Starting phenix.real_space_refine
on Sun May 11 13:03:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8h4i_34478/05_2025/8h4i_34478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8h4i_34478/05_2025/8h4i_34478.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8h4i_34478/05_2025/8h4i_34478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8h4i_34478/05_2025/8h4i_34478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8h4i_34478/05_2025/8h4i_34478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8h4i_34478/05_2025/8h4i_34478.cif"
  }
  resolution = 3.06
  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=   0.038 sd=   0.137
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      51      5.16       5
     C    5087      2.51       5
     N    1362      2.21       5
     O    1465      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7965
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1874
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1874
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 6, 'TRANS': 224}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 36
          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: "B"
      Number of atoms: 2547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2547
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 44
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 5, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
    Chain: "C"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 409
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "D"
      Number of atoms: 957
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 957
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "R"
      Number of atoms: 2154
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2154
          Classifications: {'peptide': 283}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 13, 'TRANS': 269}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 74
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 10, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 65
    Chain: "R"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 24
          Unusual residues: {'HXA': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.81, per 1000 atoms: 0.60
  Number of scatterers: 7965
  At special positions: 0
  Unit cell: (80.3, 102.3, 135.3, 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      51     16.00
     O    1465      8.00
     N    1362      7.00
     C    5087      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 111 " - pdb=" SG  CYS R 194 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.08
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1952

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 11 sheets defined
      40.9% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.880A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   ALA A  39 " --> pdb=" O   GLN A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 61
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.945A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 278
      removed outlier: 3.848A  pdb=" N   ALA A 269 " --> pdb=" O   ARG A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.554A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLY A 304 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
      removed outlier: 3.506A  pdb=" N   ASP A 310 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.671A  pdb=" N   TYR A 318 " --> pdb=" O   PHE A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.905A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 390 through 392
      No H-bonds generated for 'chain 'A' and resid 390 through 392'
    Processing helix  chain 'B' and resid 4 through 24
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 9 through 23
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.631A  pdb=" N   HIS C  44 " --> pdb=" O   TYR C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.589A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 62 through 65
      removed outlier: 3.647A  pdb=" N   LYS D  65 " --> pdb=" O   GLY D  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 62 through 65'
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 4.085A  pdb=" N   THR D  91 " --> pdb=" O   PRO D  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 35 through 67
      removed outlier: 4.410A  pdb=" N   ALA R  41 " --> pdb=" O   LEU R  37 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 89
      removed outlier: 4.166A  pdb=" N   VAL R  78 " --> pdb=" O   THR R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 91 through 99
    Processing helix  chain 'R' and resid 107 through 146
      removed outlier: 5.137A  pdb=" N   PHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   TYR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 151 through 170
      removed outlier: 3.779A  pdb=" N   ARG R 155 " --> pdb=" O   GLY R 151 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ALA R 170 " --> pdb=" O   SER R 166 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 176
    Processing helix  chain 'R' and resid 200 through 216
    Processing helix  chain 'R' and resid 216 through 238
      removed outlier: 3.700A  pdb=" N   GLY R 220 " --> pdb=" O   PHE R 216 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 260 through 272
      removed outlier: 3.833A  pdb=" N   LEU R 268 " --> pdb=" O   ARG R 264 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET R 270 " --> pdb=" O   LEU R 266 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER R 272 " --> pdb=" O   LEU R 268 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 272 through 277
    Processing helix  chain 'R' and resid 277 through 291
      removed outlier: 4.171A  pdb=" N   ILE R 281 " --> pdb=" O   TRP R 277 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 299 through 311
      removed outlier: 3.900A  pdb=" N   PHE R 303 " --> pdb=" O   TRP R 299 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 312 through 315
    Processing helix  chain 'R' and resid 316 through 321
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 5.050A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ALA A 243 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.873A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.640A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.167A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.468A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.523A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.002A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.177A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.118A  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 151
      removed outlier: 6.872A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.416A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.932A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.572A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.624A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.615A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   MET B 217 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.908A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.798A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.594A  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: 6.710A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.038A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASN B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 12
      removed outlier: 7.115A  pdb=" N   MET D  34 " --> pdb=" O   ASP D  50 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   ASP D  50 " --> pdb=" O   MET D  34 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   TRP D  36 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 177 through 183

    396 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: 2.14

  Time building geometry restraints manager: 2.31 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: 2113
        1.33 -     1.45: 1557
        1.45 -     1.57: 4388
        1.57 -     1.69: 0
        1.69 -     1.81: 71
  Bond restraints: 8129
  Sorted by residual:
  bond pdb=" C   ASP B  66 "
       pdb=" N   SER B  67 "
    ideal  model  delta    sigma   weight residual
    1.332  1.289  0.044 1.40e-02 5.10e+03 9.72e+00
  bond pdb=" C10 HXA R 401 "
       pdb=" C9  HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.448  0.054 2.00e-02 2.50e+03 7.32e+00
  bond pdb=" C18 HXA R 401 "
       pdb=" C19 HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.503  1.450  0.053 2.00e-02 2.50e+03 7.14e+00
  bond pdb=" C15 HXA R 401 "
       pdb=" C16 HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.449  0.053 2.00e-02 2.50e+03 7.05e+00
  bond pdb=" C11 HXA R 401 "
       pdb=" C12 HXA R 401 "
    ideal  model  delta    sigma   weight residual
    1.502  1.452  0.050 2.00e-02 2.50e+03 6.16e+00
  ... (remaining 8124 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.18: 10836
        3.18 -     6.35: 178
        6.35 -     9.53: 31
        9.53 -    12.70: 3
       12.70 -    15.88: 1
  Bond angle restraints: 11049
  Sorted by residual:
  angle pdb=" CA  LEU D  79 "
        pdb=" CB  LEU D  79 "
        pdb=" CG  LEU D  79 "
      ideal   model   delta    sigma   weight residual
     116.30  132.18  -15.88 3.50e+00 8.16e-02 2.06e+01
  angle pdb=" N   ASP B 205 "
        pdb=" CA  ASP B 205 "
        pdb=" C   ASP B 205 "
      ideal   model   delta    sigma   weight residual
     110.80  101.25    9.55 2.13e+00 2.20e-01 2.01e+01
  angle pdb=" C   ASP B  66 "
        pdb=" N   SER B  67 "
        pdb=" CA  SER B  67 "
      ideal   model   delta    sigma   weight residual
     121.54  114.34    7.20 1.91e+00 2.74e-01 1.42e+01
  angle pdb=" CA  TRP B  82 "
        pdb=" CB  TRP B  82 "
        pdb=" CG  TRP B  82 "
      ideal   model   delta    sigma   weight residual
     113.60  120.26   -6.66 1.90e+00 2.77e-01 1.23e+01
  angle pdb=" CA  SER B  67 "
        pdb=" C   SER B  67 "
        pdb=" N   ARG B  68 "
      ideal   model   delta    sigma   weight residual
     116.84  122.78   -5.94 1.71e+00 3.42e-01 1.21e+01
  ... (remaining 11044 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.69: 4401
       17.69 -    35.38: 323
       35.38 -    53.07: 59
       53.07 -    70.76: 16
       70.76 -    88.45: 7
  Dihedral angle restraints: 4806
    sinusoidal: 1798
      harmonic: 3008
  Sorted by residual:
  dihedral pdb=" CA  THR B  65 "
           pdb=" C   THR B  65 "
           pdb=" N   ASP B  66 "
           pdb=" CA  ASP B  66 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.96   27.04     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CA  LYS B  78 "
           pdb=" C   LYS B  78 "
           pdb=" N   LEU B  79 "
           pdb=" CA  LEU B  79 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.88   25.12     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  VAL D  64 "
           pdb=" C   VAL D  64 "
           pdb=" N   LYS D  65 "
           pdb=" CA  LYS D  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.86  -24.14     0      5.00e+00 4.00e-02 2.33e+01
  ... (remaining 4803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 679
       0.041 -    0.082: 392
       0.082 -    0.123: 164
       0.123 -    0.164: 38
       0.164 -    0.205: 11
  Chirality restraints: 1284
  Sorted by residual:
  chirality pdb=" CA  TRP B  82 "
            pdb=" N   TRP B  82 "
            pdb=" C   TRP B  82 "
            pdb=" CB  TRP B  82 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  VAL B 100 "
            pdb=" CA  VAL B 100 "
            pdb=" CG1 VAL B 100 "
            pdb=" CG2 VAL B 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.43   -0.20 2.00e-01 2.50e+01 9.73e-01
  chirality pdb=" CB  ILE R  92 "
            pdb=" CA  ILE R  92 "
            pdb=" CG1 ILE R  92 "
            pdb=" CG2 ILE R  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.10e-01
  ... (remaining 1281 not shown)

  Planarity restraints: 1407
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "   -0.028 2.00e-02 2.50e+03   2.02e-02 8.13e+00
        pdb=" CG  TYR B  59 "    0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "   -0.011 2.00e-02 2.50e+03   1.89e-02 7.11e+00
        pdb=" CG  TYR B 105 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN C  59 "   -0.043 5.00e-02 4.00e+02   6.45e-02 6.65e+00
        pdb=" N   PRO C  60 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO C  60 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C  60 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1404 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 205
        2.70 -     3.25: 7230
        3.25 -     3.80: 11407
        3.80 -     4.35: 14380
        4.35 -     4.90: 26074
  Nonbonded interactions: 59296
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" OE2 GLU R  43 "
            pdb=" NH2 ARG R  99 "
     model   vdw
     2.159 3.120
  nonbonded pdb=" OG  SER B 281 "
            pdb=" OD2 ASP C  48 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OE2 GLU A 209 "
            pdb=" ND1 HIS A 220 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.260 3.040
  ... (remaining 59291 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:             0.940
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.800
  Find NCS groups from input model:        0.060
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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      :  0.016   0.885   8132  Z= 1.096
  Angle     :  1.046  15.878  11053  Z= 0.551
  Chirality :  0.059   0.205   1284
  Planarity :  0.006   0.064   1407
  Dihedral  : 13.700  88.446   2848
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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: 1019
  helix:  1.17 (0.26), residues: 366
  sheet:  0.40 (0.33), residues: 226
  loop : -1.87 (0.26), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP A 234 
 HIS   0.015   0.004   HIS A 357 
 PHE   0.029   0.004   PHE D 108 
 TYR   0.045   0.004   TYR B  59 
 ARG   0.007   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15776 (  396)
  hydrogen bonds       : angle       5.83898 ( 1128)
  SS BOND              : bond        0.00448 (    2)
  SS BOND              : angle       3.05460 (    4)
  covalent geometry    : bond        0.01206 ( 8129)
  covalent geometry    : angle       1.04467 (11049)
  Misc. bond           : bond        0.88540 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.940 
Fit side-chains
REVERT: B  271 CYS cc_start: 0.7842 (m) cc_final: 0.7603 (m)
REVERT: D   17 SER cc_start: 0.8714 (p) cc_final: 0.8441 (t)
REVERT: R  197 ILE cc_start: 0.8872 (mt) cc_final: 0.8494 (tp)
REVERT: R  267 PHE cc_start: 0.7472 (t80) cc_final: 0.7264 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 93
  average time/residue: 0.2946
  time to fit residues: 34.6689
Evaluate side-chains
  84 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
R  80 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.116267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.091406 restraints weight = 12292.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.24
r_work: 0.3047 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8132  Z= 0.138
  Angle     :  0.584   8.414  11053  Z= 0.316
  Chirality :  0.044   0.164   1284
  Planarity :  0.004   0.046   1407
  Dihedral  :  5.534  58.335   1124
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.36 %
    Allowed  :  5.24 %
    Favored  : 94.40 %
  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:  0.42 (0.26), residues: 1019
  helix:  2.11 (0.27), residues: 368
  sheet:  0.72 (0.33), residues: 225
  loop : -1.72 (0.27), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.030   0.002   TYR B  59 
 ARG   0.005   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06278 (  396)
  hydrogen bonds       : angle       4.35648 ( 1128)
  SS BOND              : bond        0.00349 (    2)
  SS BOND              : angle       1.24657 (    4)
  covalent geometry    : bond        0.00286 ( 8129)
  covalent geometry    : angle       0.58392 (11049)
  Misc. bond           : bond        0.00087 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.836 
Fit side-chains
REVERT: A  272 ASP cc_start: 0.8448 (m-30) cc_final: 0.8182 (m-30)
REVERT: A  314 GLU cc_start: 0.7463 (pm20) cc_final: 0.7249 (pm20)
REVERT: B  271 CYS cc_start: 0.8375 (m) cc_final: 0.8148 (m)
REVERT: R  118 MET cc_start: 0.7660 (mtp) cc_final: 0.7434 (mtm)
REVERT: R  197 ILE cc_start: 0.8929 (mt) cc_final: 0.8530 (tp)
  outliers start: 3
  outliers final: 0
  residues processed: 99
  average time/residue: 0.2808
  time to fit residues: 35.0333
Evaluate side-chains
  87 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 84 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   overall best weight:    1.7990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.113205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.087976 restraints weight = 12589.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3117 rms_B_bonded: 2.27
r_work: 0.2983 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8132  Z= 0.219
  Angle     :  0.674   8.576  11053  Z= 0.355
  Chirality :  0.046   0.152   1284
  Planarity :  0.005   0.045   1407
  Dihedral  :  5.620  57.718   1124
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.22 %
    Favored  : 90.46 %
  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:  0.45 (0.26), residues: 1019
  helix:  2.14 (0.27), residues: 364
  sheet:  0.79 (0.34), residues: 230
  loop : -1.73 (0.27), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B  82 
 HIS   0.008   0.002   HIS A 357 
 PHE   0.018   0.002   PHE A 212 
 TYR   0.038   0.002   TYR B  59 
 ARG   0.005   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07353 (  396)
  hydrogen bonds       : angle       4.39844 ( 1128)
  SS BOND              : bond        0.00412 (    2)
  SS BOND              : angle       1.30875 (    4)
  covalent geometry    : bond        0.00535 ( 8129)
  covalent geometry    : angle       0.67393 (11049)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.840 
Fit side-chains
REVERT: B  271 CYS cc_start: 0.8553 (m) cc_final: 0.8291 (m)
REVERT: R  118 MET cc_start: 0.7810 (mtp) cc_final: 0.7604 (mtm)
REVERT: R  197 ILE cc_start: 0.8910 (mt) cc_final: 0.8467 (tp)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.2952
  time to fit residues: 35.8892
Evaluate side-chains
  89 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   67 ARG
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue   95 VAL
Chi-restraints excluded: chain R residue  213 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 57 optimal weight:   10.0000
   chunk 13 optimal weight:    0.9990
   chunk 100 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 93 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.116102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.090794 restraints weight = 12334.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 2.26
r_work: 0.3043 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8132  Z= 0.132
  Angle     :  0.544   7.898  11053  Z= 0.291
  Chirality :  0.043   0.154   1284
  Planarity :  0.004   0.042   1407
  Dihedral  :  5.317  59.723   1124
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  9.77 %
    Favored  : 89.39 %
  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:  0.67 (0.26), residues: 1019
  helix:  2.37 (0.27), residues: 370
  sheet:  0.84 (0.34), residues: 235
  loop : -1.70 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.015   0.001   PHE A 212 
 TYR   0.030   0.002   TYR B  59 
 ARG   0.005   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05652 (  396)
  hydrogen bonds       : angle       4.10483 ( 1128)
  SS BOND              : bond        0.00404 (    2)
  SS BOND              : angle       0.86193 (    4)
  covalent geometry    : bond        0.00290 ( 8129)
  covalent geometry    : angle       0.54419 (11049)
  Misc. bond           : bond        0.00031 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 0.825 
Fit side-chains
REVERT: A  272 ASP cc_start: 0.8445 (m-30) cc_final: 0.8186 (m-30)
REVERT: B  271 CYS cc_start: 0.8388 (m) cc_final: 0.8142 (m)
REVERT: C   38 MET cc_start: 0.8001 (mtm) cc_final: 0.7707 (mmm)
REVERT: R  276 MET cc_start: 0.8195 (mmm) cc_final: 0.7971 (mmm)
  outliers start: 7
  outliers final: 4
  residues processed: 96
  average time/residue: 0.2764
  time to fit residues: 33.8087
Evaluate side-chains
  92 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 88
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain R residue   92 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 21 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
D  77 ASN
R 182 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.114062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.088670 restraints weight = 12352.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.27
r_work: 0.3000 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.1458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8132  Z= 0.190
  Angle     :  0.622   7.914  11053  Z= 0.328
  Chirality :  0.045   0.148   1284
  Planarity :  0.004   0.043   1407
  Dihedral  :  5.449  59.945   1124
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 10.97 %
    Favored  : 87.37 %
  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:  0.62 (0.26), residues: 1019
  helix:  2.26 (0.27), residues: 369
  sheet:  0.83 (0.34), residues: 232
  loop : -1.64 (0.28), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.006   0.002   HIS A 357 
 PHE   0.019   0.002   PHE A 212 
 TYR   0.036   0.002   TYR B  59 
 ARG   0.005   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06610 (  396)
  hydrogen bonds       : angle       4.22068 ( 1128)
  SS BOND              : bond        0.00369 (    2)
  SS BOND              : angle       1.04504 (    4)
  covalent geometry    : bond        0.00460 ( 8129)
  covalent geometry    : angle       0.62181 (11049)
  Misc. bond           : bond        0.00034 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.931 
Fit side-chains
REVERT: B  271 CYS cc_start: 0.8603 (m) cc_final: 0.8370 (m)
  outliers start: 14
  outliers final: 9
  residues processed: 99
  average time/residue: 0.2780
  time to fit residues: 35.0202
Evaluate side-chains
  91 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue   67 ARG
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  213 THR
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 23 optimal weight:   20.0000
   chunk 79 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
D  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.114893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.089522 restraints weight = 12219.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 2.27
r_work: 0.3019 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8186
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8132  Z= 0.155
  Angle     :  0.576   7.498  11053  Z= 0.306
  Chirality :  0.044   0.151   1284
  Planarity :  0.004   0.043   1407
  Dihedral  :  5.355  59.577   1124
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 11.68 %
    Favored  : 87.25 %
  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:  0.66 (0.26), residues: 1019
  helix:  2.34 (0.27), residues: 370
  sheet:  0.77 (0.33), residues: 238
  loop : -1.66 (0.28), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.017   0.002   PHE A 212 
 TYR   0.028   0.002   TYR B  59 
 ARG   0.005   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06047 (  396)
  hydrogen bonds       : angle       4.13432 ( 1128)
  SS BOND              : bond        0.00390 (    2)
  SS BOND              : angle       0.85584 (    4)
  covalent geometry    : bond        0.00361 ( 8129)
  covalent geometry    : angle       0.57546 (11049)
  Misc. bond           : bond        0.00022 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 81
  time to evaluate  : 0.815 
Fit side-chains
REVERT: B  271 CYS cc_start: 0.8542 (m) cc_final: 0.8268 (m)
REVERT: R   67 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8282 (ttp80)
  outliers start: 9
  outliers final: 4
  residues processed: 87
  average time/residue: 0.2746
  time to fit residues: 30.5218
Evaluate side-chains
  90 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain R residue   67 ARG
Chi-restraints excluded: chain R residue   92 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 20 optimal weight:    0.0040
   chunk 99 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 53 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 65 optimal weight:    0.1980
   overall best weight:    0.3792

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
D  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.119702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.094532 restraints weight = 12287.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 2.27
r_work: 0.3094 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8132  Z= 0.100
  Angle     :  0.485   7.450  11053  Z= 0.260
  Chirality :  0.041   0.196   1284
  Planarity :  0.004   0.041   1407
  Dihedral  :  4.917  58.353   1124
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.16 %
    Favored  : 86.41 %
  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 (0.27), residues: 1019
  helix:  2.68 (0.28), residues: 369
  sheet:  0.95 (0.33), residues: 237
  loop : -1.59 (0.28), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.012   0.001   PHE A 212 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04342 (  396)
  hydrogen bonds       : angle       3.83138 ( 1128)
  SS BOND              : bond        0.00407 (    2)
  SS BOND              : angle       0.71469 (    4)
  covalent geometry    : bond        0.00202 ( 8129)
  covalent geometry    : angle       0.48476 (11049)
  Misc. bond           : bond        0.00005 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.8438 (m-30) cc_final: 0.8150 (m-30)
REVERT: B  271 CYS cc_start: 0.8414 (m) cc_final: 0.8138 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 98
  average time/residue: 0.2525
  time to fit residues: 32.3442
Evaluate side-chains
  94 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain A residue  387 HIS
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue   92 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 91 optimal weight:    4.9990
   chunk 95 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 47 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 96 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0030
   chunk 15 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9980
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.118365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.093615 restraints weight = 12439.148|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 2.29
r_work: 0.3072 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2920 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8135
moved from start:          0.2133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8132  Z= 0.114
  Angle     :  0.530   9.362  11053  Z= 0.277
  Chirality :  0.042   0.188   1284
  Planarity :  0.004   0.042   1407
  Dihedral  :  4.897  59.765   1124
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 12.63 %
    Favored  : 86.41 %
  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:  1.08 (0.27), residues: 1019
  helix:  2.81 (0.28), residues: 365
  sheet:  1.00 (0.33), residues: 237
  loop : -1.48 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.019   0.001   TYR B  59 
 ARG   0.006   0.000   ARG R  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04725 (  396)
  hydrogen bonds       : angle       3.80025 ( 1128)
  SS BOND              : bond        0.00346 (    2)
  SS BOND              : angle       0.72527 (    4)
  covalent geometry    : bond        0.00243 ( 8129)
  covalent geometry    : angle       0.53035 (11049)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.8487 (m-30) cc_final: 0.8198 (m-30)
REVERT: B  271 CYS cc_start: 0.8504 (m) cc_final: 0.8240 (m)
REVERT: D   17 SER cc_start: 0.8533 (p) cc_final: 0.7983 (t)
  outliers start: 8
  outliers final: 6
  residues processed: 95
  average time/residue: 0.2613
  time to fit residues: 31.9211
Evaluate side-chains
  95 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 0.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue   92 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0670
   chunk 55 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.6520

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.118151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.093062 restraints weight = 12582.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 2.37
r_work: 0.3073 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2921 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8132  Z= 0.119
  Angle     :  0.537   9.591  11053  Z= 0.281
  Chirality :  0.042   0.188   1284
  Planarity :  0.004   0.042   1407
  Dihedral  :  4.923  59.173   1124
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.11 %
    Favored  : 85.70 %
  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:  1.10 (0.27), residues: 1019
  helix:  2.80 (0.28), residues: 365
  sheet:  0.97 (0.34), residues: 226
  loop : -1.35 (0.27), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.020   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04784 (  396)
  hydrogen bonds       : angle       3.82742 ( 1128)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       1.53081 (    4)
  covalent geometry    : bond        0.00258 ( 8129)
  covalent geometry    : angle       0.53611 (11049)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.8511 (m-30) cc_final: 0.8228 (m-30)
REVERT: B  271 CYS cc_start: 0.8498 (m) cc_final: 0.8243 (m)
REVERT: D   17 SER cc_start: 0.8524 (p) cc_final: 0.8004 (t)
  outliers start: 10
  outliers final: 7
  residues processed: 93
  average time/residue: 0.2517
  time to fit residues: 30.4192
Evaluate side-chains
  92 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue   29 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0870
   chunk 91 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.118445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.093078 restraints weight = 12281.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.26
r_work: 0.3079 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8132  Z= 0.115
  Angle     :  0.538   9.575  11053  Z= 0.280
  Chirality :  0.042   0.192   1284
  Planarity :  0.004   0.056   1407
  Dihedral  :  4.860  56.807   1124
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.23 %
    Favored  : 85.94 %
  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:  1.13 (0.27), residues: 1019
  helix:  2.83 (0.28), residues: 365
  sheet:  0.98 (0.33), residues: 229
  loop : -1.35 (0.28), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.004   0.001   HIS R 112 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.015   0.001   TYR D  80 
 ARG   0.006   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04708 (  396)
  hydrogen bonds       : angle       3.78289 ( 1128)
  SS BOND              : bond        0.00398 (    2)
  SS BOND              : angle       1.51314 (    4)
  covalent geometry    : bond        0.00249 ( 8129)
  covalent geometry    : angle       0.53725 (11049)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2038 Ramachandran restraints generated.
    1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 83
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
REVERT: A  272 ASP cc_start: 0.8483 (m-30) cc_final: 0.8195 (m-30)
REVERT: B  271 CYS cc_start: 0.8485 (m) cc_final: 0.8230 (m)
REVERT: D   17 SER cc_start: 0.8540 (p) cc_final: 0.8024 (t)
REVERT: R  178 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.7267 (mtp85)
  outliers start: 7
  outliers final: 6
  residues processed: 88
  average time/residue: 0.2434
  time to fit residues: 28.5441
Evaluate side-chains
  91 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 GLU
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  186 ASP
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain R residue   92 ILE
Chi-restraints excluded: chain R residue  298 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 71 optimal weight:    0.4980
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 10 optimal weight:    0.4980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.118622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.093262 restraints weight = 12432.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 2.25
r_work: 0.3085 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8132  Z= 0.113
  Angle     :  0.527   9.439  11053  Z= 0.275
  Chirality :  0.042   0.191   1284
  Planarity :  0.004   0.045   1407
  Dihedral  :  4.762  52.442   1124
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 2.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 13.83 %
    Favored  : 85.34 %
  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:  1.17 (0.27), residues: 1019
  helix:  2.86 (0.28), residues: 366
  sheet:  0.95 (0.33), residues: 229
  loop : -1.31 (0.28), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.003   0.001   HIS R 112 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.016   0.001   TYR B  59 
 ARG   0.006   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04591 (  396)
  hydrogen bonds       : angle       3.76006 ( 1128)
  SS BOND              : bond        0.00387 (    2)
  SS BOND              : angle       1.31193 (    4)
  covalent geometry    : bond        0.00242 ( 8129)
  covalent geometry    : angle       0.52679 (11049)
  Misc. bond           : bond        0.00005 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4540.44 seconds
wall clock time: 79 minutes 4.39 seconds (4744.39 seconds total)