Starting phenix.real_space_refine
on Thu Jul 18 18:53:16 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve4_43164/07_2024/8ve4_43164.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve4_43164/07_2024/8ve4_43164.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve4_43164/07_2024/8ve4_43164.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve4_43164/07_2024/8ve4_43164.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve4_43164/07_2024/8ve4_43164.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ve4_43164/07_2024/8ve4_43164.cif"
  }
  resolution = 3.3
  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=   0.002
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: 4
    Type Number    sf(0)   Gaussians
     S       3      5.16       5
     C    2067      2.51       5
     N     548      2.21       5
     O     530      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   72": "OE1" <-> "OE2"
    Residue "A PHE   87": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  116": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  114": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C PHE   64": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   78": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D PHE   87": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib"
  Total number of atoms: 3148
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 807
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 75
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 60
    Chain: "B"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 791
          Classifications: {'peptide': 117}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 7, 'TRANS': 109}
          Unresolved non-hydrogen bonds: 116
          Unresolved non-hydrogen angles: 145
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 71
    Chain: "C"
      Number of atoms: 781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 781
          Classifications: {'peptide': 116}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 7, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 117
          Unresolved non-hydrogen angles: 148
          Unresolved non-hydrogen dihedrals: 91
          Unresolved non-hydrogen chiralities: 9
          Planarities with less than four sites: {'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 75
    Chain: "D"
      Number of atoms: 769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 769
          Classifications: {'peptide': 115}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 6, 'TRANS': 108}
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 153
          Unresolved non-hydrogen dihedrals: 93
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 10, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 78
  Time building chain proxies: 2.59, per 1000 atoms: 0.82
  Number of scatterers: 3148
  At special positions: 0
  Unit cell: (75.308, 71.936, 62.382, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       3     16.00
     O     530      8.00
     N     548      7.00
     C    2067      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: 0.96
  Conformation dependent library (CDL) restraints added in 764.2 milliseconds
  

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  874

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 6 sheets defined
      8.4% alpha, 61.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 83
    Processing helix  chain 'B' and resid 75 through 83
      removed outlier: 3.551A  pdb=" N   TRP B  79 " --> pdb=" O   THR B  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 74 through 83
      removed outlier: 3.850A  pdb=" N   TYR C  78 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   TRP C  79 " --> pdb=" O   THR C  75 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LYS C  80 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 74 through 83
      removed outlier: 3.533A  pdb=" N   TYR D  78 " --> pdb=" O   ASP D  74 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ALA D  81 " --> pdb=" O   SER D  77 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55
      removed outlier: 6.336A  pdb=" N   MET A  13 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ALA A 109 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LYS A  15 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   MET B  13 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ALA B 109 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   LEU B  17 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55
      removed outlier: 6.336A  pdb=" N   MET A  13 " --> pdb=" O   ILE A 107 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ALA A 109 " --> pdb=" O   MET A  13 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LYS A  15 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   LEU A 111 " --> pdb=" O   LYS A  15 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   MET B  13 " --> pdb=" O   ILE B 107 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ALA B 109 " --> pdb=" O   MET B  13 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   LYS B  15 " --> pdb=" O   ALA B 109 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU B 111 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   LEU B  17 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   VAL B  14 " --> pdb=" O   LEU B  55 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B  55 " --> pdb=" O   VAL B  14 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 48
      removed outlier: 6.224A  pdb=" N   ARG A  34 " --> pdb=" O   PRO A  43 " (cutoff:3.500A)
      removed outlier: 5.321A  pdb=" N   ILE A  68 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE A  95 " --> pdb=" O   TYR A  69 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   VAL B  94 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   ALA A  91 " --> pdb=" O   GLU B  92 " (cutoff:3.500A)
      removed outlier: 8.588A  pdb=" N   GLU B  92 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   VAL A  93 " --> pdb=" O   HIS B  90 " (cutoff:3.500A)
      removed outlier: 8.055A  pdb=" N   HIS B  90 " --> pdb=" O   VAL A  93 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   PHE A  95 " --> pdb=" O   HIS B  88 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   HIS B  88 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ALA B  29 " --> pdb=" O   ASP B  74 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   ARG B  34 " --> pdb=" O   PRO B  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 56
      removed outlier: 6.297A  pdb=" N   MET C  13 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   ALA C 109 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LYS C  15 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU C 111 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   LEU C  17 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR C 106 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   MET D  13 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ALA D 109 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LYS D  15 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   LEU D 111 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU D  17 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 54 through 56
      removed outlier: 6.297A  pdb=" N   MET C  13 " --> pdb=" O   ILE C 107 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   ALA C 109 " --> pdb=" O   MET C  13 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   LYS C  15 " --> pdb=" O   ALA C 109 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU C 111 " --> pdb=" O   LYS C  15 " (cutoff:3.500A)
      removed outlier: 6.286A  pdb=" N   LEU C  17 " --> pdb=" O   LEU C 111 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR C 106 " --> pdb=" O   VAL C 121 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   MET D  13 " --> pdb=" O   ILE D 107 " (cutoff:3.500A)
      removed outlier: 7.478A  pdb=" N   ALA D 109 " --> pdb=" O   MET D  13 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LYS D  15 " --> pdb=" O   ALA D 109 " (cutoff:3.500A)
      removed outlier: 7.262A  pdb=" N   LEU D 111 " --> pdb=" O   LYS D  15 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LEU D  17 " --> pdb=" O   LEU D 111 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL D  14 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 41 through 48
      removed outlier: 6.655A  pdb=" N   VAL C  32 " --> pdb=" O   PHE C  44 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   SER C  46 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   VAL C  30 " --> pdb=" O   SER C  46 " (cutoff:3.500A)
      removed outlier: 5.357A  pdb=" N   ILE C  68 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLY C  67 " --> pdb=" O   ALA C  97 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE C  95 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 7.485A  pdb=" N   HIS C  88 " --> pdb=" O   PHE D  95 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   PHE D  95 " --> pdb=" O   HIS C  88 " (cutoff:3.500A)
      removed outlier: 7.882A  pdb=" N   HIS C  90 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL D  93 " --> pdb=" O   HIS C  90 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   GLU C  92 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ALA D  91 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   VAL C  94 " --> pdb=" O   GLU D  89 " (cutoff:3.500A)
      removed outlier: 5.626A  pdb=" N   ILE D  68 " --> pdb=" O   LYS D  35 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   ARG D  34 " --> pdb=" O   PRO D  43 " (cutoff:3.500A)

    178 hydrogen bonds defined for protein.
    489 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.11

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 997
        1.35 -     1.46: 822
        1.46 -     1.58: 1416
        1.58 -     1.70: 0
        1.70 -     1.81: 3
  Bond restraints: 3238
  Sorted by residual:
  bond pdb=" CB  ASP A  18 "
       pdb=" CG  ASP A  18 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.88e-01
  bond pdb=" CG  ARG A  21 "
       pdb=" CD  ARG A  21 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 6.03e-01
  bond pdb=" N   PHE A  44 "
       pdb=" CA  PHE A  44 "
    ideal  model  delta    sigma   weight residual
    1.458  1.467 -0.009 1.27e-02 6.20e+03 4.78e-01
  bond pdb=" CB  VAL C  28 "
       pdb=" CG1 VAL C  28 "
    ideal  model  delta    sigma   weight residual
    1.521  1.500  0.021 3.30e-02 9.18e+02 4.18e-01
  bond pdb=" N   GLU C  42 "
       pdb=" CA  GLU C  42 "
    ideal  model  delta    sigma   weight residual
    1.458  1.447  0.011 1.69e-02 3.50e+03 4.09e-01
  ... (remaining 3233 not shown)

  Histogram of bond angle deviations from ideal:
      102.10 -   108.48: 228
      108.48 -   114.86: 1810
      114.86 -   121.25: 1443
      121.25 -   127.63: 942
      127.63 -   134.01: 44
  Bond angle restraints: 4467
  Sorted by residual:
  angle pdb=" N   PHE A  44 "
        pdb=" CA  PHE A  44 "
        pdb=" C   PHE A  44 "
      ideal   model   delta    sigma   weight residual
     112.68  110.26    2.42 1.33e+00 5.65e-01 3.30e+00
  angle pdb=" CB  ARG A  21 "
        pdb=" CG  ARG A  21 "
        pdb=" CD  ARG A  21 "
      ideal   model   delta    sigma   weight residual
     111.30  115.41   -4.11 2.30e+00 1.89e-01 3.19e+00
  angle pdb=" N   ASP A  18 "
        pdb=" CA  ASP A  18 "
        pdb=" C   ASP A  18 "
      ideal   model   delta    sigma   weight residual
     109.59  106.76    2.83 1.61e+00 3.86e-01 3.10e+00
  angle pdb=" CA  PRO A  86 "
        pdb=" C   PRO A  86 "
        pdb=" N   PHE A  87 "
      ideal   model   delta    sigma   weight residual
     114.58  116.48   -1.90 1.16e+00 7.43e-01 2.68e+00
  angle pdb=" N   LEU C  82 "
        pdb=" CA  LEU C  82 "
        pdb=" C   LEU C  82 "
      ideal   model   delta    sigma   weight residual
     113.18  111.23    1.95 1.21e+00 6.83e-01 2.60e+00
  ... (remaining 4462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.47: 1664
       10.47 -    20.94: 106
       20.94 -    31.41: 53
       31.41 -    41.87: 19
       41.87 -    52.34: 4
  Dihedral angle restraints: 1846
    sinusoidal: 492
      harmonic: 1354
  Sorted by residual:
  dihedral pdb=" CG  ARG C  21 "
           pdb=" CD  ARG C  21 "
           pdb=" NE  ARG C  21 "
           pdb=" CZ  ARG C  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   50.92   39.08     2      1.50e+01 4.44e-03 8.48e+00
  dihedral pdb=" CG  ARG B  34 "
           pdb=" CD  ARG B  34 "
           pdb=" NE  ARG B  34 "
           pdb=" CZ  ARG B  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   51.02   38.98     2      1.50e+01 4.44e-03 8.44e+00
  dihedral pdb=" CA  LYS A  15 "
           pdb=" CB  LYS A  15 "
           pdb=" CG  LYS A  15 "
           pdb=" CD  LYS A  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.83  -42.17     3      1.50e+01 4.44e-03 7.56e+00
  ... (remaining 1843 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 281
       0.025 -    0.049: 142
       0.049 -    0.074: 46
       0.074 -    0.098: 29
       0.098 -    0.123: 40
  Chirality restraints: 538
  Sorted by residual:
  chirality pdb=" CA  ILE C  73 "
            pdb=" N   ILE C  73 "
            pdb=" C   ILE C  73 "
            pdb=" CB  ILE C  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.78e-01
  chirality pdb=" CA  ILE B  73 "
            pdb=" N   ILE B  73 "
            pdb=" C   ILE B  73 "
            pdb=" CB  ILE B  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  chirality pdb=" CA  ILE A 107 "
            pdb=" N   ILE A 107 "
            pdb=" C   ILE A 107 "
            pdb=" CB  ILE A 107 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.67e-01
  ... (remaining 535 not shown)

  Planarity restraints: 566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B  85 "    0.035 5.00e-02 4.00e+02   5.39e-02 4.64e+00
        pdb=" N   PRO B  86 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO B  86 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B  86 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  21 "    0.146 9.50e-02 1.11e+02   6.58e-02 3.13e+00
        pdb=" NE  ARG A  21 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  21 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  21 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  21 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  85 "   -0.022 5.00e-02 4.00e+02   3.35e-02 1.79e+00
        pdb=" N   PRO A  86 "    0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A  86 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  86 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 563 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 968
        2.82 -     3.34: 2518
        3.34 -     3.86: 4949
        3.86 -     4.38: 5316
        4.38 -     4.90: 10111
  Nonbonded interactions: 23862
  Sorted by model distance:
  nonbonded pdb=" O   VAL B  65 "
            pdb=" OH  TYR B  69 "
     model   vdw
     2.302 2.440
  nonbonded pdb=" N   VAL B  28 "
            pdb=" OG1 THR B  49 "
     model   vdw
     2.329 2.520
  nonbonded pdb=" O   PHE B  64 "
            pdb=" ND2 ASN B  98 "
     model   vdw
     2.335 2.520
  nonbonded pdb=" O   VAL C  65 "
            pdb=" OH  TYR C  69 "
     model   vdw
     2.398 2.440
  nonbonded pdb=" O   TRP C  79 "
            pdb=" N   ILE C  84 "
     model   vdw
     2.414 2.520
  ... (remaining 23857 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' and ((resid 10 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 11 or (resid 12 through 13 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 14 or (resid 15 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 16 through 17 or (resid 18 through 20 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 21 through 33 or (resid 34 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 35 through 41 or \ 
 (resid 42 and (name N or name CA or name C or name O or name CB )) or resid 43  \ 
through 54 or (resid 55 through 56 and (name N or name CA or name C or name O or \ 
 name CB )) or resid 57 through 58 or (resid 59 through 63 and (name N or name C \ 
A or name C or name O or name CB )) or resid 64 through 67 or (resid 68 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 69 through 71 or (resi \ 
d 72 and (name N or name CA or name C or name O or name CB )) or resid 73 throug \ 
h 74 or (resid 75 and (name N or name CA or name C or name O or name CB )) or re \ 
sid 76 through 79 or (resid 80 through 81 and (name N or name CA or name C or na \ 
me O or name CB )) or resid 82 through 86 or (resid 87 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 88 through 111 or (resid 112 and (name  \ 
N or name CA or name C or name O or name CB )) or resid 113 or (resid 114 throug \ 
h 115 and (name N or name CA or name C or name O or name CB )) or resid 116 thro \ 
ugh 122 or (resid 123 and (name N or name CA or name C or name O or name CB )))) \ 

  selection = (chain 'B' and (resid 10 through 17 or (resid 18 through 20 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 21 through 33 or (resid 34 and (na \ 
me N or name CA or name C or name O or name CB )) or resid 35 through 47 or (res \ 
id 48 and (name N or name CA or name C or name O or name CB )) or resid 49 throu \ 
gh 54 or (resid 55 through 56 and (name N or name CA or name C or name O or name \ 
 CB )) or resid 57 through 67 or (resid 68 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 69 through 76 or (resid 77 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 78 through 79 or (resid 80 through 81  \ 
and (name N or name CA or name C or name O or name CB )) or resid 82 through 95  \ 
or (resid 96 through 97 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 98 through 102 or (resid 103 through 104 and (name N or name CA or nam \ 
e C or name O or name CB )) or resid 105 through 113 or (resid 114 through 115 a \ 
nd (name N or name CA or name C or name O or name CB )) or resid 116 through 117 \ 
 or (resid 118 through 120 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 121 through 122 or (resid 123 and (name N or name CA or name C or n \ 
ame O or name CB ))))
  selection = (chain 'C' and ((resid 10 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 11 or (resid 12 through 13 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 14 through 19 or (resid 20 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 21 through 33 or (resid 34 and (name N or  \ 
name CA or name C or name O or name CB )) or resid 35 through 47 or (resid 48 an \ 
d (name N or name CA or name C or name O or name CB )) or resid 49 through 53 or \ 
 (resid 54 through 56 and (name N or name CA or name C or name O or name CB )) o \ 
r resid 57 through 58 or (resid 59 through 63 and (name N or name CA or name C o \ 
r name O or name CB )) or resid 64 through 65 or (resid 66 and (name N or name C \ 
A or name C or name O or name CB )) or resid 67 through 79 or (resid 80 through  \ 
81 and (name N or name CA or name C or name O or name CB )) or resid 82 through  \ 
86 or (resid 87 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 88 through 95 or (resid 96 through 97 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 98 through 111 or (resid 112 and (name N or name CA or \ 
 name C or name O or name CB )) or resid 113 through 122 or (resid 123 and (name \ 
 N or name CA or name C or name O or name CB ))))
  selection = (chain 'D' and ((resid 10 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 11 or (resid 12 through 13 and (name N or name CA or name C or name  \ 
O or name CB )) or resid 14 or (resid 15 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 16 through 47 or (resid 48 and (name N or name CA or  \ 
name C or name O or name CB )) or resid 49 or (resid 50 through 52 and (name N o \ 
r name CA or name C or name O or name CB )) or (resid 53 through 56 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 57 through 58 or (resid 59 \ 
 through 63 and (name N or name CA or name C or name O or name CB )) or resid 64 \ 
 through 76 or (resid 77 and (name N or name CA or name C or name O or name CB ) \ 
) or resid 78 through 86 or (resid 87 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 88 through 111 or (resid 112 and (name N or name CA or n \ 
ame C or name O or name CB )) or resid 113 or (resid 114 through 115 and (name N \ 
 or name CA or name C or name O or name CB )) or resid 116 through 117 or (resid \ 
 118 through 120 and (name N or name CA or name C or name O or name CB )) or res \ 
id 121 through 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             0.800
  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:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.720
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7389
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3238  Z= 0.181
  Angle     :  0.564   6.194   4467  Z= 0.315
  Chirality :  0.045   0.123    538
  Planarity :  0.006   0.066    566
  Dihedral  : 10.449  52.342    972
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  1.77 (0.40), residues: 457
  helix:  1.17 (1.06), residues: 30
  sheet:  2.08 (0.36), residues: 228
  loop :  0.08 (0.43), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.006   0.001   PHE C  87 
 TYR   0.017   0.002   TYR C  78 
 ARG   0.012   0.002   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   34 ARG cc_start: 0.7894 (tmm-80) cc_final: 0.7631 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2186
  time to fit residues: 18.1593
Evaluate side-chains
  60 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 33 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 22 optimal weight:    0.3980
   chunk 17 optimal weight:    8.9990
   chunk 34 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.0562

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3238  Z= 0.172
  Angle     :  0.573   6.547   4467  Z= 0.292
  Chirality :  0.048   0.141    538
  Planarity :  0.004   0.038    566
  Dihedral  :  3.909  15.368    488
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  :  8.90 %
    Favored  : 88.98 %
  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:  1.50 (0.40), residues: 457
  helix:  0.30 (0.98), residues: 36
  sheet:  2.15 (0.37), residues: 215
  loop : -0.17 (0.41), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  79 
 HIS   0.002   0.001   HIS D  90 
 PHE   0.019   0.002   PHE B  64 
 TYR   0.016   0.002   TYR C  78 
 ARG   0.007   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 64
  time to evaluate  : 0.362 
Fit side-chains
REVERT: D   15 LYS cc_start: 0.7731 (tttt) cc_final: 0.7403 (ttpp)
  outliers start: 5
  outliers final: 4
  residues processed: 66
  average time/residue: 0.2505
  time to fit residues: 18.7068
Evaluate side-chains
  61 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 57
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   chunk 35 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3238  Z= 0.203
  Angle     :  0.550   6.518   4467  Z= 0.282
  Chirality :  0.048   0.140    538
  Planarity :  0.004   0.041    566
  Dihedral  :  3.903  14.843    488
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 11.86 %
    Favored  : 86.02 %
  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:  1.01 (0.39), residues: 457
  helix:  0.13 (0.96), residues: 36
  sheet:  1.86 (0.37), residues: 200
  loop : -0.39 (0.39), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.011   0.002   PHE B  64 
 TYR   0.013   0.001   TYR B  78 
 ARG   0.007   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.339 
Fit side-chains
REVERT: C   34 ARG cc_start: 0.7614 (ttp80) cc_final: 0.7314 (ttp-170)
REVERT: D   15 LYS cc_start: 0.7823 (tttt) cc_final: 0.7576 (tttm)
  outliers start: 5
  outliers final: 5
  residues processed: 63
  average time/residue: 0.2282
  time to fit residues: 16.2797
Evaluate side-chains
  66 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 61
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 39 optimal weight:    7.9990
   chunk 30 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    0.3980
   chunk 35 optimal weight:    0.1980
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3238  Z= 0.279
  Angle     :  0.583   6.625   4467  Z= 0.306
  Chirality :  0.050   0.146    538
  Planarity :  0.005   0.047    566
  Dihedral  :  4.202  16.291    488
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 11.44 %
    Favored  : 83.47 %
  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:  0.56 (0.39), residues: 457
  helix: -0.18 (0.90), residues: 36
  sheet:  1.52 (0.37), residues: 199
  loop : -0.63 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP D  79 
 HIS   0.003   0.001   HIS D  90 
 PHE   0.012   0.002   PHE A  95 
 TYR   0.014   0.002   TYR C 116 
 ARG   0.007   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.338 
Fit side-chains
REVERT: D   15 LYS cc_start: 0.7807 (tttt) cc_final: 0.7568 (tttm)
  outliers start: 12
  outliers final: 8
  residues processed: 68
  average time/residue: 0.2123
  time to fit residues: 16.5743
Evaluate side-chains
  69 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   chunk 17 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   3238  Z= 0.378
  Angle     :  0.642   8.389   4467  Z= 0.339
  Chirality :  0.052   0.160    538
  Planarity :  0.006   0.057    566
  Dihedral  :  4.628  17.973    488
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 13.98 %
    Favored  : 81.36 %
  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:  0.08 (0.39), residues: 457
  helix: -0.22 (0.92), residues: 35
  sheet:  1.14 (0.37), residues: 197
  loop : -0.92 (0.38), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D  79 
 HIS   0.004   0.001   HIS B  31 
 PHE   0.013   0.003   PHE C  87 
 TYR   0.017   0.002   TYR C  78 
 ARG   0.008   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 58
  time to evaluate  : 0.351 
Fit side-chains
REVERT: D   15 LYS cc_start: 0.7833 (tttt) cc_final: 0.7557 (tttm)
  outliers start: 11
  outliers final: 11
  residues processed: 63
  average time/residue: 0.2155
  time to fit residues: 15.5675
Evaluate side-chains
  68 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  106 THR
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  111 LEU
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    0.4980
   chunk 19 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 31 optimal weight:    5.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7418
moved from start:          0.2304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3238  Z= 0.163
  Angle     :  0.550   8.002   4467  Z= 0.279
  Chirality :  0.048   0.137    538
  Planarity :  0.005   0.056    566
  Dihedral  :  4.027  18.362    488
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 16.53 %
    Favored  : 79.66 %
  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:  0.27 (0.39), residues: 457
  helix: -0.20 (0.92), residues: 36
  sheet:  1.28 (0.38), residues: 197
  loop : -0.78 (0.38), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.020   0.001   PHE A  44 
 TYR   0.012   0.001   TYR C 116 
 ARG   0.009   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.311 
Fit side-chains
REVERT: D   15 LYS cc_start: 0.7794 (tttt) cc_final: 0.7589 (tttm)
  outliers start: 9
  outliers final: 8
  residues processed: 67
  average time/residue: 0.2128
  time to fit residues: 16.4046
Evaluate side-chains
  66 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:    0.0870
   chunk 23 optimal weight:    9.9990
   chunk 42 optimal weight:    6.9990
   chunk 26 optimal weight:    0.0050
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 12 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    1.6176

-------------------------------------------------------------------------------
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: 0.7447
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3238  Z= 0.202
  Angle     :  0.555   6.548   4467  Z= 0.286
  Chirality :  0.049   0.140    538
  Planarity :  0.005   0.059    566
  Dihedral  :  3.969  17.402    488
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 17.37 %
    Favored  : 78.39 %
  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:  0.16 (0.39), residues: 457
  helix:  0.02 (0.95), residues: 35
  sheet:  1.17 (0.38), residues: 197
  loop : -0.87 (0.38), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.018   0.002   PHE A  44 
 TYR   0.014   0.002   TYR C 116 
 ARG   0.010   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7941 (t80) cc_final: 0.7715 (t80)
REVERT: D   15 LYS cc_start: 0.7860 (tttt) cc_final: 0.7645 (tttm)
  outliers start: 10
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2190
  time to fit residues: 16.3424
Evaluate side-chains
  66 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain A residue  106 THR
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 3 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 40 optimal weight:    7.9990
   chunk 37 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:   10.0000
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0870
   overall best weight:    1.1964

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3238  Z= 0.170
  Angle     :  0.551   6.529   4467  Z= 0.280
  Chirality :  0.048   0.142    538
  Planarity :  0.005   0.063    566
  Dihedral  :  3.853  16.650    488
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 18.64 %
    Favored  : 77.97 %
  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:  0.21 (0.39), residues: 457
  helix: -0.07 (0.92), residues: 35
  sheet:  1.23 (0.39), residues: 197
  loop : -0.85 (0.38), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.019   0.002   PHE A  44 
 TYR   0.013   0.001   TYR C 116 
 ARG   0.011   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.292 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7977 (t80) cc_final: 0.7719 (t80)
REVERT: D   15 LYS cc_start: 0.7835 (tttt) cc_final: 0.7623 (tttm)
  outliers start: 8
  outliers final: 8
  residues processed: 63
  average time/residue: 0.2167
  time to fit residues: 15.7134
Evaluate side-chains
  64 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 35 optimal weight:    0.0670
   chunk 37 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0060
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3238  Z= 0.133
  Angle     :  0.526   6.725   4467  Z= 0.264
  Chirality :  0.047   0.136    538
  Planarity :  0.005   0.062    566
  Dihedral  :  3.572  12.657    488
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 17.80 %
    Favored  : 78.81 %
  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:  0.35 (0.40), residues: 457
  helix:  0.06 (0.93), residues: 35
  sheet:  1.29 (0.38), residues: 199
  loop : -0.75 (0.39), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.019   0.001   PHE A  44 
 TYR   0.014   0.001   TYR B 116 
 ARG   0.011   0.001   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.303 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.7805 (tttt) cc_final: 0.7592 (tttm)
  outliers start: 8
  outliers final: 7
  residues processed: 63
  average time/residue: 0.2296
  time to fit residues: 16.5221
Evaluate side-chains
  63 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0270
   chunk 10 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 5 optimal weight:    9.9990
   chunk 9 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.9642

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

Flipped N/Q/H residues before XYZ refinement:
B  98 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.2630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3238  Z= 0.226
  Angle     :  0.580   6.254   4467  Z= 0.297
  Chirality :  0.049   0.143    538
  Planarity :  0.005   0.070    566
  Dihedral  :  3.865  14.295    488
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 11.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.37 %
    Favored  : 78.81 %
  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:  0.20 (0.40), residues: 457
  helix: -0.03 (0.93), residues: 35
  sheet:  1.15 (0.39), residues: 199
  loop : -0.79 (0.39), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.008   0.002   PHE C  87 
 TYR   0.014   0.002   TYR C 116 
 ARG   0.012   0.002   ARG A  21 

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

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

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  914 Ramachandran restraints generated.
    457 Oldfield, 0 Emsley, 457 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: D   15 LYS cc_start: 0.7770 (tttt) cc_final: 0.7557 (tttm)
  outliers start: 9
  outliers final: 8
  residues processed: 65
  average time/residue: 0.2277
  time to fit residues: 16.9271
Evaluate side-chains
  66 residues out of total 389 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 LEU
Chi-restraints excluded: chain A residue   75 THR
Chi-restraints excluded: chain A residue   94 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   93 VAL
Chi-restraints excluded: chain B residue  123 THR
Chi-restraints excluded: chain C residue  106 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 44
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    0.0010
   chunk 26 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    1.3392

-------------------------------------------------------------------------------
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 = 0.4362 r_free = 0.4362 target = 0.173435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.138713 restraints weight = 4783.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.73
r_work: 0.3853 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3238  Z= 0.178
  Angle     :  0.560   6.338   4467  Z= 0.283
  Chirality :  0.048   0.140    538
  Planarity :  0.005   0.067    566
  Dihedral  :  3.788  14.080    488
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 17.37 %
    Favored  : 78.81 %
  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:  0.26 (0.40), residues: 457
  helix: -0.04 (0.93), residues: 35
  sheet:  1.20 (0.39), residues: 199
  loop : -0.76 (0.39), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D  79 
 HIS   0.003   0.001   HIS C  90 
 PHE   0.022   0.002   PHE A  44 
 TYR   0.013   0.002   TYR C 116 
 ARG   0.012   0.002   ARG A  21 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1175.31 seconds
wall clock time: 24 minutes 6.34 seconds (1446.34 seconds total)