Starting phenix.real_space_refine
on Sat May 10 13:40:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yzk_39696/05_2025/8yzk_39696.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yzk_39696/05_2025/8yzk_39696.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yzk_39696/05_2025/8yzk_39696.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yzk_39696/05_2025/8yzk_39696.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yzk_39696/05_2025/8yzk_39696.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yzk_39696/05_2025/8yzk_39696.cif"
  }
  resolution = 3.4
  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=   0.002 sd=   0.028
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      42      5.16       5
     C    4204      2.51       5
     N    1064      2.21       5
     O    1160      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 6470
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2039
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 254}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 1190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1190
          Classifications: {'peptide': 169}
          Incomplete info: {'truncation_to_alanine': 30}
          Link IDs: {'PTRANS': 6, 'TRANS': 162}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 169
          Unresolved non-hydrogen dihedrals: 117
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 88
    Chain: "D"
      Number of atoms: 1202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1202
          Classifications: {'peptide': 169}
          Incomplete info: {'truncation_to_alanine': 27}
          Link IDs: {'PTRANS': 6, 'TRANS': 162}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 154
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 5, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 77
    Chain: "B"
      Number of atoms: 2039
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2039
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 254}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 4.26, per 1000 atoms: 0.66
  Number of scatterers: 6470
  At special positions: 0
  Unit cell: (73.216, 108.992, 103.168, 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      42     16.00
     O    1160      8.00
     N    1064      7.00
     C    4204      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 191 " - pdb=" SG  CYS C 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  60 " - pdb=" SG  CYS D 125 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 191 " - pdb=" SG  CYS D 265 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.60
  Conformation dependent library (CDL) restraints added in 884.1 milliseconds
  

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1612

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 9 sheets defined
      51.7% alpha, 15.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 51
      removed outlier: 4.787A  pdb=" N   LEU A  29 " --> pdb=" O   ILE A  25 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   MET A  48 " --> pdb=" O   PHE A  44 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   ARG A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LYS A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 53 through 58
      removed outlier: 3.889A  pdb=" N   ASN A  58 " --> pdb=" O   CYS A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 79
    Processing helix  chain 'A' and resid 90 through 119
      removed outlier: 4.552A  pdb=" N   PHE A  96 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      removed outlier: 4.803A  pdb=" N   GLY A  97 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ARG A 119 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 153
      removed outlier: 3.917A  pdb=" N   CYS A 136 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   SER A 137 " --> pdb=" O   ALA A 133 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   LEU A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLN A 140 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR A 149 " --> pdb=" O   THR A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 161
    Processing helix  chain 'A' and resid 162 through 167
      removed outlier: 3.615A  pdb=" N   ASN A 167 " --> pdb=" O   PRO A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 191
      removed outlier: 3.850A  pdb=" N   VAL A 171 " --> pdb=" O   ASN A 167 " (cutoff:3.500A)
      removed outlier: 5.392A  pdb=" N   TYR A 176 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   VAL A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 232
      removed outlier: 3.992A  pdb=" N   TRP A 217 " --> pdb=" O   SER A 213 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   VAL A 219 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   TRP A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE A 221 " --> pdb=" O   TRP A 217 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   SER A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   ASN A 228 " --> pdb=" O   LEU A 224 " (cutoff:3.500A)
      Proline residue:  A 229  - end of helix
    Processing helix  chain 'A' and resid 238 through 257
      removed outlier: 3.770A  pdb=" N   VAL A 242 " --> pdb=" O   ASP A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 265
    Processing helix  chain 'C' and resid 64 through 68
      removed outlier: 3.628A  pdb=" N   TYR C  68 " --> pdb=" O   LEU C  65 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 201
      removed outlier: 3.605A  pdb=" N   SER C 200 " --> pdb=" O   THR C 197 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   HIS C 201 " --> pdb=" O   PHE C 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 197 through 201'
    Processing helix  chain 'D' and resid 197 through 201
      removed outlier: 3.509A  pdb=" N   SER D 200 " --> pdb=" O   THR D 197 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   HIS D 201 " --> pdb=" O   PHE D 198 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 197 through 201'
    Processing helix  chain 'D' and resid 256 through 260
      removed outlier: 4.125A  pdb=" N   THR D 260 " --> pdb=" O   ALA D 257 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 51
      removed outlier: 4.770A  pdb=" N   LEU B  29 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   MET B  48 " --> pdb=" O   PHE B  44 " (cutoff:3.500A)
      removed outlier: 4.328A  pdb=" N   ARG B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   LYS B  50 " --> pdb=" O   PHE B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 58
      removed outlier: 3.842A  pdb=" N   ASN B  58 " --> pdb=" O   CYS B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 79
    Processing helix  chain 'B' and resid 90 through 119
      removed outlier: 4.598A  pdb=" N   PHE B  96 " --> pdb=" O   ARG B  92 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   GLY B  97 " --> pdb=" O   TYR B  93 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG B 119 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 153
      removed outlier: 3.955A  pdb=" N   CYS B 136 " --> pdb=" O   ILE B 132 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   SER B 137 " --> pdb=" O   ALA B 133 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   LEU B 139 " --> pdb=" O   GLY B 135 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLN B 140 " --> pdb=" O   CYS B 136 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   THR B 149 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 161
    Processing helix  chain 'B' and resid 162 through 167
      removed outlier: 3.562A  pdb=" N   ASN B 167 " --> pdb=" O   PRO B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 191
      removed outlier: 3.720A  pdb=" N   VAL B 171 " --> pdb=" O   ASN B 167 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   TYR B 176 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 5.051A  pdb=" N   VAL B 177 " --> pdb=" O   LEU B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 232
      removed outlier: 4.057A  pdb=" N   TRP B 217 " --> pdb=" O   SER B 213 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL B 219 " --> pdb=" O   ILE B 215 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ILE B 221 " --> pdb=" O   TRP B 217 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   SER B 222 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   ASN B 228 " --> pdb=" O   LEU B 224 " (cutoff:3.500A)
      Proline residue:  B 229  - end of helix
    Processing helix  chain 'B' and resid 238 through 257
      removed outlier: 3.789A  pdb=" N   VAL B 242 " --> pdb=" O   ASP B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 265
    Processing sheet with id=AA1, first strand: chain 'C' and resid 71 through 74
      removed outlier: 7.108A  pdb=" N   TRP C  72 " --> pdb=" O   VAL C  84 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 127 through 128
      removed outlier: 4.018A  pdb=" N   VAL C 137 " --> pdb=" O   SER C 127 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 172 through 176
      removed outlier: 3.740A  pdb=" N   GLN C 172 " --> pdb=" O   SER C 194 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   SER C 194 " --> pdb=" O   GLN C 172 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   TYR C 249 " --> pdb=" O   SER C 240 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   SER C 240 " --> pdb=" O   TYR C 249 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   THR C 238 " --> pdb=" O   GLN C 251 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 213 through 216
      removed outlier: 3.652A  pdb=" N   TYR C 277 " --> pdb=" O   ARG C 267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 213 through 216
      removed outlier: 3.519A  pdb=" N   VAL C 284 " --> pdb=" O   ALA C 261 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 82 through 86
      removed outlier: 6.969A  pdb=" N   TRP D  72 " --> pdb=" O   VAL D  84 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   SER D  71 " --> pdb=" O   ASN D 126 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   ASN D 126 " --> pdb=" O   SER D  71 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   VAL D 137 " --> pdb=" O   SER D 127 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 172 through 176
      removed outlier: 3.820A  pdb=" N   GLN D 172 " --> pdb=" O   SER D 194 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER D 194 " --> pdb=" O   GLN D 172 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   TYR D 249 " --> pdb=" O   SER D 240 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   SER D 240 " --> pdb=" O   TYR D 249 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   THR D 238 " --> pdb=" O   GLN D 251 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 213 through 216
      removed outlier: 3.829A  pdb=" N   TYR D 277 " --> pdb=" O   ARG D 267 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 213 through 216

    370 hydrogen bonds defined for protein.
    1056 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: 1.67

  Time building geometry restraints manager: 1.85 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2021
        1.34 -     1.46: 1563
        1.46 -     1.58: 2984
        1.58 -     1.69: 1
        1.69 -     1.81: 54
  Bond restraints: 6623
  Sorted by residual:
  bond pdb=" CB  PRO C 134 "
       pdb=" CG  PRO C 134 "
    ideal  model  delta    sigma   weight residual
    1.492  1.583 -0.091 5.00e-02 4.00e+02 3.31e+00
  bond pdb=" CB  ILE B 216 "
       pdb=" CG2 ILE B 216 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.77e+00
  bond pdb=" CG  PRO C 134 "
       pdb=" CD  PRO C 134 "
    ideal  model  delta    sigma   weight residual
    1.503  1.459  0.044 3.40e-02 8.65e+02 1.66e+00
  bond pdb=" CB  ILE A 141 "
       pdb=" CG2 ILE A 141 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.12e+00
  bond pdb=" CB  ILE B 141 "
       pdb=" CG2 ILE B 141 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.19e-01
  ... (remaining 6618 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.75: 8995
        3.75 -     7.50: 40
        7.50 -    11.25: 5
       11.25 -    15.01: 0
       15.01 -    18.76: 2
  Bond angle restraints: 9042
  Sorted by residual:
  angle pdb=" CA  PRO C 134 "
        pdb=" N   PRO C 134 "
        pdb=" CD  PRO C 134 "
      ideal   model   delta    sigma   weight residual
     112.00  104.10    7.90 1.40e+00 5.10e-01 3.18e+01
  angle pdb=" CA  LEU B 166 "
        pdb=" CB  LEU B 166 "
        pdb=" CG  LEU B 166 "
      ideal   model   delta    sigma   weight residual
     116.30  135.06  -18.76 3.50e+00 8.16e-02 2.87e+01
  angle pdb=" CA  LEU A 166 "
        pdb=" CB  LEU A 166 "
        pdb=" CG  LEU A 166 "
      ideal   model   delta    sigma   weight residual
     116.30  134.30  -18.00 3.50e+00 8.16e-02 2.65e+01
  angle pdb=" N   ILE B  82 "
        pdb=" CA  ILE B  82 "
        pdb=" C   ILE B  82 "
      ideal   model   delta    sigma   weight residual
     112.80  107.35    5.45 1.15e+00 7.56e-01 2.24e+01
  angle pdb=" N   ILE A  82 "
        pdb=" CA  ILE A  82 "
        pdb=" C   ILE A  82 "
      ideal   model   delta    sigma   weight residual
     112.80  107.41    5.39 1.15e+00 7.56e-01 2.19e+01
  ... (remaining 9037 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.74: 3144
       16.74 -    33.47: 475
       33.47 -    50.21: 147
       50.21 -    66.94: 20
       66.94 -    83.68: 12
  Dihedral angle restraints: 3798
    sinusoidal: 1301
      harmonic: 2497
  Sorted by residual:
  dihedral pdb=" CA  ASN C 204 "
           pdb=" C   ASN C 204 "
           pdb=" N   TRP C 205 "
           pdb=" CA  TRP C 205 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.79   19.21     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  ASN D 133 "
           pdb=" C   ASN D 133 "
           pdb=" N   PRO D 134 "
           pdb=" CA  PRO D 134 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.77  -18.23     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  SER D 218 "
           pdb=" C   SER D 218 "
           pdb=" N   SER D 219 "
           pdb=" CA  SER D 219 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.14  -16.86     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 3795 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 767
       0.046 -    0.091: 246
       0.091 -    0.137: 39
       0.137 -    0.182: 6
       0.182 -    0.228: 1
  Chirality restraints: 1059
  Sorted by residual:
  chirality pdb=" CG  LEU B 166 "
            pdb=" CB  LEU B 166 "
            pdb=" CD1 LEU B 166 "
            pdb=" CD2 LEU B 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.82    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  ILE B  82 "
            pdb=" CA  ILE B  82 "
            pdb=" CG1 ILE B  82 "
            pdb=" CG2 ILE B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 7.91e-01
  chirality pdb=" CA  VAL C 217 "
            pdb=" N   VAL C 217 "
            pdb=" C   VAL C 217 "
            pdb=" CB  VAL C 217 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.05e-01
  ... (remaining 1056 not shown)

  Planarity restraints: 1128
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C 133 "    0.062 5.00e-02 4.00e+02   8.94e-02 1.28e+01
        pdb=" N   PRO C 134 "   -0.154 5.00e-02 4.00e+02
        pdb=" CA  PRO C 134 "    0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO C 134 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 234 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO B 235 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 235 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 235 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 234 "   -0.040 5.00e-02 4.00e+02   6.06e-02 5.87e+00
        pdb=" N   PRO A 235 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1125 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 374
        2.72 -     3.27: 6547
        3.27 -     3.81: 11420
        3.81 -     4.36: 12622
        4.36 -     4.90: 21449
  Nonbonded interactions: 52412
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  39 "
            pdb=" N   SER D  40 "
     model   vdw
     2.181 3.120
  nonbonded pdb=" O   SER C 219 "
            pdb=" OG  SER C 219 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   SER D 219 "
            pdb=" OG  SER D 219 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OG  SER C 202 "
            pdb=" OG  SER C 268 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   GLY A  33 "
            pdb=" OG1 THR A  37 "
     model   vdw
     2.259 3.040
  ... (remaining 52407 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = (chain 'C' and (resid 37 through 72 or (resid 73 through 74 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 75 through 173 or (resid 174 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 175 through 180 or  \ 
(resid 181 and (name N or name CA or name C or name O or name CB )) or resid 182 \ 
 through 186 or (resid 187 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 188 through 254 or (resid 255 and (name N or name CA or name C or n \ 
ame O or name CB )) or resid 256 through 288))
  selection = (chain 'D' and (resid 37 through 40 or (resid 41 through 42 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 60 through 64 or (resid 65 through \ 
 66 and (name N or name CA or name C or name O or name CB )) or resid 67 through \ 
 73 or (resid 74 and (name N or name CA or name C or name O or name CB )) or res \ 
id 75 through 82 or (resid 83 through 84 and (name N or name CA or name C or nam \ 
e O or name CB )) or resid 85 through 134 or (resid 135 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 136 through 200 or (resid 201 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 202 through 266 or (re \ 
sid 267 and (name N or name CA or name C or name O or name CB )) or resid 268 th \ 
rough 288))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.540
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5806
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091   6627  Z= 0.151
  Angle     :  0.762  18.757   9050  Z= 0.382
  Chirality :  0.044   0.228   1059
  Planarity :  0.006   0.089   1128
  Dihedral  : 18.280  83.680   2174
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 39.05 %
    Favored  : 59.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.21 (0.30), residues: 842
  helix:  0.33 (0.28), residues: 366
  sheet: -1.23 (0.49), residues: 116
  loop : -1.82 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 220 
 HIS   0.012   0.002   HIS B 110 
 PHE   0.038   0.002   PHE B  78 
 TYR   0.018   0.001   TYR D 228 
 ARG   0.007   0.001   ARG B 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17712 (  350)
  hydrogen bonds       : angle       7.51125 ( 1056)
  SS BOND              : bond        0.00042 (    4)
  SS BOND              : angle       0.29295 (    8)
  covalent geometry    : bond        0.00344 ( 6623)
  covalent geometry    : angle       0.76238 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.654 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 119
  average time/residue: 0.1968
  time to fit residues: 30.5131
Evaluate side-chains
  114 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 111
  time to evaluate  : 0.643 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  219 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 42 optimal weight:   10.0000
   chunk 34 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 25 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
** C 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.178700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.157742 restraints weight = 10114.126|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 2.54
r_work: 0.4115 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.4115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6201
moved from start:          0.1197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6627  Z= 0.204
  Angle     :  0.689  12.673   9050  Z= 0.358
  Chirality :  0.044   0.221   1059
  Planarity :  0.005   0.061   1128
  Dihedral  :  5.614  44.479    919
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 37.06 %
    Favored  : 57.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.47 (0.30), residues: 842
  helix:  0.02 (0.28), residues: 372
  sheet: -1.66 (0.46), residues: 128
  loop : -1.73 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 220 
 HIS   0.004   0.001   HIS B 110 
 PHE   0.016   0.002   PHE D 198 
 TYR   0.012   0.002   TYR A  93 
 ARG   0.003   0.000   ARG C 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04811 (  350)
  hydrogen bonds       : angle       5.67563 ( 1056)
  SS BOND              : bond        0.00195 (    4)
  SS BOND              : angle       0.50975 (    8)
  covalent geometry    : bond        0.00447 ( 6623)
  covalent geometry    : angle       0.68931 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 125
  time to evaluate  : 0.648 
Fit side-chains
REVERT: A   87 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6427 (pm20)
REVERT: A  168 VAL cc_start: 0.7503 (t) cc_final: 0.7293 (p)
REVERT: D  228 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.6352 (m-10)
REVERT: B   93 TYR cc_start: 0.7182 (m-80) cc_final: 0.6817 (m-80)
REVERT: B  150 LEU cc_start: 0.7194 (tp) cc_final: 0.6989 (tt)
  outliers start: 37
  outliers final: 19
  residues processed: 151
  average time/residue: 0.1851
  time to fit residues: 37.2371
Evaluate side-chains
  141 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   71 LEU
Chi-restraints excluded: chain A residue   87 GLN
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue  228 TYR
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    0.5980
   chunk 56 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0970
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
B  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.182867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.163187 restraints weight = 10195.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.4270 rms_B_bonded: 2.27
r_work: 0.4174 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.4034 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
moved from start:          0.1289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6627  Z= 0.133
  Angle     :  0.621  12.920   9050  Z= 0.315
  Chirality :  0.040   0.198   1059
  Planarity :  0.005   0.065   1128
  Dihedral  :  5.107  44.298    916
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.55 %
    Favored  : 91.45 %
  Rotamer:
    Outliers :  7.04 %
    Allowed  : 34.92 %
    Favored  : 58.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.16 (0.31), residues: 842
  helix:  0.30 (0.28), residues: 384
  sheet: -1.54 (0.46), residues: 128
  loop : -1.65 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 220 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.020   0.001   PHE A  78 
 TYR   0.009   0.001   TYR A  93 
 ARG   0.002   0.000   ARG C 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04216 (  350)
  hydrogen bonds       : angle       5.28225 ( 1056)
  SS BOND              : bond        0.00122 (    4)
  SS BOND              : angle       0.46729 (    8)
  covalent geometry    : bond        0.00292 ( 6623)
  covalent geometry    : angle       0.62143 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 118
  time to evaluate  : 0.604 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6560 (t80)
REVERT: A   87 GLN cc_start: 0.6645 (OUTLIER) cc_final: 0.6443 (pm20)
REVERT: A  224 LEU cc_start: 0.4828 (OUTLIER) cc_final: 0.4388 (mp)
REVERT: D  133 ASN cc_start: 0.5500 (OUTLIER) cc_final: 0.5298 (m-40)
REVERT: B   44 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6154 (t80)
REVERT: B  215 ILE cc_start: 0.7477 (OUTLIER) cc_final: 0.7276 (mm)
REVERT: B  224 LEU cc_start: 0.4936 (OUTLIER) cc_final: 0.4360 (tp)
  outliers start: 46
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1764
  time to fit residues: 34.7765
Evaluate side-chains
  148 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 117
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   87 GLN
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  224 LEU
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  217 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue  133 ASN
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 66 optimal weight:    0.2980
   chunk 15 optimal weight:    0.5980
   chunk 48 optimal weight:   20.0000
   chunk 18 optimal weight:    0.6980
   chunk 77 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 47 optimal weight:    8.9990
   chunk 3 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4482 r_free = 0.4482 target = 0.179368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.157410 restraints weight = 10194.971|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 2.71
r_work: 0.4109 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6219
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6627  Z= 0.161
  Angle     :  0.645  13.007   9050  Z= 0.329
  Chirality :  0.042   0.213   1059
  Planarity :  0.005   0.062   1128
  Dihedral  :  5.110  43.575    916
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 35.53 %
    Favored  : 57.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.19 (0.31), residues: 842
  helix:  0.21 (0.28), residues: 384
  sheet: -0.99 (0.50), residues: 116
  loop : -1.82 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 220 
 HIS   0.003   0.001   HIS B 110 
 PHE   0.018   0.002   PHE A  78 
 TYR   0.018   0.002   TYR D 264 
 ARG   0.002   0.000   ARG D 241 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  350)
  hydrogen bonds       : angle       5.19494 ( 1056)
  SS BOND              : bond        0.00101 (    4)
  SS BOND              : angle       0.53057 (    8)
  covalent geometry    : bond        0.00360 ( 6623)
  covalent geometry    : angle       0.64509 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 121
  time to evaluate  : 0.672 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 PHE cc_start: 0.7124 (OUTLIER) cc_final: 0.6251 (t80)
REVERT: D  203 MET cc_start: 0.4585 (OUTLIER) cc_final: 0.4119 (mtt)
REVERT: B   44 PHE cc_start: 0.6798 (OUTLIER) cc_final: 0.5860 (t80)
REVERT: B  224 LEU cc_start: 0.4742 (OUTLIER) cc_final: 0.4247 (tp)
  outliers start: 47
  outliers final: 32
  residues processed: 150
  average time/residue: 0.1802
  time to fit residues: 35.8303
Evaluate side-chains
  155 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 119
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  127 THR
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  204 ARG
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  259 ASP
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 42 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 60 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    0.2980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.180151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.158534 restraints weight = 10116.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.4234 rms_B_bonded: 2.69
r_work: 0.4126 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6184
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6627  Z= 0.141
  Angle     :  0.637  13.602   9050  Z= 0.322
  Chirality :  0.041   0.196   1059
  Planarity :  0.004   0.063   1128
  Dihedral  :  5.002  43.153    916
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.43 %
    Favored  : 91.57 %
  Rotamer:
    Outliers :  7.50 %
    Allowed  : 35.07 %
    Favored  : 57.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.06 (0.31), residues: 842
  helix:  0.34 (0.28), residues: 384
  sheet: -0.87 (0.51), residues: 116
  loop : -1.82 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 220 
 HIS   0.002   0.001   HIS B 110 
 PHE   0.018   0.001   PHE A 158 
 TYR   0.017   0.001   TYR D 264 
 ARG   0.004   0.000   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04088 (  350)
  hydrogen bonds       : angle       5.05407 ( 1056)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.43792 (    8)
  covalent geometry    : bond        0.00317 ( 6623)
  covalent geometry    : angle       0.63764 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 PHE cc_start: 0.7085 (OUTLIER) cc_final: 0.6219 (t80)
REVERT: D  203 MET cc_start: 0.4509 (OUTLIER) cc_final: 0.4063 (mtt)
REVERT: B   44 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5832 (t80)
REVERT: B  224 LEU cc_start: 0.4561 (OUTLIER) cc_final: 0.4205 (tp)
  outliers start: 49
  outliers final: 30
  residues processed: 159
  average time/residue: 0.1841
  time to fit residues: 38.4591
Evaluate side-chains
  156 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 122
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  180 LEU
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 41 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 26 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.6260

-------------------------------------------------------------------------------
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 = 0.4496 r_free = 0.4496 target = 0.180336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.159506 restraints weight = 10057.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.4246 rms_B_bonded: 2.54
r_work: 0.4141 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work (final): 0.4141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6169
moved from start:          0.1730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6627  Z= 0.139
  Angle     :  0.658  14.180   9050  Z= 0.328
  Chirality :  0.041   0.203   1059
  Planarity :  0.004   0.061   1128
  Dihedral  :  4.971  42.366    916
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  7.96 %
    Allowed  : 35.22 %
    Favored  : 56.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.02 (0.31), residues: 842
  helix:  0.36 (0.28), residues: 384
  sheet: -0.81 (0.51), residues: 116
  loop : -1.81 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.019   0.001   PHE A 158 
 TYR   0.019   0.001   TYR D 264 
 ARG   0.004   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04060 (  350)
  hydrogen bonds       : angle       4.97962 ( 1056)
  SS BOND              : bond        0.00119 (    4)
  SS BOND              : angle       0.44410 (    8)
  covalent geometry    : bond        0.00309 ( 6623)
  covalent geometry    : angle       0.65835 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 125
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6204 (t80)
REVERT: A   95 LEU cc_start: 0.7665 (mt) cc_final: 0.7338 (mp)
REVERT: D  203 MET cc_start: 0.4496 (OUTLIER) cc_final: 0.4083 (mtt)
REVERT: D  207 ARG cc_start: 0.6595 (ptp-170) cc_final: 0.6345 (ttm170)
REVERT: B   44 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5845 (t80)
REVERT: B  224 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.4184 (tp)
  outliers start: 52
  outliers final: 38
  residues processed: 157
  average time/residue: 0.1796
  time to fit residues: 37.3194
Evaluate side-chains
  167 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 125
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  217 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  259 ASP
Chi-restraints excluded: chain D residue  262 VAL
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  248 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 59 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 1 optimal weight:    0.3980
   chunk 75 optimal weight:    0.1980
   chunk 17 optimal weight:    0.4980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4505 r_free = 0.4505 target = 0.181094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.160077 restraints weight = 10024.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.4253 rms_B_bonded: 2.64
r_work: 0.4145 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6143
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6627  Z= 0.128
  Angle     :  0.659  14.808   9050  Z= 0.326
  Chirality :  0.041   0.193   1059
  Planarity :  0.004   0.061   1128
  Dihedral  :  4.852  41.595    916
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.08 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  7.66 %
    Allowed  : 35.68 %
    Favored  : 56.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.89 (0.31), residues: 842
  helix:  0.53 (0.29), residues: 382
  sheet: -0.77 (0.51), residues: 116
  loop : -1.79 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.025   0.001   PHE B  78 
 TYR   0.017   0.001   TYR D 264 
 ARG   0.006   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03821 (  350)
  hydrogen bonds       : angle       4.88126 ( 1056)
  SS BOND              : bond        0.00133 (    4)
  SS BOND              : angle       0.40795 (    8)
  covalent geometry    : bond        0.00291 ( 6623)
  covalent geometry    : angle       0.65869 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 122
  time to evaluate  : 0.606 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6145 (t80)
REVERT: A   95 LEU cc_start: 0.7654 (mt) cc_final: 0.7312 (mp)
REVERT: A  267 ARG cc_start: 0.7278 (ttp80) cc_final: 0.6868 (tmm160)
REVERT: D  203 MET cc_start: 0.4427 (OUTLIER) cc_final: 0.4044 (mtt)
REVERT: B   44 PHE cc_start: 0.6775 (OUTLIER) cc_final: 0.5823 (t80)
REVERT: B   93 TYR cc_start: 0.7216 (m-80) cc_final: 0.6696 (m-80)
REVERT: B  224 LEU cc_start: 0.4442 (OUTLIER) cc_final: 0.4211 (tp)
  outliers start: 50
  outliers final: 33
  residues processed: 153
  average time/residue: 0.1819
  time to fit residues: 36.4271
Evaluate side-chains
  159 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  259 ASP
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  165 GLN
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 VAL
Chi-restraints excluded: chain B residue  248 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 8 optimal weight:    0.0570
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9990
   chunk 41 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.7702

-------------------------------------------------------------------------------
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 = 0.4489 r_free = 0.4489 target = 0.179997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.158284 restraints weight = 10051.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.4227 rms_B_bonded: 2.70
r_work: 0.4118 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6192
moved from start:          0.1929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6627  Z= 0.156
  Angle     :  0.688  16.054   9050  Z= 0.339
  Chirality :  0.043   0.390   1059
  Planarity :  0.004   0.059   1128
  Dihedral  :  4.920  40.735    916
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 15.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  7.81 %
    Allowed  : 34.92 %
    Favored  : 57.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.97 (0.31), residues: 842
  helix:  0.41 (0.28), residues: 384
  sheet: -0.80 (0.50), residues: 116
  loop : -1.78 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A 220 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.025   0.001   PHE A 158 
 TYR   0.013   0.002   TYR B 147 
 ARG   0.005   0.000   ARG A 204 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04017 (  350)
  hydrogen bonds       : angle       4.90324 ( 1056)
  SS BOND              : bond        0.00127 (    4)
  SS BOND              : angle       0.37685 (    8)
  covalent geometry    : bond        0.00361 ( 6623)
  covalent geometry    : angle       0.68865 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 125
  time to evaluate  : 0.619 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6082 (t80)
REVERT: A   95 LEU cc_start: 0.7677 (mt) cc_final: 0.7339 (mp)
REVERT: A  267 ARG cc_start: 0.7294 (ttp80) cc_final: 0.6934 (tmm160)
REVERT: D  203 MET cc_start: 0.4494 (OUTLIER) cc_final: 0.4052 (mtt)
REVERT: D  207 ARG cc_start: 0.7633 (ttm170) cc_final: 0.7273 (ttm170)
REVERT: B   44 PHE cc_start: 0.6805 (OUTLIER) cc_final: 0.5931 (t80)
REVERT: B   93 TYR cc_start: 0.7292 (m-80) cc_final: 0.6733 (m-80)
REVERT: B  224 LEU cc_start: 0.4539 (OUTLIER) cc_final: 0.4213 (tp)
  outliers start: 51
  outliers final: 37
  residues processed: 158
  average time/residue: 0.1799
  time to fit residues: 37.7273
Evaluate side-chains
  165 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 124
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 SER
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  238 ASP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  259 ASP
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  259 ASP
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  165 GLN
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  238 ASP
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9980
   chunk 31 optimal weight:    5.9990
   chunk 28 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 43 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.4465 r_free = 0.4465 target = 0.177959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.155955 restraints weight = 10140.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.4195 rms_B_bonded: 2.70
r_work: 0.4086 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.4086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6240
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6627  Z= 0.192
  Angle     :  0.722  15.864   9050  Z= 0.360
  Chirality :  0.045   0.376   1059
  Planarity :  0.005   0.059   1128
  Dihedral  :  4.875  22.586    914
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.33 %
    Favored  : 89.67 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 35.07 %
    Favored  : 57.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.16 (0.30), residues: 842
  helix:  0.22 (0.28), residues: 380
  sheet: -0.84 (0.50), residues: 116
  loop : -1.82 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP B 220 
 HIS   0.002   0.001   HIS A 202 
 PHE   0.022   0.002   PHE B  78 
 TYR   0.018   0.002   TYR B 147 
 ARG   0.004   0.001   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04381 (  350)
  hydrogen bonds       : angle       5.05404 ( 1056)
  SS BOND              : bond        0.00120 (    4)
  SS BOND              : angle       0.41921 (    8)
  covalent geometry    : bond        0.00439 ( 6623)
  covalent geometry    : angle       0.72257 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 126
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7086 (OUTLIER) cc_final: 0.6096 (t80)
REVERT: D  203 MET cc_start: 0.4609 (OUTLIER) cc_final: 0.4121 (mtt)
REVERT: D  207 ARG cc_start: 0.7780 (ttm170) cc_final: 0.7423 (ttm170)
REVERT: B   44 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6108 (t80)
REVERT: B  224 LEU cc_start: 0.4662 (OUTLIER) cc_final: 0.4180 (tp)
  outliers start: 47
  outliers final: 34
  residues processed: 155
  average time/residue: 0.2008
  time to fit residues: 40.9872
Evaluate side-chains
  164 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 126
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 ILE
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  143 ILE
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  186 PHE
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  259 ASP
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   13 PHE
Chi-restraints excluded: chain B residue   25 ILE
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  165 GLN
Chi-restraints excluded: chain B residue  168 VAL
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 6 optimal weight:    0.8980
   chunk 26 optimal weight:    9.9990
   chunk 51 optimal weight:    0.9980
   chunk 43 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0870
   chunk 79 optimal weight:    0.2980
   chunk 60 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   overall best weight:    0.5758

-------------------------------------------------------------------------------
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 = 0.4495 r_free = 0.4495 target = 0.180330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.158642 restraints weight = 10230.797|
|-----------------------------------------------------------------------------|
r_work (start): 0.4250 rms_B_bonded: 2.72
r_work: 0.4130 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6200
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6627  Z= 0.142
  Angle     :  0.712  16.308   9050  Z= 0.348
  Chirality :  0.043   0.275   1059
  Planarity :  0.004   0.060   1128
  Dihedral  :  4.778  21.642    914
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.67 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  5.97 %
    Allowed  : 36.29 %
    Favored  : 57.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -1.10 (0.30), residues: 842
  helix:  0.34 (0.28), residues: 388
  sheet: -0.85 (0.49), residues: 116
  loop : -1.94 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 220 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.025   0.001   PHE B  78 
 TYR   0.013   0.001   TYR B  93 
 ARG   0.003   0.000   ARG C 128 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  350)
  hydrogen bonds       : angle       4.92760 ( 1056)
  SS BOND              : bond        0.00142 (    4)
  SS BOND              : angle       0.35628 (    8)
  covalent geometry    : bond        0.00324 ( 6623)
  covalent geometry    : angle       0.71245 ( 9042)

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

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

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1684 Ramachandran restraints generated.
    842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A   44 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6127 (t80)
REVERT: A   95 LEU cc_start: 0.7690 (mt) cc_final: 0.7360 (mp)
REVERT: A  267 ARG cc_start: 0.7198 (tmm160) cc_final: 0.6916 (tmm160)
REVERT: D  203 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.4001 (mtt)
REVERT: D  207 ARG cc_start: 0.7671 (ttm170) cc_final: 0.7331 (ttm170)
REVERT: B   44 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6113 (t80)
REVERT: B  224 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4325 (tp)
  outliers start: 39
  outliers final: 29
  residues processed: 150
  average time/residue: 0.2101
  time to fit residues: 41.5493
Evaluate side-chains
  155 residues out of total 754 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 PHE
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  126 TRP
Chi-restraints excluded: chain A residue  138 LEU
Chi-restraints excluded: chain A residue  154 ARG
Chi-restraints excluded: chain A residue  165 GLN
Chi-restraints excluded: chain A residue  170 PHE
Chi-restraints excluded: chain A residue  220 TRP
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain C residue  206 VAL
Chi-restraints excluded: chain C residue  238 THR
Chi-restraints excluded: chain C residue  286 VAL
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  182 HIS
Chi-restraints excluded: chain D residue  203 MET
Chi-restraints excluded: chain D residue  206 VAL
Chi-restraints excluded: chain D residue  238 THR
Chi-restraints excluded: chain D residue  259 ASP
Chi-restraints excluded: chain D residue  283 LEU
Chi-restraints excluded: chain D residue  286 VAL
Chi-restraints excluded: chain B residue   44 PHE
Chi-restraints excluded: chain B residue   47 LEU
Chi-restraints excluded: chain B residue   67 LEU
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 TRP
Chi-restraints excluded: chain B residue  154 ARG
Chi-restraints excluded: chain B residue  165 GLN
Chi-restraints excluded: chain B residue  178 LEU
Chi-restraints excluded: chain B residue  211 LEU
Chi-restraints excluded: chain B residue  213 SER
Chi-restraints excluded: chain B residue  224 LEU
Chi-restraints excluded: chain B residue  247 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 15 optimal weight:    0.2980
   chunk 33 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 46 optimal weight:    4.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4497 r_free = 0.4497 target = 0.180345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.158980 restraints weight = 10264.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.4251 rms_B_bonded: 2.70
r_work: 0.4144 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6167
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6627  Z= 0.141
  Angle     :  0.704  16.162   9050  Z= 0.343
  Chirality :  0.042   0.252   1059
  Planarity :  0.004   0.060   1128
  Dihedral  :  4.762  21.632    914
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.91 %
    Favored  : 91.09 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 37.06 %
    Favored  : 57.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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: -0.99 (0.31), residues: 842
  helix:  0.44 (0.28), residues: 384
  sheet: -0.93 (0.48), residues: 116
  loop : -1.80 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 220 
 HIS   0.003   0.001   HIS A 202 
 PHE   0.026   0.001   PHE B  78 
 TYR   0.012   0.001   TYR B  93 
 ARG   0.003   0.000   ARG B 226 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  350)
  hydrogen bonds       : angle       4.89968 ( 1056)
  SS BOND              : bond        0.00114 (    4)
  SS BOND              : angle       0.38128 (    8)
  covalent geometry    : bond        0.00324 ( 6623)
  covalent geometry    : angle       0.70409 ( 9042)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3452.15 seconds
wall clock time: 60 minutes 33.34 seconds (3633.34 seconds total)