Starting phenix.real_space_refine
on Sat Dec 28 08:11:12 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iy9_35817/12_2024/8iy9_35817.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iy9_35817/12_2024/8iy9_35817.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.37
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iy9_35817/12_2024/8iy9_35817.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iy9_35817/12_2024/8iy9_35817.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iy9_35817/12_2024/8iy9_35817.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iy9_35817/12_2024/8iy9_35817.cif"
  }
  resolution = 3.37
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.045
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      47      5.16       5
     C    5175      2.51       5
     N    1412      2.21       5
     O    1487      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8121
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1551
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 208, 1551
          Classifications: {'peptide': 208}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 4, 'TRANS': 203}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 99
          Unresolved non-hydrogen angles: 121
          Unresolved non-hydrogen dihedrals: 79
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 57
    Chain: "B"
      Number of atoms: 2399
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2399
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 62}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 202
          Unresolved non-hydrogen angles: 251
          Unresolved non-hydrogen dihedrals: 153
          Unresolved non-hydrogen chiralities: 18
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 2, 'ASP:plan': 12}
          Unresolved non-hydrogen planarities: 118
    Chain: "G"
      Number of atoms: 392
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 392
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 31
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "H"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1655
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 120
          Unresolved non-hydrogen angles: 144
          Unresolved non-hydrogen dihedrals: 96
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 56
    Chain: "R"
      Number of atoms: 2115
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2115
          Classifications: {'peptide': 297}
          Incomplete info: {'truncation_to_alanine': 84}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 341
          Unresolved non-hydrogen angles: 430
          Unresolved non-hydrogen dihedrals: 298
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 185
    Chain: "R"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 9
          Unusual residues: {'NIO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.13, per 1000 atoms: 0.63
  Number of scatterers: 8121
  At special positions: 0
  Unit cell: (123.47, 95.0719, 128.409, 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      47     16.00
     O    1487      8.00
     N    1412      7.00
     C    5175      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 159 " - pdb=" SG  CYS H 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " 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: 2.05
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 16 sheets defined
      38.1% alpha, 26.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 31
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.656A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 219
      removed outlier: 3.852A  pdb=" N   LYS A 211 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   ILE A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU A 217 " --> pdb=" O   HIS A 214 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ASP A 218 " --> pdb=" O   CYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 255
    Processing helix  chain 'A' and resid 271 through 280
    Processing helix  chain 'A' and resid 283 through 287
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 4.296A  pdb=" N   ALA A 302 " --> pdb=" O   GLU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.628A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 35 through 37
      No H-bonds generated for 'chain 'B' and resid 35 through 37'
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.709A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 4.144A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 3.966A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 53 through 56
      removed outlier: 3.772A  pdb=" N   GLY H  56 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 53 through 56'
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.974A  pdb=" N   THR H  91 " --> pdb=" O   SER H  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 220 through 224
    Processing helix  chain 'R' and resid 24 through 55
      removed outlier: 4.178A  pdb=" N   LYS R  28 " --> pdb=" O   ASP R  24 " (cutoff:3.500A)
      Proline residue:  R  31  - end of helix
      removed outlier: 4.096A  pdb=" N   LEU R  47 " --> pdb=" O   LEU R  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 89
      removed outlier: 3.608A  pdb=" N   LEU R  80 " --> pdb=" O   LEU R  76 " (cutoff:3.500A)
      Proline residue:  R  81  - end of helix
    Processing helix  chain 'R' and resid 96 through 130
    Processing helix  chain 'R' and resid 134 through 139
      removed outlier: 3.581A  pdb=" N   ILE R 139 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 158
    Processing helix  chain 'R' and resid 159 through 164
    Processing helix  chain 'R' and resid 187 through 218
      removed outlier: 3.996A  pdb=" N   ALA R 191 " --> pdb=" O   GLN R 187 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 223 through 262
      removed outlier: 3.678A  pdb=" N   ALA R 237 " --> pdb=" O   ILE R 233 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
      removed outlier: 3.529A  pdb=" N   VAL R 250 " --> pdb=" O   PRO R 246 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 265 through 268
    Processing helix  chain 'R' and resid 269 through 289
      removed outlier: 3.907A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   THR R 283 " --> pdb=" O   THR R 279 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   TYR R 284 " --> pdb=" O   LEU R 280 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   SER R 287 " --> pdb=" O   THR R 283 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 290 through 295
      removed outlier: 3.926A  pdb=" N   TYR R 294 " --> pdb=" O   ASP R 290 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 304
    Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.353A  pdb=" N   VAL A  34 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 9.608A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   ASP A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.586A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.048A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.005A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.817A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.855A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.763A  pdb=" N   GLN B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.120A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 4.147A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.808A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.601A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.962A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.472A  pdb=" N   PHE H 110 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141
      removed outlier: 3.694A  pdb=" N   ALA H 211 " --> pdb=" O   SER H 208 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149
      removed outlier: 6.617A  pdb=" N   LEU H 174 " --> pdb=" O   TYR H 190 " (cutoff:3.500A)
      removed outlier: 4.808A  pdb=" N   TYR H 190 " --> pdb=" O   LEU H 174 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   TRP H 176 " --> pdb=" O   LEU H 188 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 149
      removed outlier: 3.962A  pdb=" N   THR H 238 " --> pdb=" O   GLN H 231 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 11 through 13
    Processing sheet with id=AB7, first strand: chain 'R' and resid 169 through 171

    463 hydrogen bonds defined for protein.
    1266 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: 2.51

  Time building geometry restraints manager: 2.36 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1320
        1.32 -     1.45: 2364
        1.45 -     1.58: 4551
        1.58 -     1.71: 0
        1.71 -     1.84: 62
  Bond restraints: 8297
  Sorted by residual:
  bond pdb=" C   GLY B 330 "
       pdb=" O   GLY B 330 "
    ideal  model  delta    sigma   weight residual
    1.235  1.187  0.048 1.35e-02 5.49e+03 1.27e+01
  bond pdb=" CA  ILE R  98 "
       pdb=" CB  ILE R  98 "
    ideal  model  delta    sigma   weight residual
    1.539  1.521  0.018 5.40e-03 3.43e+04 1.10e+01
  bond pdb=" CA  ALA A   7 "
       pdb=" CB  ALA A   7 "
    ideal  model  delta    sigma   weight residual
    1.530  1.475  0.056 1.69e-02 3.50e+03 1.08e+01
  bond pdb=" C   SER B 331 "
       pdb=" O   SER B 331 "
    ideal  model  delta    sigma   weight residual
    1.235  1.199  0.036 1.14e-02 7.69e+03 9.96e+00
  bond pdb=" C6  NIO R 401 "
       pdb=" O2  NIO R 401 "
    ideal  model  delta    sigma   weight residual
    1.245  1.307 -0.062 2.00e-02 2.50e+03 9.56e+00
  ... (remaining 8292 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.13: 10883
        2.13 -     4.26: 383
        4.26 -     6.40: 42
        6.40 -     8.53: 8
        8.53 -    10.66: 2
  Bond angle restraints: 11318
  Sorted by residual:
  angle pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" C   GLU A   8 "
      ideal   model   delta    sigma   weight residual
     112.97  104.97    8.00 1.06e+00 8.90e-01 5.69e+01
  angle pdb=" C   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" CB  GLU A   8 "
      ideal   model   delta    sigma   weight residual
     111.17  100.51   10.66 1.53e+00 4.27e-01 4.85e+01
  angle pdb=" N   GLU A   9 "
        pdb=" CA  GLU A   9 "
        pdb=" C   GLU A   9 "
      ideal   model   delta    sigma   weight residual
     112.88  103.91    8.97 1.29e+00 6.01e-01 4.84e+01
  angle pdb=" N   ARG A  10 "
        pdb=" CA  ARG A  10 "
        pdb=" C   ARG A  10 "
      ideal   model   delta    sigma   weight residual
     113.12  106.55    6.57 1.25e+00 6.40e-01 2.76e+01
  angle pdb=" N   CYS R 183 "
        pdb=" CA  CYS R 183 "
        pdb=" C   CYS R 183 "
      ideal   model   delta    sigma   weight residual
     107.73  114.19   -6.46 1.61e+00 3.86e-01 1.61e+01
  ... (remaining 11313 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 4466
       17.19 -    34.38: 290
       34.38 -    51.57: 54
       51.57 -    68.76: 5
       68.76 -    85.95: 9
  Dihedral angle restraints: 4824
    sinusoidal: 1558
      harmonic: 3266
  Sorted by residual:
  dihedral pdb=" C   GLU A   8 "
           pdb=" N   GLU A   8 "
           pdb=" CA  GLU A   8 "
           pdb=" CB  GLU A   8 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.49  -13.11     0      2.50e+00 1.60e-01 2.75e+01
  dihedral pdb=" CA  CYS R  79 "
           pdb=" C   CYS R  79 "
           pdb=" N   LEU R  80 "
           pdb=" CA  LEU R  80 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.80  -23.20     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" CA  TRP R  91 "
           pdb=" C   TRP R  91 "
           pdb=" N   ASP R  92 "
           pdb=" CA  ASP R  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.28   22.72     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 4821 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1089
       0.066 -    0.132: 208
       0.132 -    0.198: 21
       0.198 -    0.264: 2
       0.264 -    0.330: 1
  Chirality restraints: 1321
  Sorted by residual:
  chirality pdb=" CA  GLU A   8 "
            pdb=" N   GLU A   8 "
            pdb=" C   GLU A   8 "
            pdb=" CB  GLU A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.84   -0.33 2.00e-01 2.50e+01 2.72e+00
  chirality pdb=" CB  THR R 279 "
            pdb=" CA  THR R 279 "
            pdb=" OG1 THR R 279 "
            pdb=" CG2 THR R 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  ILE A 344 "
            pdb=" CA  ILE A 344 "
            pdb=" CG1 ILE A 344 "
            pdb=" CG2 ILE A 344 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 1318 not shown)

  Planarity restraints: 1455
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A   7 "   -0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   ALA A   7 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ALA A   7 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A   8 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 282 "   -0.054 5.00e-02 4.00e+02   8.00e-02 1.02e+01
        pdb=" N   PRO A 283 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  40 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.64e+00
        pdb=" C   GLY A  40 "    0.041 2.00e-02 2.50e+03
        pdb=" O   GLY A  40 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ALA A  41 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1452 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 138
        2.68 -     3.23: 8142
        3.23 -     3.79: 12014
        3.79 -     4.34: 16283
        4.34 -     4.90: 28057
  Nonbonded interactions: 64634
  Sorted by model distance:
  nonbonded pdb=" O   ASN R 175 "
            pdb=" OD1 ASN R 175 "
     model   vdw
     2.123 3.040
  nonbonded pdb=" OG1 THR A 183 "
            pdb=" OD1 ASN B 119 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER B  67 "
            pdb=" OG  SER B  67 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OD1 ASP R  23 "
            pdb=" N   ASP R  24 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" O   PHE R 282 "
            pdb=" N   MET R 285 "
     model   vdw
     2.324 3.120
  ... (remaining 64629 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:             1.290
  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:          0.280
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.000
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7550
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      :  0.005   0.077   8297  Z= 0.361
  Angle     :  0.904  10.659  11318  Z= 0.531
  Chirality :  0.052   0.330   1321
  Planarity :  0.007   0.080   1455
  Dihedral  : 12.938  85.946   2697
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  :  7.99 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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: -0.48 (0.24), residues: 1112
  helix: -0.14 (0.25), residues: 361
  sheet: -0.07 (0.30), residues: 274
  loop : -0.44 (0.28), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP B  63 
 HIS   0.016   0.003   HIS R 189 
 PHE   0.034   0.003   PHE B 235 
 TYR   0.029   0.003   TYR R 294 
 ARG   0.007   0.001   ARG R 218 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A   53 MET cc_start: 0.8338 (mpp) cc_final: 0.7905 (mpp)
REVERT: A  303 TYR cc_start: 0.8632 (t80) cc_final: 0.8411 (t80)
REVERT: G   20 LYS cc_start: 0.7202 (mtpt) cc_final: 0.6304 (mmmt)
REVERT: R   90 ARG cc_start: 0.6276 (mmm-85) cc_final: 0.6065 (tmt-80)
REVERT: R  294 TYR cc_start: 0.7218 (OUTLIER) cc_final: 0.5188 (m-80)
  outliers start: 8
  outliers final: 4
  residues processed: 132
  average time/residue: 0.1916
  time to fit residues: 35.2170
Evaluate side-chains
  113 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 108
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   24 LYS
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain B residue   33 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.0770
   chunk 83 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7942

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

Flipped N/Q/H residues before XYZ refinement:
A 312 ASN
B  17 GLN
B 119 ASN
B 155 ASN
R 141 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.1543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8297  Z= 0.267
  Angle     :  0.633  11.247  11318  Z= 0.341
  Chirality :  0.045   0.174   1321
  Planarity :  0.004   0.044   1455
  Dihedral  :  5.479  53.623   1207
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  8.79 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.09 (0.24), residues: 1112
  helix:  0.91 (0.26), residues: 369
  sheet: -0.30 (0.29), residues: 282
  loop : -0.25 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B  82 
 HIS   0.006   0.001   HIS B  91 
 PHE   0.018   0.002   PHE B 180 
 TYR   0.019   0.002   TYR A 354 
 ARG   0.004   0.000   ARG R 216 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A   10 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.8175 (mtm-85)
REVERT: A  312 ASN cc_start: 0.8266 (p0) cc_final: 0.7948 (p0)
REVERT: B  170 ASP cc_start: 0.7832 (t70) cc_final: 0.7445 (t0)
REVERT: G   20 LYS cc_start: 0.7419 (mtpt) cc_final: 0.6254 (mmmt)
REVERT: G   51 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8248 (pp)
REVERT: R  210 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.7158 (mmm160)
REVERT: R  294 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.4778 (m-80)
  outliers start: 19
  outliers final: 9
  residues processed: 137
  average time/residue: 0.1904
  time to fit residues: 36.5026
Evaluate side-chains
  121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 109
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain G residue   51 LEU
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  234 MET
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 108 optimal weight:    1.9990
   chunk 89 optimal weight:    0.4980
   chunk 99 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 175 GLN
R 112 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.1973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8297  Z= 0.344
  Angle     :  0.632   8.324  11318  Z= 0.341
  Chirality :  0.045   0.163   1321
  Planarity :  0.004   0.049   1455
  Dihedral  :  5.091  54.729   1199
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.32 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.14 (0.25), residues: 1112
  helix:  1.27 (0.27), residues: 370
  sheet: -0.70 (0.28), residues: 289
  loop : -0.19 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B  82 
 HIS   0.006   0.001   HIS H  35 
 PHE   0.026   0.002   PHE R 117 
 TYR   0.018   0.002   TYR H 190 
 ARG   0.004   0.000   ARG R  90 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 116
  time to evaluate  : 0.813 
Fit side-chains
REVERT: A   10 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8339 (mtp180)
REVERT: A  303 TYR cc_start: 0.8771 (t80) cc_final: 0.8492 (t80)
REVERT: A  312 ASN cc_start: 0.8498 (OUTLIER) cc_final: 0.8049 (p0)
REVERT: B   96 ARG cc_start: 0.7158 (ttm170) cc_final: 0.6735 (ttm170)
REVERT: G   20 LYS cc_start: 0.7520 (mtpt) cc_final: 0.6243 (mmmt)
REVERT: R  210 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7119 (mmm160)
REVERT: R  251 ARG cc_start: 0.7534 (mmm160) cc_final: 0.7301 (tpt170)
REVERT: R  294 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.4905 (m-80)
  outliers start: 20
  outliers final: 8
  residues processed: 132
  average time/residue: 0.1961
  time to fit residues: 35.6758
Evaluate side-chains
  119 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 ARG
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 67 optimal weight:    0.7980
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 28 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN
B 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8297  Z= 0.218
  Angle     :  0.547   8.494  11318  Z= 0.293
  Chirality :  0.043   0.149   1321
  Planarity :  0.004   0.044   1455
  Dihedral  :  4.641  55.625   1199
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.45 %
    Favored  : 84.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.36 (0.25), residues: 1112
  helix:  1.67 (0.27), residues: 368
  sheet: -0.76 (0.28), residues: 289
  loop : -0.12 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B  82 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.017   0.001   PHE R 117 
 TYR   0.018   0.001   TYR H 190 
 ARG   0.004   0.000   ARG R  90 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8293 (p0) cc_final: 0.7784 (p0)
REVERT: B   96 ARG cc_start: 0.7133 (ttm170) cc_final: 0.6708 (ttm170)
REVERT: B  170 ASP cc_start: 0.7938 (t70) cc_final: 0.7620 (t0)
REVERT: B  198 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7777 (pp)
  outliers start: 18
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1880
  time to fit residues: 33.6508
Evaluate side-chains
  121 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 79 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 0 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8297  Z= 0.260
  Angle     :  0.557   8.769  11318  Z= 0.298
  Chirality :  0.043   0.149   1321
  Planarity :  0.004   0.045   1455
  Dihedral  :  4.590  57.172   1199
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 13.72 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.25), residues: 1112
  helix:  1.78 (0.27), residues: 368
  sheet: -0.88 (0.28), residues: 295
  loop : -0.08 (0.29), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.027   0.002   PHE R 117 
 TYR   0.017   0.001   TYR H 190 
 ARG   0.005   0.000   ARG R  90 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.925 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7903 (p0)
REVERT: B   96 ARG cc_start: 0.7211 (ttm170) cc_final: 0.6778 (ttm170)
REVERT: B  198 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7821 (pp)
REVERT: G   20 LYS cc_start: 0.7626 (mtpt) cc_final: 0.6555 (mmmt)
  outliers start: 29
  outliers final: 21
  residues processed: 135
  average time/residue: 0.1705
  time to fit residues: 33.4022
Evaluate side-chains
  131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 88 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 102 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B 155 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8297  Z= 0.296
  Angle     :  0.567   9.087  11318  Z= 0.305
  Chirality :  0.043   0.153   1321
  Planarity :  0.004   0.045   1455
  Dihedral  :  4.604  59.350   1199
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 13.85 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.28 (0.25), residues: 1112
  helix:  1.74 (0.27), residues: 370
  sheet: -1.01 (0.29), residues: 295
  loop : -0.14 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  82 
 HIS   0.005   0.001   HIS H  35 
 PHE   0.024   0.002   PHE R 117 
 TYR   0.017   0.002   TYR H 190 
 ARG   0.004   0.000   ARG R 216 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.930 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8499 (OUTLIER) cc_final: 0.7908 (p0)
REVERT: B  198 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7856 (pp)
REVERT: B  234 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8444 (m-80)
  outliers start: 32
  outliers final: 26
  residues processed: 142
  average time/residue: 0.1706
  time to fit residues: 34.9586
Evaluate side-chains
  137 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0970
   chunk 65 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.2757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8297  Z= 0.223
  Angle     :  0.539   9.606  11318  Z= 0.286
  Chirality :  0.042   0.149   1321
  Planarity :  0.004   0.042   1455
  Dihedral  :  4.410  57.910   1199
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 15.58 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.42 (0.26), residues: 1112
  helix:  1.87 (0.27), residues: 373
  sheet: -1.02 (0.29), residues: 283
  loop : -0.05 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  82 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.022   0.001   PHE R 117 
 TYR   0.017   0.001   TYR H 190 
 ARG   0.004   0.000   ARG R 216 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.854 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8447 (OUTLIER) cc_final: 0.7848 (p0)
REVERT: B   96 ARG cc_start: 0.7208 (ttm170) cc_final: 0.6775 (ttm170)
REVERT: B  198 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7812 (pp)
REVERT: B  234 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8537 (m-80)
  outliers start: 24
  outliers final: 20
  residues processed: 131
  average time/residue: 0.1716
  time to fit residues: 32.6417
Evaluate side-chains
  128 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 20 optimal weight:    5.9990
   chunk 67 optimal weight:    0.9980
   chunk 72 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 9 optimal weight:    0.7980
   chunk 83 optimal weight:    0.6980
   chunk 96 optimal weight:    8.9990
   chunk 101 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8297  Z= 0.236
  Angle     :  0.541   9.815  11318  Z= 0.288
  Chirality :  0.042   0.150   1321
  Planarity :  0.004   0.043   1455
  Dihedral  :  4.336  54.284   1199
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 14.25 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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 (0.26), residues: 1112
  helix:  1.82 (0.27), residues: 373
  sheet: -1.06 (0.29), residues: 283
  loop : -0.05 (0.29), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  82 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.022   0.001   PHE R 117 
 TYR   0.017   0.001   TYR H 190 
 ARG   0.004   0.000   ARG R 216 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.7801 (p0)
REVERT: B   96 ARG cc_start: 0.7201 (ttm170) cc_final: 0.6773 (ttm170)
REVERT: B  198 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7841 (pp)
REVERT: B  234 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.8518 (m-80)
REVERT: G   20 LYS cc_start: 0.7641 (mtpt) cc_final: 0.6548 (mmmt)
  outliers start: 35
  outliers final: 24
  residues processed: 143
  average time/residue: 0.1657
  time to fit residues: 34.2733
Evaluate side-chains
  132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.873 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  184 THR
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain H residue  210 THR
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 43 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 89 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0980
   chunk 64 optimal weight:    0.0170
   chunk 104 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8297  Z= 0.180
  Angle     :  0.518   9.964  11318  Z= 0.275
  Chirality :  0.041   0.162   1321
  Planarity :  0.004   0.042   1455
  Dihedral  :  4.158  51.325   1199
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 15.85 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.47 (0.26), residues: 1112
  helix:  1.94 (0.27), residues: 374
  sheet: -0.94 (0.30), residues: 277
  loop : -0.10 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.019   0.001   PHE R 117 
 TYR   0.017   0.001   TYR H 190 
 ARG   0.004   0.000   ARG R 216 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.872 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7573 (p0)
REVERT: B   96 ARG cc_start: 0.7255 (ttm170) cc_final: 0.6879 (ttm170)
REVERT: B  170 ASP cc_start: 0.7878 (t70) cc_final: 0.7601 (t0)
REVERT: B  198 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7839 (pp)
REVERT: B  234 PHE cc_start: 0.9034 (OUTLIER) cc_final: 0.8489 (m-80)
REVERT: G   20 LYS cc_start: 0.7655 (mtpt) cc_final: 0.6600 (mmmt)
REVERT: H  178 LEU cc_start: 0.8790 (tt) cc_final: 0.8507 (tp)
  outliers start: 25
  outliers final: 20
  residues processed: 134
  average time/residue: 0.1679
  time to fit residues: 32.6361
Evaluate side-chains
  132 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain H residue  210 THR
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain R residue   76 LEU
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  143 THR
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 109 optimal weight:    0.3980
   chunk 100 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.3059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8297  Z= 0.251
  Angle     :  0.543  10.193  11318  Z= 0.289
  Chirality :  0.042   0.157   1321
  Planarity :  0.004   0.046   1455
  Dihedral  :  4.256  48.140   1199
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.25 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    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:  0.41 (0.25), residues: 1112
  helix:  1.86 (0.27), residues: 374
  sheet: -0.96 (0.30), residues: 273
  loop : -0.14 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 214 
 PHE   0.016   0.002   PHE B 235 
 TYR   0.016   0.001   TYR H 190 
 ARG   0.004   0.000   ARG R 216 

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

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

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2224 Ramachandran restraints generated.
    1112 Oldfield, 0 Emsley, 1112 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 0.915 
Fit side-chains
REVERT: A  312 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7721 (p0)
REVERT: B  198 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7854 (pp)
REVERT: B  234 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8455 (m-80)
REVERT: G   20 LYS cc_start: 0.7670 (mtpt) cc_final: 0.6572 (mmmt)
REVERT: R   93 TRP cc_start: 0.6087 (t-100) cc_final: 0.5694 (t-100)
  outliers start: 25
  outliers final: 20
  residues processed: 136
  average time/residue: 0.1665
  time to fit residues: 32.7546
Evaluate side-chains
  131 residues out of total 973 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ASN
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue  312 ASN
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  191 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain H residue   22 CYS
Chi-restraints excluded: chain H residue   51 ILE
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  141 THR
Chi-restraints excluded: chain H residue  162 SER
Chi-restraints excluded: chain H residue  197 SER
Chi-restraints excluded: chain H residue  210 THR
Chi-restraints excluded: chain H residue  226 VAL
Chi-restraints excluded: chain R residue  104 LEU
Chi-restraints excluded: chain R residue  204 ILE
Chi-restraints excluded: chain R residue  292 VAL
Chi-restraints excluded: chain R residue  293 VAL
Chi-restraints excluded: chain R residue  294 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    0.4980
   chunk 76 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0270
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** A 256 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 = 0.4162 r_free = 0.4162 target = 0.189163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.146647 restraints weight = 9253.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.98
r_work: 0.3386 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.3163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8297  Z= 0.195
  Angle     :  0.517  10.119  11318  Z= 0.275
  Chirality :  0.042   0.159   1321
  Planarity :  0.004   0.043   1455
  Dihedral  :  4.103  44.788   1199
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.64 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.06 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1112
  helix:  1.94 (0.27), residues: 374
  sheet: -0.92 (0.30), residues: 273
  loop : -0.06 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.015   0.001   PHE R  38 
 TYR   0.017   0.001   TYR H 190 
 ARG   0.004   0.000   ARG R 216 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1743.72 seconds
wall clock time: 32 minutes 27.85 seconds (1947.85 seconds total)