP cc_start: 0.8603 (t0) cc_final: 0.8400 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 120
  average time/residue: 0.3449
  time to fit residues: 53.1744
Evaluate side-chains
  119 residues out of total 623 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain D residue   35 GLU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  139 LEU
Chi-restraints excluded: chain F residue   80 THR
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:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 79 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9980
   chunk 81 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
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 = 0.4116 r_free = 0.4116 target = 0.175841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.111155 restraints weight = 15557.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3270 rms_B_bonded: 1.62
r_work: 0.3033 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.3289

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= 0.194
  Angle     :  0.552   9.714  18512  Z= 0.330
  Chirality :  0.033   0.144   2101
  Planarity :  0.003   0.038   1335
  Dihedral  : 30.261 179.747   4115
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 14.13 %
    Favored  : 84.91 %
  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 (0.31), residues: 745
  helix:  0.76 (0.23), residues: 530
  sheet:  None (None), residues: 0
  loop : -0.86 (0.39), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP E  86 
 HIS   0.006   0.000   HIS F  75 
 PHE   0.007   0.001   PHE G  25 
 TYR   0.030   0.001   TYR H  40 
 ARG   0.004   0.000   ARG F  36 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2122.60 seconds
wall clock time: 38 minutes 24.98 seconds (2304.98 seconds total)