Starting phenix.real_space_refine
on Wed Mar 12 11:58:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kbb_22788/03_2025/7kbb_22788_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kbb_22788/03_2025/7kbb_22788.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.02
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kbb_22788/03_2025/7kbb_22788.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kbb_22788/03_2025/7kbb_22788.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kbb_22788/03_2025/7kbb_22788_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kbb_22788/03_2025/7kbb_22788_neut.cif"
  }
  resolution = 4.02
  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=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1776 atoms to isotropic.
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      29      5.16       5
     C    4046      2.51       5
     N    1139      2.21       5
     O    1208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6422
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 979
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
    Chain: "B"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 818
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "C"
      Number of atoms: 567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 567
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1384
          Classifications: {'peptide': 170}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 158}
    Chain: "E"
      Number of atoms: 893
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 893
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 3, 'TRANS': 104}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 957
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "L"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 824
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100}
  Time building chain proxies: 4.93, per 1000 atoms: 0.77
  Number of scatterers: 6422
  At special positions: 0
  Unit cell: (78.525, 106.794, 126.687, 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      29     16.00
     O    1208      8.00
     N    1139      7.00
     C    4046      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  96 " - pdb=" SG  CYS C 111 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D  57 " - pdb=" SG  CYS D  83 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 172 " - pdb=" SG  CYS D 207 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  20 " - pdb=" SG  CYS E  40 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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: 1.50
  Conformation dependent library (CDL) restraints added in 949.7 milliseconds
  

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1492

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 14 sheets defined
      19.2% alpha, 36.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.92
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 30
      No H-bonds generated for 'chain 'A' and resid 28 through 30'
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'A' and resid 100 through 100D
      removed outlier: 3.509A  pdb=" N   GLY A 100C" --> pdb=" O   ASP A 100 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   TYR A 100D" --> pdb=" O   ARG A 100A" (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 100 through 100D'
    Processing helix  chain 'B' and resid 79 through 83
      removed outlier: 4.083A  pdb=" N   PHE B  83 " --> pdb=" O   PRO B  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 92
    Processing helix  chain 'C' and resid 93 through 97
    Processing helix  chain 'C' and resid 145 through 155
      removed outlier: 4.038A  pdb=" N   LYS C 155 " --> pdb=" O   GLU C 151 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 55
    Processing helix  chain 'D' and resid 67 through 69
      No H-bonds generated for 'chain 'D' and resid 67 through 69'
    Processing helix  chain 'D' and resid 80 through 84
    Processing helix  chain 'D' and resid 104 through 118
      removed outlier: 4.325A  pdb=" N   ASN D 118 " --> pdb=" O   LEU D 114 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 131
      Proline residue:  D 126  - end of helix
    Processing helix  chain 'D' and resid 140 through 151
    Processing helix  chain 'E' and resid 35 through 41
    Processing helix  chain 'E' and resid 45 through 69
    Processing helix  chain 'E' and resid 73 through 79
      removed outlier: 3.635A  pdb=" N   LEU E  77 " --> pdb=" O   ASN E  73 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   ARG E  79 " --> pdb=" O   ASP E  75 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 95
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.671A  pdb=" N   PHE L  83 " --> pdb=" O   SER L  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 8
    Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12
      removed outlier: 4.759A  pdb=" N   ASP A  33 " --> pdb=" O   GLY A  95 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   MET A  34 " --> pdb=" O   ARG A  50 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   ARG A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 4.458A  pdb=" N   ILE A 102 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 7
      removed outlier: 3.572A  pdb=" N   THR B  74 " --> pdb=" O   SER B  63 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   SER B  63 " --> pdb=" O   THR B  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.682A  pdb=" N   GLU B 105 " --> pdb=" O   VAL B  11 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   LEU B  33 " --> pdb=" O   TYR B  49 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   TYR B  49 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 109 through 111
    Processing sheet with id=AA7, first strand: chain 'C' and resid 130 through 131
    Processing sheet with id=AA8, first strand: chain 'D' and resid 71 through 78
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.526A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.586A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.624A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 112 " (cutoff:3.500A)
      removed outlier: 4.730A  pdb=" N   TRP H 112 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
      removed outlier: 6.544A  pdb=" N   LYS H  98 " --> pdb=" O   ASP H 110 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   LEU H 106 " --> pdb=" O   LEU H 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.624A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   PHE H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   MET H  34 " --> pdb=" O   PHE H  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.615A  pdb=" N   GLU L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13
      removed outlier: 7.121A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    288 hydrogen bonds defined for protein.
    753 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: 1.93

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.17 -     1.31: 1030
        1.31 -     1.44: 1965
        1.44 -     1.58: 3540
        1.58 -     1.71: 2
        1.71 -     1.85: 41
  Bond restraints: 6578
  Sorted by residual:
  bond pdb=" CA  ARG H  87 "
       pdb=" C   ARG H  87 "
    ideal  model  delta    sigma   weight residual
    1.523  1.639 -0.116 1.34e-02 5.57e+03 7.48e+01
  bond pdb=" CA  LEU H  86 "
       pdb=" C   LEU H  86 "
    ideal  model  delta    sigma   weight residual
    1.524  1.619 -0.095 1.26e-02 6.30e+03 5.65e+01
  bond pdb=" N   ARG H  87 "
       pdb=" CA  ARG H  87 "
    ideal  model  delta    sigma   weight residual
    1.457  1.552 -0.094 1.29e-02 6.01e+03 5.34e+01
  bond pdb=" C   LEU B  78 "
       pdb=" N   GLN B  79 "
    ideal  model  delta    sigma   weight residual
    1.327  1.228  0.098 1.71e-02 3.42e+03 3.31e+01
  bond pdb=" C   ARG H  87 "
       pdb=" O   ARG H  87 "
    ideal  model  delta    sigma   weight residual
    1.235  1.173  0.063 1.26e-02 6.30e+03 2.46e+01
  ... (remaining 6573 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.70: 8888
        5.70 -    11.39: 21
       11.39 -    17.09: 3
       17.09 -    22.79: 1
       22.79 -    28.48: 1
  Bond angle restraints: 8914
  Sorted by residual:
  angle pdb=" N   LEU H  86 "
        pdb=" CA  LEU H  86 "
        pdb=" C   LEU H  86 "
      ideal   model   delta    sigma   weight residual
     111.14  139.62  -28.48 1.08e+00 8.57e-01 6.96e+02
  angle pdb=" N   ARG H  87 "
        pdb=" CA  ARG H  87 "
        pdb=" C   ARG H  87 "
      ideal   model   delta    sigma   weight residual
     110.80  129.85  -19.05 2.13e+00 2.20e-01 8.00e+01
  angle pdb=" C   ALA H  88 "
        pdb=" N   GLU H  89 "
        pdb=" CA  GLU H  89 "
      ideal   model   delta    sigma   weight residual
     122.33  110.68   11.65 1.68e+00 3.54e-01 4.81e+01
  angle pdb=" N   ALA H  88 "
        pdb=" CA  ALA H  88 "
        pdb=" C   ALA H  88 "
      ideal   model   delta    sigma   weight residual
     107.98  120.97  -12.99 1.88e+00 2.83e-01 4.77e+01
  angle pdb=" O   SER H  85 "
        pdb=" C   SER H  85 "
        pdb=" N   LEU H  86 "
      ideal   model   delta    sigma   weight residual
     123.32  114.89    8.43 1.27e+00 6.20e-01 4.41e+01
  ... (remaining 8909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.91: 3460
       16.91 -    33.81: 321
       33.81 -    50.72: 72
       50.72 -    67.63: 19
       67.63 -    84.54: 16
  Dihedral angle restraints: 3888
    sinusoidal: 1553
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" CB  CYS D  57 "
           pdb=" SG  CYS D  57 "
           pdb=" SG  CYS D  83 "
           pdb=" CB  CYS D  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -135.12   49.12     1      1.00e+01 1.00e-02 3.32e+01
  dihedral pdb=" CB  CYS C  96 "
           pdb=" SG  CYS C  96 "
           pdb=" SG  CYS C 111 "
           pdb=" CB  CYS C 111 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -115.98   29.98     1      1.00e+01 1.00e-02 1.28e+01
  dihedral pdb=" CB  CYS D 172 "
           pdb=" SG  CYS D 172 "
           pdb=" SG  CYS D 207 "
           pdb=" CB  CYS D 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -58.04  -27.96     1      1.00e+01 1.00e-02 1.12e+01
  ... (remaining 3885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.150: 940
       0.150 -    0.301: 9
       0.301 -    0.451: 1
       0.451 -    0.602: 2
       0.602 -    0.752: 1
  Chirality restraints: 953
  Sorted by residual:
  chirality pdb=" CA  LEU H  86 "
            pdb=" N   LEU H  86 "
            pdb=" C   LEU H  86 "
            pdb=" CB  LEU H  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.76    0.75 2.00e-01 2.50e+01 1.42e+01
  chirality pdb=" CG  LEU E  59 "
            pdb=" CB  LEU E  59 "
            pdb=" CD1 LEU E  59 "
            pdb=" CD2 LEU E  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.06   -0.53 2.00e-01 2.50e+01 7.04e+00
  chirality pdb=" CG  LEU L  78 "
            pdb=" CB  LEU L  78 "
            pdb=" CD1 LEU L  78 "
            pdb=" CD2 LEU L  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.11   -0.48 2.00e-01 2.50e+01 5.80e+00
  ... (remaining 950 not shown)

  Planarity restraints: 1151
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  67 "    0.152 9.50e-02 1.11e+02   8.78e-02 4.10e+01
        pdb=" NE  ARG H  67 "   -0.045 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  67 "    0.105 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  67 "   -0.037 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  67 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  71 "   -0.133 9.50e-02 1.11e+02   7.66e-02 3.14e+01
        pdb=" NE  ARG A  71 "    0.039 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  71 "   -0.092 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  71 "    0.033 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  71 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  38 "    0.106 9.50e-02 1.11e+02   6.19e-02 2.12e+01
        pdb=" NE  ARG H  38 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  38 "    0.076 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  38 "   -0.027 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  38 "   -0.022 2.00e-02 2.50e+03
  ... (remaining 1148 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 121
        2.64 -     3.20: 5851
        3.20 -     3.77: 9713
        3.77 -     4.33: 13531
        4.33 -     4.90: 22229
  Nonbonded interactions: 51445
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG H  38 "
            pdb=" OE1 GLU H  89 "
     model   vdw
     2.073 3.120
  nonbonded pdb=" O   SER E  41 "
            pdb=" NH1 ARG E  94 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" OG1 THR D 120 "
            pdb=" OG  SER L  52 "
     model   vdw
     2.090 3.040
  nonbonded pdb=" OH  TYR A 100E"
            pdb=" O   CYS E  40 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OH  TYR D  46 "
            pdb=" O   ARG H 104 "
     model   vdw
     2.144 3.040
  ... (remaining 51440 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:             3.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.680
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5721
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      :  0.006   0.116   6578  Z= 0.420
  Angle     :  1.156  28.484   8914  Z= 0.718
  Chirality :  0.065   0.752    953
  Planarity :  0.009   0.088   1151
  Dihedral  : 14.883  84.536   2372
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 14.81
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  5.42 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  9.20 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -1.59 (0.26), residues: 794
  helix: -1.40 (0.40), residues: 109
  sheet: -0.16 (0.31), residues: 259
  loop : -1.53 (0.25), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.004   TRP H 100 
 HIS   0.008   0.002   HIS D 150 
 PHE   0.027   0.003   PHE D 183 
 TYR   0.031   0.006   TYR L  91 
 ARG   0.107   0.014   ARG H  67 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.678 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 TRP cc_start: 0.7113 (t60) cc_final: 0.6913 (t60)
REVERT: B    4 MET cc_start: 0.6754 (mmm) cc_final: 0.6538 (mmp)
REVERT: B   44 PRO cc_start: 0.8464 (Cg_exo) cc_final: 0.8049 (Cg_endo)
REVERT: B   94 PHE cc_start: 0.7638 (m-80) cc_final: 0.7151 (m-10)
REVERT: D  106 TRP cc_start: 0.7328 (p-90) cc_final: 0.6637 (p-90)
REVERT: D  118 ASN cc_start: 0.6021 (m-40) cc_final: 0.5507 (t0)
REVERT: D  174 MET cc_start: 0.5646 (ttp) cc_final: 0.5307 (ttp)
REVERT: H    6 GLU cc_start: 0.6182 (mp0) cc_final: 0.5740 (mp0)
REVERT: H  112 TRP cc_start: 0.6880 (m100) cc_final: 0.6641 (m100)
REVERT: L    4 MET cc_start: 0.6375 (mmm) cc_final: 0.6121 (mmt)
REVERT: L   18 ARG cc_start: 0.7241 (mtm110) cc_final: 0.6924 (ttm110)
REVERT: L   39 LYS cc_start: 0.7907 (mttt) cc_final: 0.7679 (ttmt)
REVERT: L   56 SER cc_start: 0.8230 (m) cc_final: 0.7919 (p)
  outliers start: 11
  outliers final: 7
  residues processed: 132
  average time/residue: 0.1949
  time to fit residues: 33.2571
Evaluate side-chains
  114 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.0980
   chunk 37 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  37 GLN
** C  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
E  35 HIS
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  37 GLN
L  89 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.181001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.168743 restraints weight = 11472.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.171568 restraints weight = 6919.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.173463 restraints weight = 4524.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.4163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5829
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6578  Z= 0.310
  Angle     :  0.766  11.490   8914  Z= 0.407
  Chirality :  0.048   0.281    953
  Planarity :  0.007   0.136   1151
  Dihedral  :  5.451  28.533    901
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.02 %
    Favored  : 96.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.57 (0.28), residues: 794
  helix:  0.44 (0.48), residues: 116
  sheet:  0.22 (0.31), residues: 267
  loop : -1.01 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  47 
 HIS   0.006   0.001   HIS D 150 
 PHE   0.024   0.002   PHE L  99 
 TYR   0.023   0.002   TYR L  91 
 ARG   0.009   0.001   ARG A  66 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    4 MET cc_start: 0.7012 (mmm) cc_final: 0.6707 (mmp)
REVERT: B   44 PRO cc_start: 0.8438 (Cg_exo) cc_final: 0.7960 (Cg_endo)
REVERT: D   77 VAL cc_start: 0.7912 (t) cc_final: 0.7473 (m)
REVERT: D  131 LYS cc_start: 0.7256 (mmtt) cc_final: 0.7007 (mmtt)
REVERT: H    6 GLU cc_start: 0.6366 (mp0) cc_final: 0.5513 (mp0)
REVERT: H   16 ARG cc_start: 0.6039 (mmt-90) cc_final: 0.5445 (mtt90)
REVERT: L    4 MET cc_start: 0.6247 (mmm) cc_final: 0.6029 (mmt)
REVERT: L   18 ARG cc_start: 0.7412 (mtm110) cc_final: 0.7036 (ttm110)
REVERT: L   56 SER cc_start: 0.8312 (m) cc_final: 0.8008 (p)
REVERT: L   63 SER cc_start: 0.7894 (p) cc_final: 0.7447 (t)
  outliers start: 2
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2179
  time to fit residues: 32.8997
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 67 optimal weight:    0.4980
   chunk 30 optimal weight:    0.0670
   chunk 66 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 115 ASN
D  97 GLN
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.179247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.167157 restraints weight = 11413.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.169938 restraints weight = 6845.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.171737 restraints weight = 4467.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5873
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6578  Z= 0.279
  Angle     :  0.677   7.348   8914  Z= 0.363
  Chirality :  0.046   0.276    953
  Planarity :  0.006   0.056   1151
  Dihedral  :  5.502  28.140    901
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 794
  helix:  0.67 (0.47), residues: 116
  sheet:  0.50 (0.31), residues: 264
  loop : -1.03 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  47 
 HIS   0.011   0.002   HIS H  35 
 PHE   0.018   0.002   PHE D 183 
 TYR   0.024   0.002   TYR L  91 
 ARG   0.005   0.001   ARG E  42 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: B    4 MET cc_start: 0.7081 (mmm) cc_final: 0.6809 (mmp)
REVERT: D  127 GLN cc_start: 0.6961 (tt0) cc_final: 0.6665 (tt0)
REVERT: D  131 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6982 (mmtt)
REVERT: D  174 MET cc_start: 0.6059 (ttp) cc_final: 0.5648 (ttp)
REVERT: H   72 ARG cc_start: 0.4465 (ttm-80) cc_final: 0.4091 (ttm-80)
REVERT: L   18 ARG cc_start: 0.7369 (mtm110) cc_final: 0.7083 (ttp-170)
REVERT: L   56 SER cc_start: 0.8349 (m) cc_final: 0.8061 (p)
REVERT: L   63 SER cc_start: 0.7916 (p) cc_final: 0.7502 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2801
  time to fit residues: 41.1630
Evaluate side-chains
  107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0980
   chunk 16 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0060
   chunk 35 optimal weight:    0.2980
   chunk 29 optimal weight:    0.0070
   chunk 27 optimal weight:    1.9990
   chunk 60 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   overall best weight:    0.1414

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E  96 ASN
E 129 ASN
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.187640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.179422 restraints weight = 13443.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.180311 restraints weight = 11034.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.181756 restraints weight = 9033.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.4276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5731
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   6578  Z= 0.156
  Angle     :  0.580   5.462   8914  Z= 0.309
  Chirality :  0.043   0.175    953
  Planarity :  0.005   0.052   1151
  Dihedral  :  5.040  25.619    901
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.30), residues: 794
  helix:  0.89 (0.47), residues: 123
  sheet:  0.67 (0.31), residues: 260
  loop : -0.84 (0.31), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A  47 
 HIS   0.005   0.001   HIS A  98 
 PHE   0.010   0.001   PHE E 122 
 TYR   0.024   0.001   TYR E  63 
 ARG   0.004   0.000   ARG A  66 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
REVERT: B    4 MET cc_start: 0.7076 (mmm) cc_final: 0.6759 (mmp)
REVERT: D  174 MET cc_start: 0.5993 (ttp) cc_final: 0.5478 (ttp)
REVERT: H   45 LEU cc_start: 0.7916 (tt) cc_final: 0.7600 (tp)
REVERT: H  112 TRP cc_start: 0.7095 (m100) cc_final: 0.6831 (m100)
REVERT: L   18 ARG cc_start: 0.7223 (mtm110) cc_final: 0.6960 (ttm110)
REVERT: L   20 THR cc_start: 0.7668 (m) cc_final: 0.7241 (p)
REVERT: L   56 SER cc_start: 0.8203 (m) cc_final: 0.7991 (p)
REVERT: L   63 SER cc_start: 0.7745 (p) cc_final: 0.7340 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.3106
  time to fit residues: 45.6326
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.2980
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0870
   chunk 46 optimal weight:    0.0980
   chunk 18 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** 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 = 0.4341 r_free = 0.4341 target = 0.186197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.178199 restraints weight = 13177.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.178595 restraints weight = 12897.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.179962 restraints weight = 10593.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5768
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6578  Z= 0.191
  Angle     :  0.579   5.268   8914  Z= 0.308
  Chirality :  0.043   0.164    953
  Planarity :  0.005   0.046   1151
  Dihedral  :  4.988  24.716    901
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.07 (0.30), residues: 794
  helix:  0.86 (0.47), residues: 123
  sheet:  0.74 (0.32), residues: 255
  loop : -0.83 (0.31), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  47 
 HIS   0.010   0.001   HIS H  35 
 PHE   0.013   0.002   PHE H  68 
 TYR   0.020   0.001   TYR E  63 
 ARG   0.004   0.000   ARG L  61 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.784 
Fit side-chains
REVERT: B    4 MET cc_start: 0.7245 (mmm) cc_final: 0.6861 (mmp)
REVERT: D  174 MET cc_start: 0.6007 (ttp) cc_final: 0.5592 (ttp)
REVERT: H    6 GLU cc_start: 0.6567 (mp0) cc_final: 0.6291 (mt-10)
REVERT: H  112 TRP cc_start: 0.7035 (m100) cc_final: 0.6764 (m100)
REVERT: L   18 ARG cc_start: 0.7244 (mtm110) cc_final: 0.6949 (ttm110)
REVERT: L   20 THR cc_start: 0.7661 (m) cc_final: 0.7230 (p)
REVERT: L   63 SER cc_start: 0.7939 (p) cc_final: 0.7551 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2022
  time to fit residues: 29.2849
Evaluate side-chains
  103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0050
   chunk 75 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 63 optimal weight:    0.3980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  92 ASN
D  97 GLN
E  64 HIS
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.184722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.176653 restraints weight = 13104.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.177133 restraints weight = 12614.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.178672 restraints weight = 10259.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.4247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5813
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6578  Z= 0.240
  Angle     :  0.626   6.333   8914  Z= 0.332
  Chirality :  0.044   0.171    953
  Planarity :  0.006   0.066   1151
  Dihedral  :  5.136  24.362    901
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.13 (0.30), residues: 794
  helix:  0.60 (0.46), residues: 123
  sheet:  0.64 (0.32), residues: 261
  loop : -0.76 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H  47 
 HIS   0.004   0.001   HIS A  32 
 PHE   0.017   0.002   PHE B  98 
 TYR   0.020   0.001   TYR E  63 
 ARG   0.009   0.001   ARG E  22 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.6966 (ttt180) cc_final: 0.6598 (ttt90)
REVERT: B    4 MET cc_start: 0.7222 (mmm) cc_final: 0.6795 (mmt)
REVERT: D  174 MET cc_start: 0.6079 (ttp) cc_final: 0.5699 (ttp)
REVERT: E   54 GLU cc_start: 0.7132 (tt0) cc_final: 0.6931 (tt0)
REVERT: E   61 LEU cc_start: 0.8142 (tp) cc_final: 0.7931 (tp)
REVERT: H  112 TRP cc_start: 0.7162 (m100) cc_final: 0.6818 (m100)
REVERT: L   18 ARG cc_start: 0.7227 (mtm110) cc_final: 0.6886 (ttp-170)
REVERT: L   20 THR cc_start: 0.7720 (m) cc_final: 0.7289 (p)
REVERT: L   63 SER cc_start: 0.7989 (p) cc_final: 0.7616 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.2008
  time to fit residues: 28.1639
Evaluate side-chains
  102 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** 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 = 0.4294 r_free = 0.4294 target = 0.181954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.173643 restraints weight = 12993.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.174358 restraints weight = 11048.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.174702 restraints weight = 9338.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5911
moved from start:          0.3865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6578  Z= 0.295
  Angle     :  0.663   6.242   8914  Z= 0.354
  Chirality :  0.046   0.184    953
  Planarity :  0.006   0.064   1151
  Dihedral  :  5.450  26.109    901
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.30), residues: 794
  helix:  0.35 (0.46), residues: 123
  sheet:  0.50 (0.32), residues: 264
  loop : -1.02 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  47 
 HIS   0.009   0.002   HIS H  35 
 PHE   0.022   0.002   PHE B  98 
 TYR   0.019   0.002   TYR E  63 
 ARG   0.011   0.001   ARG L  61 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.726 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7010 (ttt180) cc_final: 0.6434 (ttt90)
REVERT: D  127 GLN cc_start: 0.7550 (tp40) cc_final: 0.6931 (tp40)
REVERT: H  112 TRP cc_start: 0.7246 (m100) cc_final: 0.5963 (m100)
REVERT: L   18 ARG cc_start: 0.7101 (mtm110) cc_final: 0.6750 (ttp-170)
REVERT: L   20 THR cc_start: 0.7758 (m) cc_final: 0.7314 (p)
REVERT: L   63 SER cc_start: 0.7992 (p) cc_final: 0.7621 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2286
  time to fit residues: 33.5398
Evaluate side-chains
  105 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.0270
   chunk 2 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0980
   chunk 57 optimal weight:    0.0040
   chunk 26 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.1650

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  89 GLN
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
D 181 HIS
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  35 HIS
L  32 ASN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.185641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.177697 restraints weight = 13138.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.178777 restraints weight = 9756.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.179415 restraints weight = 7674.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.4255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5781
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6578  Z= 0.165
  Angle     :  0.582   6.003   8914  Z= 0.310
  Chirality :  0.044   0.168    953
  Planarity :  0.005   0.070   1151
  Dihedral  :  5.039  23.652    901
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 (0.30), residues: 794
  helix:  0.55 (0.46), residues: 123
  sheet:  0.50 (0.31), residues: 264
  loop : -0.76 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 112 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.016   0.002   PHE B  71 
 TYR   0.022   0.001   TYR E  63 
 ARG   0.006   0.000   ARG H  72 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A   35 ASP cc_start: 0.5466 (m-30) cc_final: 0.5237 (m-30)
REVERT: A   45 PHE cc_start: 0.7527 (m-80) cc_final: 0.7048 (m-10)
REVERT: A   94 ARG cc_start: 0.7038 (ttt180) cc_final: 0.6730 (ttt90)
REVERT: D  131 LYS cc_start: 0.6995 (pttt) cc_final: 0.6761 (pttm)
REVERT: D  174 MET cc_start: 0.5891 (tmm) cc_final: 0.5413 (tmm)
REVERT: H  112 TRP cc_start: 0.7018 (m100) cc_final: 0.6688 (m100)
REVERT: L   18 ARG cc_start: 0.7049 (mtm110) cc_final: 0.6752 (ttp-170)
REVERT: L   20 THR cc_start: 0.7644 (m) cc_final: 0.7191 (p)
REVERT: L   63 SER cc_start: 0.7899 (p) cc_final: 0.7597 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2164
  time to fit residues: 30.0749
Evaluate side-chains
  104 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0030
   chunk 62 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0970
   chunk 75 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 36 optimal weight:    0.1980
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0020
   overall best weight:    0.0996

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

Flipped N/Q/H residues before XYZ refinement:
** A   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.186953 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.178936 restraints weight = 13320.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.179253 restraints weight = 12549.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.179827 restraints weight = 10575.404|
|-----------------------------------------------------------------------------|
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5743
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.058   6578  Z= 0.163
  Angle     :  0.569   8.444   8914  Z= 0.300
  Chirality :  0.043   0.159    953
  Planarity :  0.005   0.047   1151
  Dihedral  :  4.785  23.703    901
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.04 (0.30), residues: 794
  helix:  0.79 (0.46), residues: 123
  sheet:  0.60 (0.32), residues: 264
  loop : -0.67 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 112 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.013   0.001   PHE E 122 
 TYR   0.021   0.001   TYR E  63 
 ARG   0.006   0.000   ARG A  38 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.684 
Fit side-chains
REVERT: A   94 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6712 (ttt90)
REVERT: D  131 LYS cc_start: 0.7129 (pttt) cc_final: 0.6834 (pttm)
REVERT: D  174 MET cc_start: 0.6086 (tmm) cc_final: 0.5791 (tmm)
REVERT: L   20 THR cc_start: 0.7501 (m) cc_final: 0.7020 (p)
REVERT: L   37 GLN cc_start: 0.7488 (tp40) cc_final: 0.6891 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1982
  time to fit residues: 28.1525
Evaluate side-chains
  103 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 67 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 55 optimal weight:    0.4980
   chunk 68 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 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 = 0.4318 r_free = 0.4318 target = 0.184021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.176214 restraints weight = 13158.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.176643 restraints weight = 12145.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.177718 restraints weight = 10120.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.4236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5822
moved from start:          0.4284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6578  Z= 0.246
  Angle     :  0.619   8.371   8914  Z= 0.328
  Chirality :  0.045   0.197    953
  Planarity :  0.006   0.085   1151
  Dihedral  :  5.027  24.717    901
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 (0.30), residues: 794
  helix:  0.62 (0.46), residues: 123
  sheet:  0.58 (0.32), residues: 262
  loop : -0.83 (0.31), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 103 
 HIS   0.008   0.001   HIS H  35 
 PHE   0.032   0.002   PHE B  98 
 TYR   0.027   0.002   TYR L  86 
 ARG   0.006   0.001   ARG A  66 

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

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

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1588 Ramachandran restraints generated.
    794 Oldfield, 0 Emsley, 794 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.622 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 ARG cc_start: 0.6912 (ttt180) cc_final: 0.6623 (ttt90)
REVERT: D  100 VAL cc_start: 0.7824 (p) cc_final: 0.7563 (m)
REVERT: D  174 MET cc_start: 0.6169 (tmm) cc_final: 0.5680 (tmm)
REVERT: H  112 TRP cc_start: 0.7178 (m100) cc_final: 0.6880 (m100)
REVERT: L   20 THR cc_start: 0.7616 (m) cc_final: 0.7197 (p)
REVERT: L   37 GLN cc_start: 0.7561 (tp40) cc_final: 0.6953 (tt0)
REVERT: L   63 SER cc_start: 0.7936 (p) cc_final: 0.7599 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1983
  time to fit residues: 29.2438
Evaluate side-chains
  107 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 72 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 64 optimal weight:    0.5980
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  97 GLN
** E  69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  32 ASN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.181338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.173616 restraints weight = 13267.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.173953 restraints weight = 12314.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.175083 restraints weight = 10312.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5891
moved from start:          0.4479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6578  Z= 0.296
  Angle     :  0.668   9.819   8914  Z= 0.357
  Chirality :  0.047   0.208    953
  Planarity :  0.006   0.073   1151
  Dihedral  :  5.461  24.599    901
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.05 %
    Favored  : 92.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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: -0.51 (0.29), residues: 794
  helix:  0.46 (0.46), residues: 123
  sheet:  0.37 (0.32), residues: 260
  loop : -1.06 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP H  47 
 HIS   0.010   0.002   HIS H  35 
 PHE   0.036   0.003   PHE B  98 
 TYR   0.026   0.002   TYR L  86 
 ARG   0.007   0.001   ARG E  22 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2460.37 seconds
wall clock time: 45 minutes 39.75 seconds (2739.75 seconds total)