Starting phenix.real_space_refine
on Wed Sep 17 05:01:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9d6f_46596/09_2025/9d6f_46596.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9d6f_46596/09_2025/9d6f_46596.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9d6f_46596/09_2025/9d6f_46596.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9d6f_46596/09_2025/9d6f_46596.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9d6f_46596/09_2025/9d6f_46596.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9d6f_46596/09_2025/9d6f_46596.map"
  }
  resolution = 4.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.015
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      18      5.16       5
     C    2967      2.51       5
     N     772      2.21       5
     O     915      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4672
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 832
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 934
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 934
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 884
          Classifications: {'peptide': 113}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 796
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 4, 'TRANS': 100}
    Chain: "D"
      Number of atoms: 1226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1226
          Classifications: {'peptide': 164}
          Link IDs: {'PTRANS': 10, 'TRANS': 153}
  Time building chain proxies: 1.34, per 1000 atoms: 0.29
  Number of scatterers: 4672
  At special positions: 0
  Unit cell: (107.01, 106.14, 72.21, 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      18     16.00
     O     915      8.00
     N     772      7.00
     C    2967      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   3 " - pdb=" SG  CYS D  44 " distance=2.03

  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: 0.35
  Conformation dependent library (CDL) restraints added in 184.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1102

  Finding SS restraints...
    Secondary structure from input PDB file:
      2 helices and 17 sheets defined
      1.6% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'L' and resid 84 through 88
      removed outlier: 3.739A  pdb=" N   VAL L  88 " --> pdb=" O   THR L  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.632A  pdb=" N   ASP A  90 " --> pdb=" O   THR A  87 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER A  91 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 87 through 91'
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 5
      removed outlier: 3.844A  pdb=" N   THR L   5 " --> pdb=" O   SER L  24 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   SER L  24 " --> pdb=" O   THR L   5 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'L' and resid 58 through 59
      removed outlier: 3.663A  pdb=" N   ASN L  58 " --> pdb=" O   TYR L  54 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR L  54 " --> pdb=" O   ASN L  58 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   TRP L  40 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   TYR L  54 " --> pdb=" O   LEU L  38 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   LEU L  38 " --> pdb=" O   TYR L  54 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLN L  95 " --> pdb=" O   THR L 102 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   THR L 102 " --> pdb=" O   GLN L  95 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 58 through 59
      removed outlier: 3.663A  pdb=" N   ASN L  58 " --> pdb=" O   TYR L  54 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR L  54 " --> pdb=" O   ASN L  58 " (cutoff:3.500A)
      removed outlier: 7.062A  pdb=" N   TRP L  40 " --> pdb=" O   LEU L  52 " (cutoff:3.500A)
      removed outlier: 5.552A  pdb=" N   TYR L  54 " --> pdb=" O   LEU L  38 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   LEU L  38 " --> pdb=" O   TYR L  54 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLN L  43 " --> pdb=" O   VAL L  90 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   VAL L  90 " --> pdb=" O   GLN L  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 68 through 71
      removed outlier: 3.561A  pdb=" N   SER L  68 " --> pdb=" O   ARG L  79 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.542A  pdb=" N   THR H 119 " --> pdb=" O   GLU H  10 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 22 through 23
      removed outlier: 3.559A  pdb=" N   CYS H  22 " --> pdb=" O   ALA H  79 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.207A  pdb=" N   LEU H  45 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ARG H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TRP H  36 " --> pdb=" O   GLY H  49 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLN H  39 " --> pdb=" O   VAL H  93 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL H  93 " --> pdb=" O   GLN H  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.207A  pdb=" N   LEU H  45 " --> pdb=" O   ARG H  40 " (cutoff:3.500A)
      removed outlier: 7.964A  pdb=" N   ARG H  40 " --> pdb=" O   LEU H  45 " (cutoff:3.500A)
      removed outlier: 5.540A  pdb=" N   TRP H  47 " --> pdb=" O   LYS H  38 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   LYS H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TRP H  36 " --> pdb=" O   GLY H  49 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 4 through 6
    Processing sheet with id=AB1, first strand: chain 'A' and resid 17 through 19
      removed outlier: 3.555A  pdb=" N   VAL A  18 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 45 through 51
      removed outlier: 6.359A  pdb=" N   TRP A  36 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   TYR A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   MET A  34 " --> pdb=" O   TYR A  50 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   VAL A  37 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 5
      removed outlier: 3.908A  pdb=" N   VAL C  19 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   ILE C  75 " --> pdb=" O   VAL C  19 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   PHE C  71 " --> pdb=" O   CYS C  23 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   SER C  65 " --> pdb=" O   SER C  72 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS C  74 " --> pdb=" O   SER C  63 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   SER C  63 " --> pdb=" O   LYS C  74 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 48
      removed outlier: 6.028A  pdb=" N   LEU C  46 " --> pdb=" O   GLN C  37 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   GLN C  37 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   TRP C  35 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 5
      removed outlier: 3.609A  pdb=" N   LYS D   4 " --> pdb=" O   PHE D  43 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   PHE D  43 " --> pdb=" O   LYS D   4 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 17 through 22
      removed outlier: 6.588A  pdb=" N   ALA D  18 " --> pdb=" O   ASN D 147 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   TYR D 149 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 6.534A  pdb=" N   VAL D  20 " --> pdb=" O   TYR D 149 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE D 142 " --> pdb=" O   GLN D 133 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ALA D 127 " --> pdb=" O   ILE D 148 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ALA D 150 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
      removed outlier: 6.801A  pdb=" N   LEU D 125 " --> pdb=" O   ALA D 150 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP D  54 " --> pdb=" O   TYR D  95 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL D  56 " --> pdb=" O   VAL D  93 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   VAL D  93 " --> pdb=" O   VAL D  56 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 36 through 37
      removed outlier: 3.814A  pdb=" N   VAL D  36 " --> pdb=" O   LEU D 107 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 75 through 76

    70 hydrogen bonds defined for protein.
    171 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: 0.50

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1474
        1.34 -     1.46: 1247
        1.46 -     1.58: 2040
        1.58 -     1.70: 0
        1.70 -     1.82: 25
  Bond restraints: 4786
  Sorted by residual:
  bond pdb=" CA  ASP C  49 "
       pdb=" C   ASP C  49 "
    ideal  model  delta    sigma   weight residual
    1.528  1.488  0.040 1.34e-02 5.57e+03 8.86e+00
  bond pdb=" CA  ASP L  75 "
       pdb=" C   ASP L  75 "
    ideal  model  delta    sigma   weight residual
    1.522  1.496  0.026 1.21e-02 6.83e+03 4.45e+00
  bond pdb=" CA  ASP D 153 "
       pdb=" CB  ASP D 153 "
    ideal  model  delta    sigma   weight residual
    1.525  1.554 -0.029 1.47e-02 4.63e+03 3.95e+00
  bond pdb=" N   ASP L  75 "
       pdb=" CA  ASP L  75 "
    ideal  model  delta    sigma   weight residual
    1.454  1.430  0.025 1.27e-02 6.20e+03 3.78e+00
  bond pdb=" N   ALA C   9 "
       pdb=" CA  ALA C   9 "
    ideal  model  delta    sigma   weight residual
    1.457  1.482 -0.025 1.29e-02 6.01e+03 3.68e+00
  ... (remaining 4781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.91: 6190
        1.91 -     3.82: 257
        3.82 -     5.73: 42
        5.73 -     7.64: 15
        7.64 -     9.55: 5
  Bond angle restraints: 6509
  Sorted by residual:
  angle pdb=" C   GLU L  98 "
        pdb=" CA  GLU L  98 "
        pdb=" CB  GLU L  98 "
      ideal   model   delta    sigma   weight residual
     116.34  110.71    5.63 1.40e+00 5.10e-01 1.62e+01
  angle pdb=" C   LEU D 109 "
        pdb=" N   THR D 110 "
        pdb=" CA  THR D 110 "
      ideal   model   delta    sigma   weight residual
     121.61  127.17   -5.56 1.39e+00 5.18e-01 1.60e+01
  angle pdb=" N   SER C   7 "
        pdb=" CA  SER C   7 "
        pdb=" C   SER C   7 "
      ideal   model   delta    sigma   weight residual
     109.81  117.43   -7.62 2.21e+00 2.05e-01 1.19e+01
  angle pdb=" CA  LEU C  11 "
        pdb=" C   LEU C  11 "
        pdb=" N   SER C  12 "
      ideal   model   delta    sigma   weight residual
     119.56  117.61    1.95 5.80e-01 2.97e+00 1.13e+01
  angle pdb=" C   GLU C 105 "
        pdb=" N   MET C 106 "
        pdb=" CA  MET C 106 "
      ideal   model   delta    sigma   weight residual
     121.70  127.61   -5.91 1.80e+00 3.09e-01 1.08e+01
  ... (remaining 6504 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.58: 2470
       16.58 -    33.17: 246
       33.17 -    49.75: 51
       49.75 -    66.33: 10
       66.33 -    82.92: 4
  Dihedral angle restraints: 2781
    sinusoidal: 1039
      harmonic: 1742
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  93 "
           pdb=" CB  CYS L  93 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  137.99  -44.99     1      1.00e+01 1.00e-02 2.81e+01
  dihedral pdb=" CA  PHE D  84 "
           pdb=" C   PHE D  84 "
           pdb=" N   PRO D  85 "
           pdb=" CA  PRO D  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.28   21.72     0      5.00e+00 4.00e-02 1.89e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   57.62   35.38     1      1.00e+01 1.00e-02 1.77e+01
  ... (remaining 2778 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 516
       0.046 -    0.092: 142
       0.092 -    0.138: 49
       0.138 -    0.184: 7
       0.184 -    0.230: 1
  Chirality restraints: 715
  Sorted by residual:
  chirality pdb=" CB  THR C  52 "
            pdb=" CA  THR C  52 "
            pdb=" OG1 THR C  52 "
            pdb=" CG2 THR C  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  THR H 116 "
            pdb=" CA  THR H 116 "
            pdb=" OG1 THR H 116 "
            pdb=" CG2 THR H 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.16 2.00e-01 2.50e+01 6.77e-01
  chirality pdb=" CA  THR C  94 "
            pdb=" N   THR C  94 "
            pdb=" C   THR C  94 "
            pdb=" CB  THR C  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.16 2.00e-01 2.50e+01 6.14e-01
  ... (remaining 712 not shown)

  Planarity restraints: 830
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN L  11 "    0.063 5.00e-02 4.00e+02   9.59e-02 1.47e+01
        pdb=" N   PRO L  12 "   -0.166 5.00e-02 4.00e+02
        pdb=" CA  PRO L  12 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO L  12 "    0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  33 "    0.016 2.00e-02 2.50e+03   1.41e-02 4.97e+00
        pdb=" CG  TRP A  33 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  33 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  33 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  33 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  33 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  33 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  33 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D  84 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.16e+00
        pdb=" N   PRO D  85 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO D  85 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D  85 "    0.025 5.00e-02 4.00e+02
  ... (remaining 827 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 480
        2.75 -     3.29: 4131
        3.29 -     3.83: 6870
        3.83 -     4.36: 7216
        4.36 -     4.90: 12932
  Nonbonded interactions: 31629
  Sorted by model distance:
  nonbonded pdb=" O   ALA H  24 "
            pdb=" OG  SER H  77 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   SER D  72 "
            pdb=" OG1 THR D 110 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" OG  SER D  80 "
            pdb=" N   SER D  81 "
     model   vdw
     2.345 3.120
  nonbonded pdb=" NZ  LYS D  76 "
            pdb=" OH  TYR D 108 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" OG  SER C  14 "
            pdb=" OE2 GLU C  17 "
     model   vdw
     2.373 3.040
  ... (remaining 31624 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 group one per residue
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:             3.030
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.250
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4791  Z= 0.202
  Angle     :  0.921   9.551   6519  Z= 0.489
  Chirality :  0.049   0.230    715
  Planarity :  0.007   0.096    830
  Dihedral  : 13.893  82.918   1664
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.34 %
    Allowed  :  8.42 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.32), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.28 (0.39), residues: 193
  loop : -2.09 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  98 
 TYR   0.019   0.002   TYR L 101 
 PHE   0.015   0.002   PHE H  76 
 TRP   0.038   0.003   TRP A  33 
 HIS   0.005   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 4786)
  covalent geometry    : angle       0.92147 ( 6509)
  SS BOND              : bond        0.00408 (    5)
  SS BOND              : angle       0.92059 (   10)
  hydrogen bonds       : bond        0.28563 (   63)
  hydrogen bonds       : angle      10.40380 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   53 ILE cc_start: 0.8206 (mm) cc_final: 0.8004 (mm)
REVERT: L   54 TYR cc_start: 0.6238 (p90) cc_final: 0.6038 (p90)
REVERT: C   27 GLU cc_start: 0.8128 (mp0) cc_final: 0.7901 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 109
  average time/residue: 0.0642
  time to fit residues: 9.5011
Evaluate side-chains
  75 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 54 optimal weight:    0.0670
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    0.0870
   chunk 16 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.4896

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 135 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.129422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.109117 restraints weight = 10656.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.112114 restraints weight = 6480.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.114304 restraints weight = 4533.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.115740 restraints weight = 3461.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.116951 restraints weight = 2843.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4791  Z= 0.114
  Angle     :  0.602   6.511   6519  Z= 0.309
  Chirality :  0.041   0.124    715
  Planarity :  0.005   0.066    830
  Dihedral  :  4.892  21.716    657
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.85 (0.33), residues: 594
  helix:  None (None), residues: 0
  sheet:  0.09 (0.38), residues: 208
  loop : -2.13 (0.28), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  55 
 TYR   0.013   0.001   TYR H  94 
 PHE   0.010   0.001   PHE A 104 
 TRP   0.013   0.002   TRP A  33 
 HIS   0.002   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4786)
  covalent geometry    : angle       0.60073 ( 6509)
  SS BOND              : bond        0.00464 (    5)
  SS BOND              : angle       0.99535 (   10)
  hydrogen bonds       : bond        0.05213 (   63)
  hydrogen bonds       : angle       7.80236 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   86 GLU cc_start: 0.8583 (pm20) cc_final: 0.8275 (pm20)
REVERT: C    6 GLN cc_start: 0.8304 (pm20) cc_final: 0.7622 (pm20)
REVERT: D  153 ASP cc_start: 0.8695 (t0) cc_final: 0.8469 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.0540
  time to fit residues: 7.9808
Evaluate side-chains
  79 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0070
   chunk 28 optimal weight:    0.0040
   chunk 44 optimal weight:    0.0770
   chunk 17 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   overall best weight:    0.4170

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

Flipped N/Q/H residues before XYZ refinement:
** D  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.109367 restraints weight = 10530.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.112618 restraints weight = 6185.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.114974 restraints weight = 4207.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.116401 restraints weight = 3147.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.117758 restraints weight = 2571.118|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4791  Z= 0.100
  Angle     :  0.566   5.863   6519  Z= 0.289
  Chirality :  0.041   0.152    715
  Planarity :  0.004   0.042    830
  Dihedral  :  4.682  21.090    657
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.25 %
    Favored  : 91.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.33), residues: 594
  helix:  None (None), residues: 0
  sheet:  0.10 (0.37), residues: 213
  loop : -2.00 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  24 
 TYR   0.011   0.001   TYR H  59 
 PHE   0.011   0.001   PHE A 104 
 TRP   0.012   0.001   TRP C  35 
 HIS   0.003   0.001   HIS D  45 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4786)
  covalent geometry    : angle       0.56583 ( 6509)
  SS BOND              : bond        0.00380 (    5)
  SS BOND              : angle       0.77333 (   10)
  hydrogen bonds       : bond        0.04403 (   63)
  hydrogen bonds       : angle       7.15412 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   56 MET cc_start: 0.8670 (tpt) cc_final: 0.8467 (tpt)
REVERT: L   86 GLU cc_start: 0.8580 (pm20) cc_final: 0.8316 (pm20)
REVERT: A   34 MET cc_start: 0.7950 (tpp) cc_final: 0.7738 (tpt)
REVERT: D  153 ASP cc_start: 0.8687 (t0) cc_final: 0.8445 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.0587
  time to fit residues: 8.7669
Evaluate side-chains
  78 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0870
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
** D  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.127550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.107419 restraints weight = 10588.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.110379 restraints weight = 6387.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.112544 restraints weight = 4443.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.114178 restraints weight = 3376.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.115171 restraints weight = 2735.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7561
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4791  Z= 0.111
  Angle     :  0.563   5.989   6519  Z= 0.288
  Chirality :  0.041   0.125    715
  Planarity :  0.004   0.038    830
  Dihedral  :  4.727  21.046    657
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.33), residues: 594
  helix:  None (None), residues: 0
  sheet:  0.26 (0.37), residues: 212
  loop : -1.99 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 132 
 TYR   0.011   0.001   TYR A  32 
 PHE   0.012   0.001   PHE A 104 
 TRP   0.016   0.002   TRP H  36 
 HIS   0.004   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4786)
  covalent geometry    : angle       0.56292 ( 6509)
  SS BOND              : bond        0.00430 (    5)
  SS BOND              : angle       0.84578 (   10)
  hydrogen bonds       : bond        0.03920 (   63)
  hydrogen bonds       : angle       6.56067 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   54 TYR cc_start: 0.6235 (p90) cc_final: 0.6000 (p90)
REVERT: L   86 GLU cc_start: 0.8549 (pm20) cc_final: 0.8295 (pm20)
REVERT: D  153 ASP cc_start: 0.8718 (t0) cc_final: 0.8494 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0580
  time to fit residues: 8.2495
Evaluate side-chains
  77 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0970
   chunk 52 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0050
   chunk 9 optimal weight:    0.0370
   chunk 35 optimal weight:    4.9990
   chunk 50 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0980
   chunk 56 optimal weight:    4.9990
   overall best weight:    0.2270

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

Flipped N/Q/H residues before XYZ refinement:
H   6 GLN
** D  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.130563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110030 restraints weight = 10760.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.112946 restraints weight = 6242.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.115549 restraints weight = 4379.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.117320 restraints weight = 3202.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.118638 restraints weight = 2537.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   4791  Z= 0.092
  Angle     :  0.561   6.820   6519  Z= 0.280
  Chirality :  0.041   0.145    715
  Planarity :  0.004   0.038    830
  Dihedral  :  4.482  19.616    657
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.33), residues: 594
  helix:  None (None), residues: 0
  sheet:  0.25 (0.40), residues: 191
  loop : -1.79 (0.29), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  82 
 TYR   0.012   0.001   TYR D  64 
 PHE   0.006   0.001   PHE A 104 
 TRP   0.017   0.001   TRP C  35 
 HIS   0.002   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00204 ( 4786)
  covalent geometry    : angle       0.56069 ( 6509)
  SS BOND              : bond        0.00606 (    5)
  SS BOND              : angle       0.72378 (   10)
  hydrogen bonds       : bond        0.03567 (   63)
  hydrogen bonds       : angle       6.27513 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   54 TYR cc_start: 0.6088 (p90) cc_final: 0.5856 (p90)
REVERT: L   86 GLU cc_start: 0.8548 (pm20) cc_final: 0.8302 (pm20)
REVERT: C    6 GLN cc_start: 0.8203 (pm20) cc_final: 0.7936 (pm20)
REVERT: D  153 ASP cc_start: 0.8725 (t0) cc_final: 0.8515 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.0679
  time to fit residues: 9.3265
Evaluate side-chains
  75 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 50 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.9984

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

Flipped N/Q/H residues before XYZ refinement:
L  95 GLN
H   6 GLN
C  45 GLN
C  76 ASN
** D  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.119104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.099759 restraints weight = 11049.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.102539 restraints weight = 6677.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104512 restraints weight = 4660.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.105815 restraints weight = 3568.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.106942 restraints weight = 2958.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4791  Z= 0.238
  Angle     :  0.728   8.744   6519  Z= 0.376
  Chirality :  0.045   0.181    715
  Planarity :  0.005   0.033    830
  Dihedral  :  5.554  26.504    657
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.35 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.04 (0.32), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.24 (0.35), residues: 222
  loop : -2.19 (0.28), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  82 
 TYR   0.021   0.002   TYR L 101 
 PHE   0.027   0.002   PHE A  60 
 TRP   0.026   0.003   TRP H  36 
 HIS   0.011   0.002   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 ( 4786)
  covalent geometry    : angle       0.72565 ( 6509)
  SS BOND              : bond        0.00766 (    5)
  SS BOND              : angle       1.67684 (   10)
  hydrogen bonds       : bond        0.04938 (   63)
  hydrogen bonds       : angle       6.65898 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   54 TYR cc_start: 0.6149 (p90) cc_final: 0.5817 (p90)
REVERT: L   75 ASP cc_start: 0.8575 (t0) cc_final: 0.8323 (t0)
REVERT: L   86 GLU cc_start: 0.8500 (pm20) cc_final: 0.8296 (pm20)
REVERT: H   48 ILE cc_start: 0.6856 (mt) cc_final: 0.6542 (mt)
REVERT: H  110 ASP cc_start: 0.8413 (p0) cc_final: 0.8189 (p0)
REVERT: C    6 GLN cc_start: 0.8411 (pm20) cc_final: 0.8208 (pm20)
REVERT: C   27 GLU cc_start: 0.8461 (pm20) cc_final: 0.8134 (pm20)
REVERT: C   35 TRP cc_start: 0.8303 (m100) cc_final: 0.7991 (m100)
  outliers start: 1
  outliers final: 1
  residues processed: 97
  average time/residue: 0.0658
  time to fit residues: 8.3913
Evaluate side-chains
  70 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 12 optimal weight:    0.0870
   chunk 30 optimal weight:    1.9990
   chunk 6 optimal weight:   10.0000
   chunk 27 optimal weight:    0.4980
   chunk 34 optimal weight:    0.0770
   chunk 20 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0000
   chunk 57 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.2720

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.126348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.106873 restraints weight = 10601.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.109981 restraints weight = 6257.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.112108 restraints weight = 4258.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.113725 restraints weight = 3221.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.114706 restraints weight = 2590.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   4791  Z= 0.100
  Angle     :  0.609   6.777   6519  Z= 0.301
  Chirality :  0.042   0.124    715
  Planarity :  0.004   0.037    830
  Dihedral  :  4.848  22.327    657
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.59 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.33), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.13 (0.35), residues: 226
  loop : -2.09 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  82 
 TYR   0.014   0.001   TYR D  64 
 PHE   0.013   0.001   PHE L  67 
 TRP   0.019   0.002   TRP C  35 
 HIS   0.002   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 4786)
  covalent geometry    : angle       0.60834 ( 6509)
  SS BOND              : bond        0.00404 (    5)
  SS BOND              : angle       0.73421 (   10)
  hydrogen bonds       : bond        0.03516 (   63)
  hydrogen bonds       : angle       6.22157 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   54 TYR cc_start: 0.6035 (p90) cc_final: 0.5700 (p90)
REVERT: L   75 ASP cc_start: 0.8436 (t0) cc_final: 0.8164 (t0)
REVERT: L   82 ARG cc_start: 0.7473 (mmm160) cc_final: 0.7238 (mmm160)
REVERT: L   86 GLU cc_start: 0.8480 (pm20) cc_final: 0.8242 (pm20)
REVERT: H  101 TYR cc_start: 0.7793 (t80) cc_final: 0.7530 (t80)
REVERT: C   27 GLU cc_start: 0.8275 (pm20) cc_final: 0.7977 (pm20)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.0646
  time to fit residues: 8.9206
Evaluate side-chains
  71 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0370
   chunk 43 optimal weight:    4.9990
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0770
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.7820

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.124202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104666 restraints weight = 10858.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.107682 restraints weight = 6470.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.109742 restraints weight = 4414.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.111303 restraints weight = 3373.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112387 restraints weight = 2728.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4791  Z= 0.123
  Angle     :  0.630  10.560   6519  Z= 0.313
  Chirality :  0.042   0.126    715
  Planarity :  0.004   0.032    830
  Dihedral  :  4.825  21.957    657
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.92 (0.32), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.14 (0.35), residues: 220
  loop : -2.11 (0.28), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  82 
 TYR   0.012   0.001   TYR D  64 
 PHE   0.009   0.001   PHE C  71 
 TRP   0.014   0.001   TRP C  35 
 HIS   0.005   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 4786)
  covalent geometry    : angle       0.62897 ( 6509)
  SS BOND              : bond        0.00439 (    5)
  SS BOND              : angle       0.96488 (   10)
  hydrogen bonds       : bond        0.03738 (   63)
  hydrogen bonds       : angle       6.25112 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   54 TYR cc_start: 0.6062 (p90) cc_final: 0.5680 (p90)
REVERT: L   75 ASP cc_start: 0.8512 (t0) cc_final: 0.8229 (t0)
REVERT: L   86 GLU cc_start: 0.8406 (pm20) cc_final: 0.8173 (pm20)
REVERT: H  101 TYR cc_start: 0.7851 (t80) cc_final: 0.7577 (t80)
REVERT: C    6 GLN cc_start: 0.8304 (pm20) cc_final: 0.8083 (pm20)
REVERT: C   27 GLU cc_start: 0.8308 (pm20) cc_final: 0.7983 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0599
  time to fit residues: 7.9587
Evaluate side-chains
  69 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    0.5980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.123510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.104069 restraints weight = 10762.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.106938 restraints weight = 6449.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.109050 restraints weight = 4476.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.110471 restraints weight = 3406.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.111623 restraints weight = 2802.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4791  Z= 0.122
  Angle     :  0.624   9.569   6519  Z= 0.313
  Chirality :  0.042   0.184    715
  Planarity :  0.004   0.033    830
  Dihedral  :  4.830  20.690    657
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (0.32), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.17 (0.34), residues: 228
  loop : -2.14 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  82 
 TYR   0.014   0.001   TYR D  48 
 PHE   0.010   0.001   PHE H  95 
 TRP   0.012   0.002   TRP H  36 
 HIS   0.004   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4786)
  covalent geometry    : angle       0.62301 ( 6509)
  SS BOND              : bond        0.00420 (    5)
  SS BOND              : angle       0.89764 (   10)
  hydrogen bonds       : bond        0.03674 (   63)
  hydrogen bonds       : angle       6.25711 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   54 TYR cc_start: 0.6051 (p90) cc_final: 0.5720 (p90)
REVERT: L   75 ASP cc_start: 0.8527 (t0) cc_final: 0.8227 (t0)
REVERT: L   86 GLU cc_start: 0.8389 (pm20) cc_final: 0.8156 (pm20)
REVERT: H  101 TYR cc_start: 0.7832 (t80) cc_final: 0.7434 (t80)
REVERT: C    6 GLN cc_start: 0.8283 (pm20) cc_final: 0.8080 (pm20)
REVERT: C   27 GLU cc_start: 0.8270 (pm20) cc_final: 0.7947 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.0549
  time to fit residues: 7.2430
Evaluate side-chains
  70 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 1 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0570
   chunk 0 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.123974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.104454 restraints weight = 10761.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.107401 restraints weight = 6394.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.109475 restraints weight = 4420.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111048 restraints weight = 3370.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112095 restraints weight = 2721.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4791  Z= 0.113
  Angle     :  0.613   9.448   6519  Z= 0.305
  Chirality :  0.042   0.175    715
  Planarity :  0.004   0.045    830
  Dihedral  :  4.752  20.853    657
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.74 %
    Favored  : 92.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.91 (0.32), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.13 (0.34), residues: 228
  loop : -2.15 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG L  82 
 TYR   0.013   0.001   TYR D  64 
 PHE   0.009   0.001   PHE H  95 
 TRP   0.013   0.001   TRP C  35 
 HIS   0.003   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4786)
  covalent geometry    : angle       0.61263 ( 6509)
  SS BOND              : bond        0.00400 (    5)
  SS BOND              : angle       0.89670 (   10)
  hydrogen bonds       : bond        0.03581 (   63)
  hydrogen bonds       : angle       6.15836 (  171)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   53 ILE cc_start: 0.7988 (mm) cc_final: 0.7787 (mm)
REVERT: L   54 TYR cc_start: 0.5973 (p90) cc_final: 0.5605 (p90)
REVERT: L   75 ASP cc_start: 0.8504 (t0) cc_final: 0.8195 (t0)
REVERT: L   86 GLU cc_start: 0.8383 (pm20) cc_final: 0.8146 (pm20)
REVERT: H  101 TYR cc_start: 0.7821 (t80) cc_final: 0.7500 (t80)
REVERT: H  110 ASP cc_start: 0.8453 (p0) cc_final: 0.8237 (p0)
REVERT: C   27 GLU cc_start: 0.8227 (pm20) cc_final: 0.7886 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.0593
  time to fit residues: 7.4738
Evaluate side-chains
  69 residues out of total 509 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 59
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 56 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** D  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.123300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.103778 restraints weight = 10756.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.106762 restraints weight = 6494.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.108890 restraints weight = 4480.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.110362 restraints weight = 3395.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.111496 restraints weight = 2770.893|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4791  Z= 0.118
  Angle     :  0.613   6.859   6519  Z= 0.308
  Chirality :  0.042   0.169    715
  Planarity :  0.004   0.039    830
  Dihedral  :  4.754  20.806    657
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.91 %
    Favored  : 92.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (0.32), residues: 594
  helix:  None (None), residues: 0
  sheet: -0.08 (0.36), residues: 217
  loop : -2.17 (0.28), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG L  82 
 TYR   0.013   0.001   TYR D  64 
 PHE   0.010   0.001   PHE H  95 
 TRP   0.012   0.001   TRP A  33 
 HIS   0.004   0.001   HIS C  90 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4786)
  covalent geometry    : angle       0.61248 ( 6509)
  SS BOND              : bond        0.00445 (    5)
  SS BOND              : angle       0.86916 (   10)
  hydrogen bonds       : bond        0.03607 (   63)
  hydrogen bonds       : angle       6.01713 (  171)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1015.05 seconds
wall clock time: 18 minutes 14.94 seconds (1094.94 seconds total)