Starting phenix.real_space_refine
on Tue Feb 11 11:24:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rfp_24444/02_2025/7rfp_24444.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rfp_24444/02_2025/7rfp_24444.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rfp_24444/02_2025/7rfp_24444.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rfp_24444/02_2025/7rfp_24444.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rfp_24444/02_2025/7rfp_24444.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rfp_24444/02_2025/7rfp_24444.cif"
  }
  resolution = 4.4
  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=   0.001 sd=   0.044
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      50      5.16       5
     C    3252      2.51       5
     N    1114      2.21       5
     O    1116      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5532
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 591
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 10, 'TRANS': 107}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 324
          Unresolved non-hydrogen angles: 415
          Unresolved non-hydrogen dihedrals: 279
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 190
    Chain: "B"
      Number of atoms: 591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 591
          Classifications: {'peptide': 118}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PTRANS': 10, 'TRANS': 107}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 324
          Unresolved non-hydrogen angles: 415
          Unresolved non-hydrogen dihedrals: 279
          Unresolved non-hydrogen chiralities: 20
          Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 6, 'GLU:plan': 5, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 190
    Chain: "H"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1077
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 182}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204}
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 600
          Unresolved non-hydrogen angles: 775
          Unresolved non-hydrogen dihedrals: 516
          Unresolved non-hydrogen chiralities: 59
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 288
    Chain: "L"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1098
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 193}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 648
          Unresolved non-hydrogen angles: 835
          Unresolved non-hydrogen dihedrals: 539
          Unresolved non-hydrogen chiralities: 56
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 369
    Chain: "I"
      Number of atoms: 1077
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1077
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 182}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 204}
          Unresolved chain link angles: 13
          Unresolved non-hydrogen bonds: 600
          Unresolved non-hydrogen angles: 775
          Unresolved non-hydrogen dihedrals: 516
          Unresolved non-hydrogen chiralities: 59
          Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 7, 'TRP:plan': 4, 'ASP:plan': 7, 'PHE:plan': 7, 'GLU:plan': 5, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 288
    Chain: "M"
      Number of atoms: 1098
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1098
          Classifications: {'peptide': 221}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 193}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 210}
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 648
          Unresolved non-hydrogen angles: 835
          Unresolved non-hydrogen dihedrals: 539
          Unresolved non-hydrogen chiralities: 56
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 369
  Time building chain proxies: 4.59, per 1000 atoms: 0.83
  Number of scatterers: 5532
  At special positions: 0
  Unit cell: (62.472, 123.848, 168.784, 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      50     16.00
     O    1116      8.00
     N    1114      7.00
     C    3252      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=23, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  44 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  45 " - pdb=" SG  CYS A  60 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS B  55 " distance=2.19
    Simple disulfide: pdb=" SG  CYS A  62 " - pdb=" SG  CYS A  77 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  69 " - pdb=" SG  CYS A  74 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  82 " - pdb=" SG  CYS A 100 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  29 " - pdb=" SG  CYS B  44 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B  45 " - pdb=" SG  CYS B  60 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  62 " - pdb=" SG  CYS B  77 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B  69 " - pdb=" SG  CYS B  74 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  82 " - pdb=" SG  CYS B 100 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS B 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.02
    Simple disulfide: pdb=" SG  CYS H 162 " - pdb=" SG  CYS H 218 " distance=2.01
    Simple disulfide: pdb=" SG  CYS H 238 " - pdb=" SG  CYS L 240 " distance=2.08
    Simple disulfide: pdb=" SG  CYS L  41 " - pdb=" SG  CYS L 110 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 160 " - pdb=" SG  CYS L 220 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I  41 " - pdb=" SG  CYS I 115 " distance=2.02
    Simple disulfide: pdb=" SG  CYS I 162 " - pdb=" SG  CYS I 218 " distance=2.01
    Simple disulfide: pdb=" SG  CYS I 238 " - pdb=" SG  CYS M 240 " distance=2.08
    Simple disulfide: pdb=" SG  CYS M  41 " - pdb=" SG  CYS M 110 " distance=2.05
    Simple disulfide: pdb=" SG  CYS M 160 " - pdb=" SG  CYS M 220 " distance=2.02

  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: 1.40
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2048

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 29 sheets defined
      7.9% alpha, 33.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.586A  pdb=" N   PHE A 125 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 126
      removed outlier: 3.586A  pdb=" N   PHE B 125 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 93 through 96
    Processing helix  chain 'H' and resid 106 through 110
    Processing helix  chain 'H' and resid 178 through 180
      No H-bonds generated for 'chain 'H' and resid 178 through 180'
    Processing helix  chain 'H' and resid 209 through 211
      No H-bonds generated for 'chain 'H' and resid 209 through 211'
    Processing helix  chain 'H' and resid 223 through 226
    Processing helix  chain 'L' and resid 101 through 105
      removed outlier: 3.820A  pdb=" N   GLU L 105 " --> pdb=" O   MET L 102 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 147 through 153
      removed outlier: 3.854A  pdb=" N   SER L 153 " --> pdb=" O   GLU L 149 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 209 through 215
      removed outlier: 3.944A  pdb=" N   HIS L 215 " --> pdb=" O   ASP L 211 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 93 through 96
    Processing helix  chain 'I' and resid 106 through 110
    Processing helix  chain 'I' and resid 178 through 180
      No H-bonds generated for 'chain 'I' and resid 178 through 180'
    Processing helix  chain 'I' and resid 209 through 211
      No H-bonds generated for 'chain 'I' and resid 209 through 211'
    Processing helix  chain 'I' and resid 223 through 226
    Processing helix  chain 'M' and resid 101 through 105
      removed outlier: 3.821A  pdb=" N   GLU M 105 " --> pdb=" O   MET M 102 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 147 through 153
      removed outlier: 3.854A  pdb=" N   SER M 153 " --> pdb=" O   GLU M 149 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 209 through 215
      removed outlier: 3.944A  pdb=" N   HIS M 215 " --> pdb=" O   ASP M 211 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 36
    Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69
    Processing sheet with id=AA3, first strand: chain 'A' and resid 89 through 91
    Processing sheet with id=AA4, first strand: chain 'A' and resid 107 through 108
    Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 36
    Processing sheet with id=AA6, first strand: chain 'B' and resid 67 through 69
    Processing sheet with id=AA7, first strand: chain 'B' and resid 89 through 91
    Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108
    Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 131
      removed outlier: 6.693A  pdb=" N   VAL B 140 " --> pdb=" O   MET B 130 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 24 through 26
    Processing sheet with id=AB2, first strand: chain 'H' and resid 30 through 31
      removed outlier: 7.015A  pdb=" N   MET H  53 " --> pdb=" O   THR H  69 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   THR H  69 " --> pdb=" O   MET H  53 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   TRP H  55 " --> pdb=" O   VAL H  67 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 91 through 92
    Processing sheet with id=AB4, first strand: chain 'H' and resid 142 through 146
      removed outlier: 5.883A  pdb=" N   TYR H 198 " --> pdb=" O   ASP H 166 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 142 through 146
      removed outlier: 5.883A  pdb=" N   TYR H 198 " --> pdb=" O   ASP H 166 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 173 through 176
    Processing sheet with id=AB7, first strand: chain 'L' and resid 28 through 32
      removed outlier: 6.346A  pdb=" N   VAL L  29 " --> pdb=" O   THR L 129 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   LEU L 131 " --> pdb=" O   VAL L  29 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   GLY L  31 " --> pdb=" O   LEU L 131 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   TRP L  55 " --> pdb=" O   VAL L  67 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 37 through 41
      removed outlier: 3.630A  pdb=" N   ALA L  93 " --> pdb=" O   CYS L  41 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'L' and resid 140 through 144
      removed outlier: 5.637A  pdb=" N   TYR L 199 " --> pdb=" O   ASN L 164 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'L' and resid 179 through 181
      removed outlier: 4.821A  pdb=" N   TRP L 174 " --> pdb=" O   GLN L 181 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'I' and resid 24 through 26
    Processing sheet with id=AC3, first strand: chain 'I' and resid 30 through 31
      removed outlier: 7.140A  pdb=" N   MET I  53 " --> pdb=" O   THR I  69 " (cutoff:3.500A)
      removed outlier: 4.690A  pdb=" N   THR I  69 " --> pdb=" O   MET I  53 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   TRP I  55 " --> pdb=" O   VAL I  67 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'I' and resid 91 through 92
    Processing sheet with id=AC5, first strand: chain 'I' and resid 142 through 146
      removed outlier: 5.883A  pdb=" N   TYR I 198 " --> pdb=" O   ASP I 166 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'I' and resid 142 through 146
      removed outlier: 5.883A  pdb=" N   TYR I 198 " --> pdb=" O   ASP I 166 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'I' and resid 173 through 176
    Processing sheet with id=AC8, first strand: chain 'M' and resid 28 through 30
      removed outlier: 6.371A  pdb=" N   TRP M  55 " --> pdb=" O   VAL M  67 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'M' and resid 37 through 41
    Processing sheet with id=AD1, first strand: chain 'M' and resid 140 through 144
      removed outlier: 5.636A  pdb=" N   TYR M 199 " --> pdb=" O   ASN M 164 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'M' and resid 179 through 181
      removed outlier: 4.820A  pdb=" N   TRP M 174 " --> pdb=" O   GLN M 181 " (cutoff:3.500A)

    304 hydrogen bonds defined for protein.
    726 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: 1.68

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 1116
        1.26 -     1.41: 1108
        1.41 -     1.55: 2955
        1.55 -     1.69: 297
        1.69 -     1.84: 50
  Bond restraints: 5526
  Sorted by residual:
  bond pdb=" C   PRO B 143 "
       pdb=" O   PRO B 143 "
    ideal  model  delta    sigma   weight residual
    1.235  1.122  0.113 1.30e-02 5.92e+03 7.59e+01
  bond pdb=" C   PRO A 143 "
       pdb=" O   PRO A 143 "
    ideal  model  delta    sigma   weight residual
    1.235  1.126  0.109 1.30e-02 5.92e+03 7.06e+01
  bond pdb=" N   GLU A  53 "
       pdb=" CA  GLU A  53 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 6.30e-03 2.52e+04 2.25e+01
  bond pdb=" N   ILE A 142 "
       pdb=" CA  ILE A 142 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 7.70e-03 1.69e+04 1.83e+01
  bond pdb=" N   ILE M  39 "
       pdb=" CA  ILE M  39 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.033 7.70e-03 1.69e+04 1.80e+01
  ... (remaining 5521 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.33: 6929
        3.33 -     6.66: 686
        6.66 -     9.99: 34
        9.99 -    13.32: 2
       13.32 -    16.66: 3
  Bond angle restraints: 7654
  Sorted by residual:
  angle pdb=" O   PRO A 143 "
        pdb=" C   PRO A 143 "
        pdb=" N   GLU A 144 "
      ideal   model   delta    sigma   weight residual
     122.64  105.98   16.66 1.35e+00 5.49e-01 1.52e+02
  angle pdb=" O   PRO B 143 "
        pdb=" C   PRO B 143 "
        pdb=" N   GLU B 144 "
      ideal   model   delta    sigma   weight residual
     122.64  106.94   15.70 1.35e+00 5.49e-01 1.35e+02
  angle pdb=" C   TYR M 113 "
        pdb=" CA  TYR M 113 "
        pdb=" CB  TYR M 113 "
      ideal   model   delta    sigma   weight residual
     110.42   96.62   13.80 1.99e+00 2.53e-01 4.81e+01
  angle pdb=" O   ALA B  49 "
        pdb=" C   ALA B  49 "
        pdb=" N   PRO B  50 "
      ideal   model   delta    sigma   weight residual
     121.53  124.64   -3.11 4.60e-01 4.73e+00 4.57e+01
  angle pdb=" N   ASP M 114 "
        pdb=" CA  ASP M 114 "
        pdb=" C   ASP M 114 "
      ideal   model   delta    sigma   weight residual
     111.90  103.06    8.84 1.32e+00 5.74e-01 4.49e+01
  ... (remaining 7649 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    13.23: 3157
       13.23 -    26.45: 87
       26.45 -    39.67: 18
       39.67 -    52.90: 11
       52.90 -    66.12: 4
  Dihedral angle restraints: 3277
    sinusoidal: 121
      harmonic: 3156
  Sorted by residual:
  dihedral pdb=" C   TYR M 113 "
           pdb=" N   TYR M 113 "
           pdb=" CA  TYR M 113 "
           pdb=" CB  TYR M 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -102.61  -19.99     0      2.50e+00 1.60e-01 6.39e+01
  dihedral pdb=" CB  CYS B  82 "
           pdb=" SG  CYS B  82 "
           pdb=" SG  CYS B 100 "
           pdb=" CB  CYS B 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.12  -66.12     1      1.00e+01 1.00e-02 5.71e+01
  dihedral pdb=" CB  CYS A  82 "
           pdb=" SG  CYS A  82 "
           pdb=" SG  CYS A 100 "
           pdb=" CB  CYS A 100 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  159.11  -66.11     1      1.00e+01 1.00e-02 5.71e+01
  ... (remaining 3274 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.098: 589
       0.098 -    0.197: 327
       0.197 -    0.295: 92
       0.295 -    0.393: 13
       0.393 -    0.491: 3
  Chirality restraints: 1024
  Sorted by residual:
  chirality pdb=" CA  GLU A  66 "
            pdb=" N   GLU A  66 "
            pdb=" C   GLU A  66 "
            pdb=" CB  GLU A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 6.03e+00
  chirality pdb=" CA  GLU B  66 "
            pdb=" N   GLU B  66 "
            pdb=" C   GLU B  66 "
            pdb=" CB  GLU B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.02    0.49 2.00e-01 2.50e+01 5.97e+00
  chirality pdb=" CA  TYR M 113 "
            pdb=" N   TYR M 113 "
            pdb=" C   TYR M 113 "
            pdb=" CB  TYR M 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.95   -0.44 2.00e-01 2.50e+01 4.75e+00
  ... (remaining 1021 not shown)

  Planarity restraints: 1110
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 143 "    0.089 2.00e-02 2.50e+03   1.75e-01 3.05e+02
        pdb=" C   PRO B 143 "   -0.301 2.00e-02 2.50e+03
        pdb=" O   PRO B 143 "    0.132 2.00e-02 2.50e+03
        pdb=" N   GLU B 144 "    0.080 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 143 "    0.088 2.00e-02 2.50e+03   1.68e-01 2.83e+02
        pdb=" C   PRO A 143 "   -0.289 2.00e-02 2.50e+03
        pdb=" O   PRO A 143 "    0.127 2.00e-02 2.50e+03
        pdb=" N   GLU A 144 "    0.075 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS H 115 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.15e+00
        pdb=" C   CYS H 115 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   CYS H 115 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ALA H 116 "    0.017 2.00e-02 2.50e+03
  ... (remaining 1107 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.24: 1
        2.24 -     2.91: 2474
        2.91 -     3.57: 6557
        3.57 -     4.24: 8969
        4.24 -     4.90: 15471
  Nonbonded interactions: 33472
  Sorted by model distance:
  nonbonded pdb=" CB  THR A 120 "
            pdb=" O   PHE B 125 "
     model   vdw
     1.581 3.470
  nonbonded pdb=" CB  TYR M 113 "
            pdb=" N   ASP M 114 "
     model   vdw
     2.275 2.816
  nonbonded pdb=" CB  SER M 112 "
            pdb=" N   TYR M 113 "
     model   vdw
     2.396 2.816
  nonbonded pdb=" N   TYR L  69 "
            pdb=" O   TYR L  69 "
     model   vdw
     2.428 2.496
  nonbonded pdb=" N   TYR M  69 "
            pdb=" O   TYR M  69 "
     model   vdw
     2.428 2.496
  ... (remaining 33467 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'M'
}

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:             2.910
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.200
  Find NCS groups from input model:        0.400
  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:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
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      :  0.014   0.113   5526  Z= 1.053
  Angle     :  2.065  16.656   7654  Z= 1.455
  Chirality :  0.123   0.491   1024
  Planarity :  0.009   0.175   1110
  Dihedral  :  7.118  47.710   1160
  Min Nonbonded Distance : 1.581

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  2.99 %
    Allowed  :  9.53 %
    Favored  : 87.48 %
  Rotamer:
    Outliers :  8.00 %
    Allowed  :  4.00 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.78 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.46 (0.25), residues: 1102
  helix:  0.60 (0.89), residues: 26
  sheet: -0.02 (0.25), residues: 413
  loop : -1.75 (0.24), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 19
  time to evaluate  : 0.513 
Fit side-chains
REVERT: B  116 CYS cc_start: 0.6860 (m) cc_final: 0.5847 (p)
  outliers start: 4
  outliers final: 2
  residues processed: 23
  average time/residue: 0.0617
  time to fit residues: 3.2798
Evaluate side-chains
  17 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 15
  time to evaluate  : 0.577 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.6980
   chunk 81 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 43 optimal weight:    6.9990
   chunk 84 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.097287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.085412 restraints weight = 27774.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.084090 restraints weight = 44380.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.084711 restraints weight = 41636.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6986
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5526  Z= 0.225
  Angle     :  0.679   8.215   7654  Z= 0.397
  Chirality :  0.046   0.143   1024
  Planarity :  0.003   0.013   1110
  Dihedral  :  5.887  35.219   1110
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.91 %
    Allowed  :  6.81 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -0.54 (0.26), residues: 1102
  helix:  0.24 (0.90), residues: 30
  sheet:  0.38 (0.26), residues: 401
  loop : -0.87 (0.25), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.608 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0539
  time to fit residues: 2.4229
Evaluate side-chains
  14 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 84 optimal weight:   20.0000
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 88 optimal weight:    0.9990
   chunk 41 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 79 optimal weight:    4.9990
   overall best weight:    5.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.086874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.074866 restraints weight = 27867.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.073351 restraints weight = 47325.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.073771 restraints weight = 45560.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7455
moved from start:          0.6279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064   5526  Z= 0.543
  Angle     :  1.047  14.519   7654  Z= 0.618
  Chirality :  0.051   0.155   1024
  Planarity :  0.006   0.031   1110
  Dihedral  :  9.120  48.426   1110
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  1.09 %
    Allowed  : 13.70 %
    Favored  : 85.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.48 %

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: -1.83 (0.25), residues: 1102
  helix:  0.79 (0.93), residues: 26
  sheet: -0.12 (0.28), residues: 350
  loop : -1.98 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  15 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.590 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 15
  average time/residue: 0.0542
  time to fit residues: 2.3074
Evaluate side-chains
  14 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 29 optimal weight:    6.9990
   chunk 59 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 100 optimal weight:    8.9990
   chunk 105 optimal weight:    9.9990
   chunk 5 optimal weight:    5.9990
   chunk 73 optimal weight:    0.8980
   chunk 94 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 66 optimal weight:    0.9980
   chunk 72 optimal weight:   10.0000
   overall best weight:    3.7786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.086893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.074020 restraints weight = 28502.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.072963 restraints weight = 40546.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.073328 restraints weight = 41759.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.6634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   5526  Z= 0.368
  Angle     :  0.814  10.909   7654  Z= 0.477
  Chirality :  0.047   0.140   1024
  Planarity :  0.004   0.017   1110
  Dihedral  :  7.665  39.532   1110
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 13.34 %
    Favored  : 86.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.24), residues: 1102
  helix:  0.26 (0.79), residues: 34
  sheet: -0.65 (0.27), residues: 365
  loop : -2.37 (0.22), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.620 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0497
  time to fit residues: 2.1481
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.639 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 59 optimal weight:    0.0060
   chunk 102 optimal weight:   10.0000
   chunk 79 optimal weight:    0.8980
   chunk 62 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 81 optimal weight:    8.9990
   overall best weight:    2.9800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.086733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.074483 restraints weight = 28319.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.073074 restraints weight = 42210.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.073523 restraints weight = 40657.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.7022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   5526  Z= 0.300
  Angle     :  0.722  10.443   7654  Z= 0.422
  Chirality :  0.046   0.136   1024
  Planarity :  0.004   0.016   1110
  Dihedral  :  7.156  46.959   1110
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 14.97 %
    Favored  : 84.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.63 (0.24), residues: 1102
  helix:  0.70 (0.83), residues: 34
  sheet: -0.88 (0.26), residues: 357
  loop : -2.49 (0.22), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.641 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0624
  time to fit residues: 2.5930
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 80 optimal weight:   10.0000
   chunk 78 optimal weight:    9.9990
   chunk 34 optimal weight:    4.9990
   chunk 81 optimal weight:    6.9990
   chunk 49 optimal weight:    0.0970
   chunk 70 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 95 optimal weight:    0.9980
   chunk 97 optimal weight:    0.1980
   chunk 52 optimal weight:    0.0970
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.2778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.088627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.076315 restraints weight = 28165.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.075599 restraints weight = 34691.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.075913 restraints weight = 34758.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7372
moved from start:          0.7003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5526  Z= 0.151
  Angle     :  0.561   6.658   7654  Z= 0.327
  Chirality :  0.044   0.137   1024
  Planarity :  0.002   0.011   1110
  Dihedral  :  5.692  32.241   1110
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 10.89 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.34 (0.24), residues: 1102
  helix:  1.37 (0.88), residues: 34
  sheet: -0.98 (0.26), residues: 371
  loop : -2.14 (0.23), residues: 697

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.666 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0536
  time to fit residues: 2.2358
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.648 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 87 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 90 optimal weight:    0.0050
   chunk 8 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 50 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 62 optimal weight:   20.0000
   chunk 63 optimal weight:    9.9990
   overall best weight:    3.6002

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.084152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.071698 restraints weight = 28267.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.070620 restraints weight = 38296.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.070881 restraints weight = 37860.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7485
moved from start:          0.7559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5526  Z= 0.343
  Angle     :  0.750   9.865   7654  Z= 0.442
  Chirality :  0.046   0.149   1024
  Planarity :  0.004   0.018   1110
  Dihedral  :  7.131  34.923   1110
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 16.42 %
    Favored  : 83.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -3.00 (0.23), residues: 1102
  helix:  0.89 (0.83), residues: 34
  sheet: -1.38 (0.26), residues: 345
  loop : -2.61 (0.21), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.722 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0485
  time to fit residues: 2.0973
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.636 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 57 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 5 optimal weight:    6.9990
   chunk 86 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 88 optimal weight:    0.8980
   overall best weight:    3.5788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.083984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.071712 restraints weight = 28342.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.070559 restraints weight = 37032.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.070387 restraints weight = 40869.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.8044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   5526  Z= 0.338
  Angle     :  0.738  11.038   7654  Z= 0.434
  Chirality :  0.046   0.141   1024
  Planarity :  0.004   0.017   1110
  Dihedral  :  7.281  37.796   1110
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.36 %
    Allowed  : 16.97 %
    Favored  : 82.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -3.42 (0.23), residues: 1102
  helix:  0.65 (0.87), residues: 34
  sheet: -1.71 (0.27), residues: 341
  loop : -2.88 (0.21), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  14 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.647 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 14
  average time/residue: 0.0540
  time to fit residues: 2.3616
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 23 optimal weight:    9.9990
   chunk 105 optimal weight:   30.0000
   chunk 48 optimal weight:    5.9990
   chunk 89 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0870
   chunk 12 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   overall best weight:    2.9364

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.084146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.070718 restraints weight = 28289.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.069432 restraints weight = 41552.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.069839 restraints weight = 38092.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.8176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5526  Z= 0.291
  Angle     :  0.690  10.830   7654  Z= 0.404
  Chirality :  0.045   0.142   1024
  Planarity :  0.003   0.017   1110
  Dihedral  :  6.869  33.136   1110
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 17.06 %
    Favored  : 82.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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: -3.49 (0.23), residues: 1102
  helix:  0.68 (0.85), residues: 34
  sheet: -1.88 (0.27), residues: 334
  loop : -2.85 (0.21), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.590 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0530
  time to fit residues: 2.2421
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 64 optimal weight:    9.9990
   chunk 48 optimal weight:    4.9990
   chunk 69 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 41 optimal weight:   20.0000
   chunk 50 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    3.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.083334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.070136 restraints weight = 28202.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.068846 restraints weight = 42274.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.069331 restraints weight = 38596.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7552
moved from start:          0.8583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   5526  Z= 0.364
  Angle     :  0.771  11.638   7654  Z= 0.454
  Chirality :  0.046   0.157   1024
  Planarity :  0.004   0.020   1110
  Dihedral  :  7.549  38.187   1110
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 19.06 %
    Favored  : 80.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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: -3.76 (0.23), residues: 1102
  helix:  0.33 (0.85), residues: 34
  sheet: -1.94 (0.27), residues: 330
  loop : -3.11 (0.20), residues: 738

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 

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

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

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2204 Ramachandran restraints generated.
    1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.617 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 13
  average time/residue: 0.0550
  time to fit residues: 2.2706
Evaluate side-chains
  13 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 99 optimal weight:    7.9990
   chunk 17 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 20 optimal weight:    6.9990
   chunk 92 optimal weight:    0.0030
   chunk 45 optimal weight:    6.9990
   chunk 67 optimal weight:    7.9990
   chunk 87 optimal weight:    8.9990
   chunk 39 optimal weight:    8.9990
   overall best weight:    2.5998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.084334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.071020 restraints weight = 28369.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.069336 restraints weight = 42668.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.069910 restraints weight = 40147.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.8572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   5526  Z= 0.261
  Angle     :  0.660  10.462   7654  Z= 0.386
  Chirality :  0.045   0.138   1024
  Planarity :  0.003   0.015   1110
  Dihedral  :  6.662  36.243   1110
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.45 %
    Allowed  : 16.33 %
    Favored  : 83.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -3.65 (0.23), residues: 1102
  helix:  0.56 (0.86), residues: 34
  sheet: -1.99 (0.27), residues: 328
  loop : -2.96 (0.21), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A 119 
 PHE   0.000   0.000   PHE A  96 
 TYR   0.000   0.000   TYR A  48 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1531.99 seconds
wall clock time: 27 minutes 48.70 seconds (1668.70 seconds total)