Starting phenix.real_space_refine
on Thu Feb 13 01:13:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hqn_34951/02_2025/8hqn_34951.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hqn_34951/02_2025/8hqn_34951.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hqn_34951/02_2025/8hqn_34951.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hqn_34951/02_2025/8hqn_34951.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hqn_34951/02_2025/8hqn_34951.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hqn_34951/02_2025/8hqn_34951.cif"
  }
  resolution = 3.0
  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=   0.005 sd=   0.019
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      64      5.16       5
     C    5468      2.51       5
     N    1460      2.21       5
     O    1613      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8605
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 296, 2246
          Classifications: {'peptide': 296}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 291}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 24
          Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 418
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "H"
      Number of atoms: 1785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1785
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 10, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2467
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2467
          Classifications: {'peptide': 310}
          Link IDs: {'PTRANS': 6, 'TRANS': 303}
    Chain: "A"
      Number of atoms: 1668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1668
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 58
          Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "R"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'9HO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.13, per 1000 atoms: 0.60
  Number of scatterers: 8605
  At special positions: 0
  Unit cell: (113.92, 111.25, 136.17, 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      64     16.00
     O    1613      8.00
     N    1460      7.00
     C    5468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 147 " - pdb=" SG  CYS H 217 " 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: 2.25
  Conformation dependent library (CDL) restraints added in 975.7 milliseconds
  

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2070

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 13 sheets defined
      36.9% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.89
  Creating SS restraints...
    Processing helix  chain 'C' and resid 10 through 21
      removed outlier: 4.211A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU C  15 " --> pdb=" O   GLN C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 45
      removed outlier: 3.698A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 4.099A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ALA C  43 " --> pdb=" O   ALA C  39 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   HIS C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'R' and resid 38 through 71
      Proline residue:  R  58  - end of helix
      removed outlier: 3.820A  pdb=" N   TRP R  65 " --> pdb=" O   CYS R  61 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 75 through 87
      removed outlier: 3.774A  pdb=" N   VAL R  79 " --> pdb=" O   ASN R  75 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 89 through 102
      Proline residue:  R  96  - end of helix
    Processing helix  chain 'R' and resid 112 through 145
    Processing helix  chain 'R' and resid 146 through 154
      removed outlier: 4.126A  pdb=" N   ARG R 151 " --> pdb=" O   ALA R 147 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   GLY R 152 " --> pdb=" O   LEU R 148 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG R 153 " --> pdb=" O   GLU R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 155 through 180
      removed outlier: 3.961A  pdb=" N   LEU R 161 " --> pdb=" O   ARG R 157 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   ILE R 162 " --> pdb=" O   THR R 158 " (cutoff:3.500A)
      removed outlier: 4.677A  pdb=" N   SER R 163 " --> pdb=" O   ALA R 159 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ALA R 164 " --> pdb=" O   ILE R 160 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   CYS R 165 " --> pdb=" O   LEU R 161 " (cutoff:3.500A)
      Proline residue:  R 176  - end of helix
    Processing helix  chain 'R' and resid 194 through 208
    Processing helix  chain 'R' and resid 208 through 228
    Processing helix  chain 'R' and resid 233 through 271
      Proline residue:  R 257  - end of helix
      removed outlier: 4.622A  pdb=" N   LYS R 265 " --> pdb=" O   VAL R 261 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ALA R 266 " --> pdb=" O   LEU R 262 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ALA R 267 " --> pdb=" O   LEU R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 280 through 311
      Proline residue:  R 305  - end of helix
      removed outlier: 3.613A  pdb=" N   ALA R 311 " --> pdb=" O   ILE R 307 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 313 through 331
      removed outlier: 3.977A  pdb=" N   GLN R 317 " --> pdb=" O   ASP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 334 through 346
      removed outlier: 3.840A  pdb=" N   GLU R 346 " --> pdb=" O   ARG R 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 6 through 31
    Processing helix  chain 'A' and resid 45 through 53
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.378A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 216
      No H-bonds generated for 'chain 'A' and resid 214 through 216'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.801A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 50
      removed outlier: 7.400A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 5.174A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63
      removed outlier: 3.527A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.878A  pdb=" N   THR B 102 " --> pdb=" O   GLY B 115 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 150
      removed outlier: 4.130A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 189 through 192
      removed outlier: 4.058A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.390A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.236A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 234
      removed outlier: 3.809A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   GLY B 244 " --> pdb=" O   ALA B 231 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   CYS B 233 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ALA B 242 " --> pdb=" O   CYS B 233 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU B 252 " --> pdb=" O   MET B 262 " (cutoff:3.500A)
      removed outlier: 4.606A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 276 through 278
    Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.883A  pdb=" N   SER H  21 " --> pdb=" O   SER H   7 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   LEU H  79 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 58 through 60
      removed outlier: 3.701A  pdb=" N   TYR H  59 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 5.792A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ALA H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ARG H  98 " --> pdb=" O   PHE H 110 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'H' and resid 129 through 130
    Processing sheet with id=AB2, first strand: chain 'H' and resid 182 through 183
      removed outlier: 6.915A  pdb=" N   TRP H 164 " --> pdb=" O   LEU H 176 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   TYR H 178 " --> pdb=" O   LEU H 162 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LEU H 162 " --> pdb=" O   TYR H 178 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY H 213 " --> pdb=" O   LEU H 233 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 194 through 195
    Processing sheet with id=AB4, first strand: chain 'A' and resid 185 through 191
      removed outlier: 5.645A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   PHE A 199 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.077A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.943A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.867A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.793A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)

    394 hydrogen bonds defined for protein.
    1128 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: 2.27

  Time building geometry restraints manager: 2.55 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2254
        1.33 -     1.46: 2033
        1.46 -     1.58: 4402
        1.58 -     1.70: 0
        1.70 -     1.83: 89
  Bond restraints: 8778
  Sorted by residual:
  bond pdb=" C11 9HO R 401 "
       pdb=" C12 9HO R 401 "
    ideal  model  delta    sigma   weight residual
    1.455  1.551 -0.096 2.00e-02 2.50e+03 2.30e+01
  bond pdb=" N   LEU R  95 "
       pdb=" CA  LEU R  95 "
    ideal  model  delta    sigma   weight residual
    1.462  1.491 -0.029 7.70e-03 1.69e+04 1.38e+01
  bond pdb=" C   ILE R 210 "
       pdb=" N   PRO R 211 "
    ideal  model  delta    sigma   weight residual
    1.334  1.389 -0.055 1.51e-02 4.39e+03 1.31e+01
  bond pdb=" N   LYS B  57 "
       pdb=" CA  LYS B  57 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.36e+00
  bond pdb=" N   VAL B 320 "
       pdb=" CA  VAL B 320 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.035 1.14e-02 7.69e+03 9.32e+00
  ... (remaining 8773 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.48: 11883
        7.48 -    14.96: 12
       14.96 -    22.45: 0
       22.45 -    29.93: 0
       29.93 -    37.41: 1
  Bond angle restraints: 11896
  Sorted by residual:
  angle pdb=" C10 9HO R 401 "
        pdb=" C11 9HO R 401 "
        pdb=" C12 9HO R 401 "
      ideal   model   delta    sigma   weight residual
     122.56   85.15   37.41 3.00e+00 1.11e-01 1.55e+02
  angle pdb=" C   GLN H 167 "
        pdb=" N   ARG H 168 "
        pdb=" CA  ARG H 168 "
      ideal   model   delta    sigma   weight residual
     120.49  130.38   -9.89 1.42e+00 4.96e-01 4.85e+01
  angle pdb=" C   LYS A 192 "
        pdb=" CA  LYS A 192 "
        pdb=" CB  LYS A 192 "
      ideal   model   delta    sigma   weight residual
     117.23  110.18    7.05 1.36e+00 5.41e-01 2.68e+01
  angle pdb=" CA  LYS A 192 "
        pdb=" C   LYS A 192 "
        pdb=" N   ASP A 193 "
      ideal   model   delta    sigma   weight residual
     119.98  115.62    4.36 8.50e-01 1.38e+00 2.64e+01
  angle pdb=" C11 9HO R 401 "
        pdb=" C10 9HO R 401 "
        pdb=" C9  9HO R 401 "
      ideal   model   delta    sigma   weight residual
     126.07  111.47   14.60 3.00e+00 1.11e-01 2.37e+01
  ... (remaining 11891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.64: 5067
       35.64 -    71.28: 113
       71.28 -   106.92: 3
      106.92 -   142.56: 0
      142.56 -   178.20: 1
  Dihedral angle restraints: 5184
    sinusoidal: 1972
      harmonic: 3212
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    6.91   86.09     1      1.00e+01 1.00e-02 8.95e+01
  dihedral pdb=" C11 9HO R 401 "
           pdb=" C10 9HO R 401 "
           pdb=" C9  9HO R 401 "
           pdb=" O3  9HO R 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
       1.74  179.94 -178.20     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" CB  CYS H 147 "
           pdb=" SG  CYS H 147 "
           pdb=" SG  CYS H 217 "
           pdb=" CB  CYS H 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.22   38.78     1      1.00e+01 1.00e-02 2.12e+01
  ... (remaining 5181 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 1218
       0.090 -    0.180: 134
       0.180 -    0.269: 8
       0.269 -    0.359: 1
       0.359 -    0.449: 2
  Chirality restraints: 1363
  Sorted by residual:
  chirality pdb=" CG  LEU R 262 "
            pdb=" CB  LEU R 262 "
            pdb=" CD1 LEU R 262 "
            pdb=" CD2 LEU R 262 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.14   -0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CG  LEU R  89 "
            pdb=" CB  LEU R  89 "
            pdb=" CD1 LEU R  89 "
            pdb=" CD2 LEU R  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.40 2.00e-01 2.50e+01 3.98e+00
  chirality pdb=" C9  9HO R 401 "
            pdb=" C10 9HO R 401 "
            pdb=" C8  9HO R 401 "
            pdb=" O3  9HO R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.23    2.50   -0.28 2.00e-01 2.50e+01 1.92e+00
  ... (remaining 1360 not shown)

  Planarity restraints: 1502
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN R  70 "   -0.013 2.00e-02 2.50e+03   2.58e-02 6.64e+00
        pdb=" C   GLN R  70 "    0.045 2.00e-02 2.50e+03
        pdb=" O   GLN R  70 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL R  71 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET H 180 "    0.012 2.00e-02 2.50e+03   2.32e-02 5.40e+00
        pdb=" C   MET H 180 "   -0.040 2.00e-02 2.50e+03
        pdb=" O   MET H 180 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER H 181 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 210 "   -0.033 5.00e-02 4.00e+02   4.93e-02 3.88e+00
        pdb=" N   PRO R 211 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R 211 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 211 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1499 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1911
        2.78 -     3.31: 8222
        3.31 -     3.84: 14161
        3.84 -     4.37: 15822
        4.37 -     4.90: 27140
  Nonbonded interactions: 67256
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 227 "
            pdb=" OD1 ASP B 228 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" CB  PHE R 123 "
            pdb=" O1  9HO R 401 "
     model   vdw
     2.259 3.440
  nonbonded pdb=" OG  SER B 201 "
            pdb=" NE1 TRP B 211 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" O   PHE A 336 "
            pdb=" OG1 THR A 340 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NE2 GLN H 167 "
            pdb=" O   ARG H 168 "
     model   vdw
     2.295 3.120
  ... (remaining 67251 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             0.620
  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:             0.000
  Extract box with map and model:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.530
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.096   8778  Z= 0.383
  Angle     :  1.055  37.410  11896  Z= 0.572
  Chirality :  0.057   0.449   1363
  Planarity :  0.006   0.049   1502
  Dihedral  : 15.246 178.201   3108
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 15.87 %
    Favored  : 83.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.23), residues: 1089
  helix: -0.18 (0.26), residues: 373
  sheet: -0.75 (0.32), residues: 236
  loop : -1.93 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP R  98 
 HIS   0.010   0.002   HIS R 242 
 PHE   0.019   0.003   PHE A 189 
 TYR   0.027   0.003   TYR R  91 
 ARG   0.006   0.001   ARG B 256 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
REVERT: C   19 LEU cc_start: 0.9058 (mt) cc_final: 0.8842 (mp)
  outliers start: 5
  outliers final: 3
  residues processed: 75
  average time/residue: 1.3700
  time to fit residues: 109.7182
Evaluate side-chains
  50 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 47
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  335 VAL
Chi-restraints excluded: chain A residue   54 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 44 optimal weight:    5.9990
   chunk 85 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 98 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C  11 GLN
A 213 HIS
A 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2965 r_free = 0.2965 target = 0.061480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.054736 restraints weight = 39400.906|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 2.95
r_work: 0.2734 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8778  Z= 0.303
  Angle     :  0.620   6.920  11896  Z= 0.331
  Chirality :  0.043   0.146   1363
  Planarity :  0.004   0.041   1502
  Dihedral  :  7.277 131.468   1225
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 16.74 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.95 (0.24), residues: 1089
  helix:  0.71 (0.27), residues: 378
  sheet: -0.74 (0.30), residues: 265
  loop : -1.69 (0.26), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.018   0.002   PHE H  29 
 TYR   0.016   0.002   TYR H 178 
 ARG   0.005   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 53
  time to evaluate  : 0.974 
Fit side-chains
   revert: symmetry clash
REVERT: A   18 MET cc_start: 0.8436 (tpp) cc_final: 0.8148 (tpp)
REVERT: A  256 ASN cc_start: 0.9015 (m-40) cc_final: 0.8566 (m-40)
  outliers start: 23
  outliers final: 7
  residues processed: 73
  average time/residue: 1.1935
  time to fit residues: 94.2968
Evaluate side-chains
  51 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.972 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 13 optimal weight:    6.9990
   chunk 80 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:   10.0000
   chunk 89 optimal weight:    0.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
R 105 GLN
A 304 GLN
A 347 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.062481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.055651 restraints weight = 40131.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 3.00
r_work: 0.2759 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8778  Z= 0.189
  Angle     :  0.546   6.045  11896  Z= 0.293
  Chirality :  0.041   0.190   1363
  Planarity :  0.003   0.038   1502
  Dihedral  :  6.707 115.321   1220
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.76 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.74 %
    Favored  : 80.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.25), residues: 1089
  helix:  1.20 (0.28), residues: 376
  sheet: -0.66 (0.30), residues: 282
  loop : -1.47 (0.28), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 297 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.013   0.001   PHE H  29 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.004   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 48
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9707 (OUTLIER) cc_final: 0.9481 (tt)
REVERT: A  256 ASN cc_start: 0.9097 (m-40) cc_final: 0.8686 (m110)
  outliers start: 27
  outliers final: 4
  residues processed: 71
  average time/residue: 1.0660
  time to fit residues: 82.1512
Evaluate side-chains
  50 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 25 optimal weight:    9.9990
   chunk 105 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 74 optimal weight:    0.7980
   chunk 69 optimal weight:   10.0000
   chunk 107 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    2.9588

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
A 213 HIS
A 347 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.061868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.055042 restraints weight = 39623.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.97
r_work: 0.2746 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2746
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8778  Z= 0.218
  Angle     :  0.541   5.973  11896  Z= 0.290
  Chirality :  0.041   0.165   1363
  Planarity :  0.003   0.038   1502
  Dihedral  :  6.609 108.940   1220
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 17.06 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.25), residues: 1089
  helix:  1.32 (0.28), residues: 377
  sheet: -0.57 (0.31), residues: 261
  loop : -1.36 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 332 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.013   0.002   PHE A 354 
 TYR   0.015   0.001   TYR H 178 
 ARG   0.003   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 46
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8675 (mm110)
REVERT: H  154 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9476 (tt)
REVERT: A  256 ASN cc_start: 0.9186 (m-40) cc_final: 0.8841 (m110)
REVERT: A  347 ASN cc_start: 0.8344 (t0) cc_final: 0.8114 (t0)
  outliers start: 34
  outliers final: 9
  residues processed: 76
  average time/residue: 0.9692
  time to fit residues: 80.5901
Evaluate side-chains
  55 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  158 THR
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 48 optimal weight:    9.9990
   chunk 97 optimal weight:    0.6980
   chunk 17 optimal weight:    6.9990
   chunk 63 optimal weight:    7.9990
   chunk 91 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 93 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 52 optimal weight:    9.9990
   chunk 76 optimal weight:    9.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
C  11 GLN
A 213 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.061809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.054977 restraints weight = 39384.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2822 rms_B_bonded: 2.98
r_work: 0.2747 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8778  Z= 0.213
  Angle     :  0.538   6.677  11896  Z= 0.285
  Chirality :  0.041   0.146   1363
  Planarity :  0.003   0.036   1502
  Dihedral  :  6.573 106.007   1220
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.32 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 19.11 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.25), residues: 1089
  helix:  1.38 (0.28), residues: 377
  sheet: -0.55 (0.31), residues: 261
  loop : -1.33 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 332 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.014   0.001   TYR H 178 
 ARG   0.002   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 47
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9478 (tt)
REVERT: A  256 ASN cc_start: 0.9170 (m-40) cc_final: 0.8855 (m110)
REVERT: A  347 ASN cc_start: 0.8326 (t0) cc_final: 0.8113 (t0)
  outliers start: 29
  outliers final: 12
  residues processed: 73
  average time/residue: 1.0037
  time to fit residues: 79.6351
Evaluate side-chains
  56 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   69 LEU
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 100 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 82 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 46 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C  11 GLN
R  73 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.062584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.055734 restraints weight = 38756.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 2.96
r_work: 0.2766 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2488

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8778  Z= 0.170
  Angle     :  0.520   9.063  11896  Z= 0.274
  Chirality :  0.040   0.135   1363
  Planarity :  0.003   0.037   1502
  Dihedral  :  6.505 103.233   1220
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.67 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 20.52 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.25), residues: 1089
  helix:  1.48 (0.28), residues: 377
  sheet: -0.60 (0.31), residues: 263
  loop : -1.23 (0.27), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 332 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.013   0.001   TYR H 178 
 ARG   0.005   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 46
  time to evaluate  : 1.055 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9485 (tt)
REVERT: A  256 ASN cc_start: 0.9166 (m-40) cc_final: 0.8879 (m110)
  outliers start: 23
  outliers final: 11
  residues processed: 67
  average time/residue: 1.0817
  time to fit residues: 79.1041
Evaluate side-chains
  54 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  338 ILE
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue  158 THR
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 90 optimal weight:    0.2980
   chunk 82 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 72 optimal weight:    4.9990
   overall best weight:    4.2588

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
C  11 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.060943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.054061 restraints weight = 39758.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 2.99
r_work: 0.2723 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8778  Z= 0.291
  Angle     :  0.569   8.175  11896  Z= 0.302
  Chirality :  0.042   0.173   1363
  Planarity :  0.003   0.037   1502
  Dihedral  :  6.596 102.872   1220
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.32 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.30 %
    Favored  : 76.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.37 (0.25), residues: 1089
  helix:  1.31 (0.28), residues: 379
  sheet: -0.74 (0.30), residues: 270
  loop : -1.26 (0.27), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.016   0.002   PHE R  38 
 TYR   0.015   0.001   TYR H 178 
 ARG   0.003   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9486 (tt)
REVERT: A  256 ASN cc_start: 0.9192 (m-40) cc_final: 0.8933 (m110)
  outliers start: 26
  outliers final: 14
  residues processed: 68
  average time/residue: 1.0265
  time to fit residues: 75.9864
Evaluate side-chains
  57 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   69 LEU
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  158 THR
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 107 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 34 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 81 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9990
   chunk 35 optimal weight:    7.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.062753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.055869 restraints weight = 39412.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 3.00
r_work: 0.2768 rms_B_bonded: 3.49 restraints_weight: 0.5000
r_work (final): 0.2768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.2629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8778  Z= 0.155
  Angle     :  0.522   7.862  11896  Z= 0.274
  Chirality :  0.040   0.167   1363
  Planarity :  0.003   0.037   1502
  Dihedral  :  6.507 102.363   1220
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 8.33
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.95 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 21.06 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.26), residues: 1089
  helix:  1.51 (0.28), residues: 377
  sheet: -0.59 (0.31), residues: 268
  loop : -1.16 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 332 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.013   0.001   TYR H 178 
 ARG   0.003   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 47
  time to evaluate  : 0.946 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9711 (OUTLIER) cc_final: 0.9475 (tt)
REVERT: A  256 ASN cc_start: 0.9146 (m-40) cc_final: 0.8883 (m110)
  outliers start: 22
  outliers final: 13
  residues processed: 69
  average time/residue: 1.0847
  time to fit residues: 81.3712
Evaluate side-chains
  57 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 43
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue   69 LEU
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  158 THR
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 9 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 85 optimal weight:    6.9990
   chunk 47 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.061014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.054147 restraints weight = 39755.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.2801 rms_B_bonded: 2.98
r_work: 0.2725 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8349
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8778  Z= 0.289
  Angle     :  0.572   8.527  11896  Z= 0.301
  Chirality :  0.042   0.156   1363
  Planarity :  0.003   0.037   1502
  Dihedral  :  6.516 101.127   1220
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.22 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 22.03 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.25), residues: 1089
  helix:  1.31 (0.28), residues: 379
  sheet: -0.68 (0.31), residues: 268
  loop : -1.24 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.017   0.002   PHE R  38 
 TYR   0.015   0.001   TYR B  59 
 ARG   0.003   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 1.092 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9713 (OUTLIER) cc_final: 0.9461 (tt)
REVERT: R   73 GLN cc_start: 0.9380 (mt0) cc_final: 0.8749 (pp30)
REVERT: A  256 ASN cc_start: 0.9187 (m-40) cc_final: 0.8959 (m110)
  outliers start: 15
  outliers final: 13
  residues processed: 60
  average time/residue: 1.1153
  time to fit residues: 72.6644
Evaluate side-chains
  55 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain H residue   57 THR
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  158 THR
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 40 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 105 optimal weight:    0.0970
   chunk 37 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 46 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    2.4184

-------------------------------------------------------------------------------
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 = 0.2988 r_free = 0.2988 target = 0.062128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.055244 restraints weight = 39736.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 3.02
r_work: 0.2753 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8778  Z= 0.190
  Angle     :  0.544   8.899  11896  Z= 0.284
  Chirality :  0.041   0.155   1363
  Planarity :  0.003   0.036   1502
  Dihedral  :  6.485 101.454   1220
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.86 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.14 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.26), residues: 1089
  helix:  1.41 (0.28), residues: 378
  sheet: -0.61 (0.31), residues: 276
  loop : -1.13 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 332 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.011   0.001   PHE H  29 
 TYR   0.013   0.001   TYR H 178 
 ARG   0.003   0.000   ARG A 205 

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 44
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
REVERT: H  154 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9469 (tt)
REVERT: R   73 GLN cc_start: 0.9372 (mt0) cc_final: 0.8749 (pp30)
REVERT: A  256 ASN cc_start: 0.9149 (m-40) cc_final: 0.8910 (m110)
  outliers start: 16
  outliers final: 12
  residues processed: 60
  average time/residue: 1.0815
  time to fit residues: 70.5927
Evaluate side-chains
  55 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   55 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain H residue  154 LEU
Chi-restraints excluded: chain H residue  162 LEU
Chi-restraints excluded: chain R residue   57 VAL
Chi-restraints excluded: chain R residue  142 VAL
Chi-restraints excluded: chain R residue  158 THR
Chi-restraints excluded: chain R residue  187 PHE
Chi-restraints excluded: chain R residue  261 VAL
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  316 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 2 optimal weight:    9.9990
   chunk 76 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 104 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 72 optimal weight:    0.3980
   chunk 69 optimal weight:   10.0000
   chunk 105 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    2.6184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
A 346 ASN
** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2988 r_free = 0.2988 target = 0.062022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.055125 restraints weight = 39926.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.03
r_work: 0.2752 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8778  Z= 0.201
  Angle     :  0.547   8.837  11896  Z= 0.285
  Chirality :  0.041   0.154   1363
  Planarity :  0.003   0.037   1502
  Dihedral  :  6.458  99.904   1220
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.04 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 22.25 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.19 (0.26), residues: 1089
  helix:  1.44 (0.28), residues: 377
  sheet: -0.62 (0.30), residues: 276
  loop : -1.13 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 332 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.012   0.001   PHE R  38 
 TYR   0.013   0.001   TYR H 178 
 ARG   0.004   0.000   ARG A 205 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4772.87 seconds
wall clock time: 85 minutes 22.50 seconds (5122.50 seconds total)