Starting phenix.real_space_refine
on Sat Jul 26 13:06:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sbf_24978/07_2025/7sbf_24978.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sbf_24978/07_2025/7sbf_24978.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2025/7sbf_24978.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2025/7sbf_24978.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2025/7sbf_24978.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sbf_24978/07_2025/7sbf_24978.cif"
  }
  resolution = 2.9
  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=   1.000
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      65      5.16       5
     C    5452      2.51       5
     N    1450      2.21       5
     O    1558      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8525
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1683
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 68
          Unresolved non-hydrogen angles: 84
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 42
    Chain: "B"
      Number of atoms: 2537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2537
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 37
    Chain: "C"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 381
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 18
    Chain: "E"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1742
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "R"
      Number of atoms: 2157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2157
          Classifications: {'peptide': 281}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 270}
          Unresolved non-hydrogen bonds: 98
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 43
    Chain: "R"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'8QY': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.34, per 1000 atoms: 0.63
  Number of scatterers: 8525
  At special positions: 0
  Unit cell: (98.58, 116.6, 115.54, 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      65     16.00
     O    1558      8.00
     N    1450      7.00
     C    5452      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 140 " - pdb=" SG  CYS R 217 " distance=2.04

  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: 2.31
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2098

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 14 sheets defined
      37.9% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 32
      removed outlier: 3.932A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 53
      removed outlier: 3.636A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 4.371A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 273 through 281
      removed outlier: 3.714A  pdb=" N   LYS A 277 " --> pdb=" O   LEU A 273 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 278 " --> pdb=" O   PHE A 274 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 4.340A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
      removed outlier: 3.980A  pdb=" N   GLN A 333 " --> pdb=" O   THR A 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 25
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 4.066A  pdb=" N   GLY B 131 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   ASN B 132 " --> pdb=" O   ARG B 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 128 through 132'
    Processing helix  chain 'C' and resid 10 through 24
      removed outlier: 3.610A  pdb=" N   LYS C  14 " --> pdb=" O   ALA C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 3.951A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.976A  pdb=" N   THR E  91 " --> pdb=" O   SER E  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 66 through 97
      removed outlier: 4.232A  pdb=" N   THR R  72 " --> pdb=" O   ALA R  68 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 105 through 120
      removed outlier: 3.906A  pdb=" N   THR R 120 " --> pdb=" O   LEU R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 120 through 131
      removed outlier: 3.548A  pdb=" N   GLN R 124 " --> pdb=" O   THR R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 135 through 140
      removed outlier: 3.978A  pdb=" N   LEU R 139 " --> pdb=" O   PHE R 135 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   CYS R 140 " --> pdb=" O   GLY R 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 135 through 140'
    Processing helix  chain 'R' and resid 142 through 171
      removed outlier: 3.617A  pdb=" N   PHE R 152 " --> pdb=" O   TYR R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 179
      removed outlier: 3.666A  pdb=" N   ASP R 177 " --> pdb=" O   VAL R 173 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 180 through 206
      removed outlier: 3.714A  pdb=" N   ALA R 197 " --> pdb=" O   ILE R 193 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   ILE R 198 " --> pdb=" O   LEU R 194 " (cutoff:3.500A)
      Proline residue:  R 201  - end of helix
    Processing helix  chain 'R' and resid 224 through 241
      removed outlier: 4.748A  pdb=" N   ASN R 230 " --> pdb=" O   TRP R 226 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU R 231 " --> pdb=" O   TYR R 227 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 241 through 260
      removed outlier: 3.870A  pdb=" N   VAL R 250 " --> pdb=" O   LEU R 246 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 261 through 266
      removed outlier: 6.767A  pdb=" N   MET R 264 " --> pdb=" O   SER R 261 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   SER R 266 " --> pdb=" O   ARG R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 306
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 311 through 337
      removed outlier: 3.772A  pdb=" N   THR R 315 " --> pdb=" O   THR R 311 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL R 316 " --> pdb=" O   THR R 312 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER R 329 " --> pdb=" O   GLY R 325 " (cutoff:3.500A)
      Proline residue:  R 333  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.523A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.572A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.547A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.445A  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: 4.182A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.759A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.356A  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: 6.836A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   CYS B 166 " --> pdb=" O   THR B 179 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   THR B 179 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   LEU B 168 " --> pdb=" O   THR B 177 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 191 through 192
      removed outlier: 6.599A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.634A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.794A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 6.645A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.801A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.208A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.837A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 116 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.837A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 116 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.456A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.422A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 208 through 209
      removed outlier: 3.583A  pdb=" N   ASP R 216 " --> pdb=" O   LYS R 209 " (cutoff:3.500A)

    435 hydrogen bonds defined for protein.
    1221 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: 2.56

  Time building geometry restraints manager: 2.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2710
        1.34 -     1.46: 1866
        1.46 -     1.58: 4032
        1.58 -     1.69: 3
        1.69 -     1.81: 94
  Bond restraints: 8705
  Sorted by residual:
  bond pdb=" C02 8QY R 501 "
       pdb=" N03 8QY R 501 "
    ideal  model  delta    sigma   weight residual
    1.365  1.441 -0.076 2.00e-02 2.50e+03 1.44e+01
  bond pdb=" C02 8QY R 501 "
       pdb=" N12 8QY R 501 "
    ideal  model  delta    sigma   weight residual
    1.360  1.423 -0.063 2.00e-02 2.50e+03 9.98e+00
  bond pdb=" N   ILE R 142 "
       pdb=" CA  ILE R 142 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.82e+00
  bond pdb=" C04 8QY R 501 "
       pdb=" N03 8QY R 501 "
    ideal  model  delta    sigma   weight residual
    1.449  1.500 -0.051 2.00e-02 2.50e+03 6.38e+00
  bond pdb=" C13 8QY R 501 "
       pdb=" C14 8QY R 501 "
    ideal  model  delta    sigma   weight residual
    1.536  1.586 -0.050 2.00e-02 2.50e+03 6.30e+00
  ... (remaining 8700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 11615
        2.02 -     4.04: 171
        4.04 -     6.06: 31
        6.06 -     8.09: 6
        8.09 -    10.11: 3
  Bond angle restraints: 11826
  Sorted by residual:
  angle pdb=" N   LYS R 141 "
        pdb=" CA  LYS R 141 "
        pdb=" C   LYS R 141 "
      ideal   model   delta    sigma   weight residual
     113.17  103.06   10.11 1.26e+00 6.30e-01 6.43e+01
  angle pdb=" C   ILE B  18 "
        pdb=" N   ARG B  19 "
        pdb=" CA  ARG B  19 "
      ideal   model   delta    sigma   weight residual
     121.14  114.16    6.98 1.75e+00 3.27e-01 1.59e+01
  angle pdb=" N   ASP B 333 "
        pdb=" CA  ASP B 333 "
        pdb=" C   ASP B 333 "
      ideal   model   delta    sigma   weight residual
     113.16  108.30    4.86 1.24e+00 6.50e-01 1.54e+01
  angle pdb=" C   ARG B  19 "
        pdb=" N   ASP B  20 "
        pdb=" CA  ASP B  20 "
      ideal   model   delta    sigma   weight residual
     121.58  114.47    7.11 1.95e+00 2.63e-01 1.33e+01
  angle pdb=" CA  ILE R 142 "
        pdb=" C   ILE R 142 "
        pdb=" O   ILE R 142 "
      ideal   model   delta    sigma   weight residual
     120.78  116.33    4.45 1.25e+00 6.40e-01 1.27e+01
  ... (remaining 11821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4715
       17.74 -    35.48: 366
       35.48 -    53.23: 36
       53.23 -    70.97: 10
       70.97 -    88.71: 7
  Dihedral angle restraints: 5134
    sinusoidal: 1883
      harmonic: 3251
  Sorted by residual:
  dihedral pdb=" CB  CYS R 140 "
           pdb=" SG  CYS R 140 "
           pdb=" SG  CYS R 217 "
           pdb=" CB  CYS R 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.14   76.14     1      1.00e+01 1.00e-02 7.30e+01
  dihedral pdb=" CA  TYR E 101 "
           pdb=" C   TYR E 101 "
           pdb=" N   TYR E 102 "
           pdb=" CA  TYR E 102 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.90   19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  SER R 268 "
           pdb=" C   SER R 268 "
           pdb=" N   LYS R 269 "
           pdb=" CA  LYS R 269 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.95  -19.05     0      5.00e+00 4.00e-02 1.45e+01
  ... (remaining 5131 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1171
       0.065 -    0.131: 192
       0.131 -    0.196: 6
       0.196 -    0.261: 0
       0.261 -    0.327: 3
  Chirality restraints: 1372
  Sorted by residual:
  chirality pdb=" C14 8QY R 501 "
            pdb=" C13 8QY R 501 "
            pdb=" C15 8QY R 501 "
            pdb=" N23 8QY R 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.36    2.69   -0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CA  ASP B 247 "
            pdb=" N   ASP B 247 "
            pdb=" C   ASP B 247 "
            pdb=" CB  ASP B 247 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.78e+00
  chirality pdb=" CA  LYS R 141 "
            pdb=" N   LYS R 141 "
            pdb=" C   LYS R 141 "
            pdb=" CB  LYS R 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.78e+00
  ... (remaining 1369 not shown)

  Planarity restraints: 1485
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 308 "   -0.039 5.00e-02 4.00e+02   5.81e-02 5.39e+00
        pdb=" N   PRO R 309 "    0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO R 309 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R 309 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.032 5.00e-02 4.00e+02   4.82e-02 3.71e+00
        pdb=" N   PRO B 236 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R  83 "   -0.009 2.00e-02 2.50e+03   1.88e-02 3.54e+00
        pdb=" C   LEU R  83 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LEU R  83 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   PHE R  84 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 1482 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 724
        2.74 -     3.28: 8503
        3.28 -     3.82: 14213
        3.82 -     4.36: 17111
        4.36 -     4.90: 30122
  Nonbonded interactions: 70673
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" OG  SER E 149 "
            pdb=" O   LYS E 151 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" NE2 HIS B  54 "
            pdb=" OG  SER B  72 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.299 3.120
  ... (remaining 70668 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:             0.790
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.210
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:12.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
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   0.082   8708  Z= 0.218
  Angle     :  0.652  10.106  11832  Z= 0.357
  Chirality :  0.047   0.327   1372
  Planarity :  0.004   0.058   1485
  Dihedral  : 12.821  88.712   3027
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.81 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  0.68 %
    Favored  : 99.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.02 (0.26), residues: 1103
  helix:  0.92 (0.28), residues: 367
  sheet: -0.37 (0.28), residues: 289
  loop : -0.41 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.015   0.001   PHE A 274 
 TYR   0.017   0.002   TYR A 296 
 ARG   0.003   0.000   ARG E  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13156 (  429)
  hydrogen bonds       : angle       6.76638 ( 1221)
  SS BOND              : bond        0.00401 (    3)
  SS BOND              : angle       1.05217 (    6)
  covalent geometry    : bond        0.00472 ( 8705)
  covalent geometry    : angle       0.65198 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 191
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A  245 GLU cc_start: 0.7139 (mp0) cc_final: 0.6905 (mp0)
REVERT: A  247 MET cc_start: 0.8579 (mtp) cc_final: 0.8330 (mtp)
REVERT: A  273 LEU cc_start: 0.8744 (tp) cc_final: 0.8522 (tm)
REVERT: A  308 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7804 (mt-10)
REVERT: A  337 ASP cc_start: 0.7884 (m-30) cc_final: 0.7655 (m-30)
REVERT: R   86 ASN cc_start: 0.7868 (m-40) cc_final: 0.7653 (m-40)
REVERT: R   87 PHE cc_start: 0.8036 (m-10) cc_final: 0.7423 (m-80)
REVERT: R  190 CYS cc_start: 0.8128 (t) cc_final: 0.7834 (t)
REVERT: R  342 ASN cc_start: 0.7970 (m-40) cc_final: 0.7714 (m-40)
  outliers start: 2
  outliers final: 0
  residues processed: 191
  average time/residue: 1.2283
  time to fit residues: 249.4921
Evaluate side-chains
  143 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 86 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
B 268 ASN
C  59 ASN
E 167 GLN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.140882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.104545 restraints weight = 11776.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 2.46
r_work: 0.3148 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8708  Z= 0.134
  Angle     :  0.561   8.006  11832  Z= 0.295
  Chirality :  0.043   0.137   1372
  Planarity :  0.003   0.043   1485
  Dihedral  :  6.327  89.283   1221
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 14.50 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: 1103
  helix:  1.15 (0.28), residues: 364
  sheet: -0.29 (0.29), residues: 277
  loop : -0.39 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  82 
 HIS   0.003   0.001   HIS R 297 
 PHE   0.013   0.001   PHE R 135 
 TYR   0.017   0.001   TYR A 296 
 ARG   0.002   0.000   ARG A 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  429)
  hydrogen bonds       : angle       5.06346 ( 1221)
  SS BOND              : bond        0.00299 (    3)
  SS BOND              : angle       1.12177 (    6)
  covalent geometry    : bond        0.00306 ( 8705)
  covalent geometry    : angle       0.56022 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 158
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8565 (tt0)
REVERT: A  245 GLU cc_start: 0.7428 (mp0) cc_final: 0.6869 (mp0)
REVERT: A  247 MET cc_start: 0.8836 (mtp) cc_final: 0.8616 (mtp)
REVERT: A  273 LEU cc_start: 0.8676 (tp) cc_final: 0.8448 (tm)
REVERT: A  337 ASP cc_start: 0.8398 (m-30) cc_final: 0.8109 (m-30)
REVERT: B   13 GLN cc_start: 0.8432 (tm-30) cc_final: 0.8207 (pp30)
REVERT: B   42 ARG cc_start: 0.7576 (tpt170) cc_final: 0.7275 (tpp-160)
REVERT: E   84 THR cc_start: 0.9331 (m) cc_final: 0.9101 (p)
REVERT: R   87 PHE cc_start: 0.8282 (m-10) cc_final: 0.7808 (m-80)
REVERT: R  130 MET cc_start: 0.8103 (mpp) cc_final: 0.7739 (mpp)
REVERT: R  258 ARG cc_start: 0.8011 (tmt170) cc_final: 0.7751 (tmt170)
  outliers start: 19
  outliers final: 10
  residues processed: 167
  average time/residue: 1.2478
  time to fit residues: 221.2494
Evaluate side-chains
  159 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue   93 ILE
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 87 optimal weight:    0.8980
   chunk 78 optimal weight:    6.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 306 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 268 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 328 ASN
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.141341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.104678 restraints weight = 11884.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.52
r_work: 0.3154 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8708  Z= 0.137
  Angle     :  0.546   7.928  11832  Z= 0.286
  Chirality :  0.042   0.137   1372
  Planarity :  0.003   0.045   1485
  Dihedral  :  6.058  87.285   1221
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 17.21 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.25), residues: 1103
  helix:  1.35 (0.28), residues: 361
  sheet: -0.21 (0.29), residues: 285
  loop : -0.50 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.014   0.001   TYR R 149 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  429)
  hydrogen bonds       : angle       4.83496 ( 1221)
  SS BOND              : bond        0.00423 (    3)
  SS BOND              : angle       1.39673 (    6)
  covalent geometry    : bond        0.00317 ( 8705)
  covalent geometry    : angle       0.54511 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 153
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (tt0)
REVERT: A   20 ASP cc_start: 0.8518 (t0) cc_final: 0.8231 (m-30)
REVERT: A  242 ARG cc_start: 0.7302 (mmp-170) cc_final: 0.7020 (mmp-170)
REVERT: A  245 GLU cc_start: 0.7500 (mp0) cc_final: 0.6848 (mp0)
REVERT: A  337 ASP cc_start: 0.8381 (m-30) cc_final: 0.8075 (m-30)
REVERT: B   42 ARG cc_start: 0.7674 (tpt170) cc_final: 0.7392 (tpp-160)
REVERT: E   38 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.7842 (ptp90)
REVERT: E   43 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8327 (mmmt)
REVERT: E   84 THR cc_start: 0.9306 (OUTLIER) cc_final: 0.9095 (p)
REVERT: R   65 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7187 (tt)
REVERT: R   87 PHE cc_start: 0.8297 (m-10) cc_final: 0.7821 (m-80)
REVERT: R  258 ARG cc_start: 0.8008 (tmt170) cc_final: 0.7735 (tmt170)
  outliers start: 27
  outliers final: 11
  residues processed: 166
  average time/residue: 1.2162
  time to fit residues: 214.7001
Evaluate side-chains
  161 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.937 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   61 MET
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 39 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 106 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 62 optimal weight:    0.6980
   chunk 88 optimal weight:    4.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 306 GLN
B  13 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 ASN
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 297 HIS
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.138610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.101869 restraints weight = 11907.397|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 2.50
r_work: 0.3105 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8207
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8708  Z= 0.218
  Angle     :  0.600   9.405  11832  Z= 0.314
  Chirality :  0.044   0.156   1372
  Planarity :  0.004   0.048   1485
  Dihedral  :  6.036  83.792   1221
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.33 %
    Favored  : 78.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.26), residues: 1103
  helix:  1.33 (0.28), residues: 359
  sheet: -0.20 (0.29), residues: 298
  loop : -0.47 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  82 
 HIS   0.004   0.001   HIS R 297 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.020   0.002   TYR A 230 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04015 (  429)
  hydrogen bonds       : angle       4.93743 ( 1221)
  SS BOND              : bond        0.00164 (    3)
  SS BOND              : angle       1.70419 (    6)
  covalent geometry    : bond        0.00520 ( 8705)
  covalent geometry    : angle       0.59869 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 158
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8660 (tt0)
REVERT: A   20 ASP cc_start: 0.8554 (t0) cc_final: 0.8265 (m-30)
REVERT: A   33 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7101 (tt0)
REVERT: A  188 HIS cc_start: 0.8379 (m90) cc_final: 0.7818 (t70)
REVERT: A  245 GLU cc_start: 0.7684 (mp0) cc_final: 0.7118 (mp0)
REVERT: A  273 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8156 (mm)
REVERT: A  337 ASP cc_start: 0.8410 (m-30) cc_final: 0.8103 (m-30)
REVERT: E   38 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.7814 (ptp90)
REVERT: E   43 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8314 (mmmm)
REVERT: E   84 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9066 (p)
REVERT: R   65 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7181 (tt)
REVERT: R   87 PHE cc_start: 0.8333 (m-10) cc_final: 0.7866 (m-80)
REVERT: R  124 GLN cc_start: 0.7605 (mp10) cc_final: 0.6999 (mp10)
REVERT: R  258 ARG cc_start: 0.8007 (tmt170) cc_final: 0.7718 (tmt170)
  outliers start: 36
  outliers final: 14
  residues processed: 173
  average time/residue: 1.1999
  time to fit residues: 220.6557
Evaluate side-chains
  167 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   84 THR
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 52 optimal weight:    0.0980
   chunk 8 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.140316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.103786 restraints weight = 11882.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.51
r_work: 0.3137 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8708  Z= 0.144
  Angle     :  0.561   9.260  11832  Z= 0.293
  Chirality :  0.043   0.147   1372
  Planarity :  0.003   0.047   1485
  Dihedral  :  5.799  79.898   1221
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.71 %
    Favored  : 77.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1103
  helix:  1.49 (0.28), residues: 359
  sheet: -0.18 (0.30), residues: 280
  loop : -0.47 (0.30), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.012   0.001   PHE A 189 
 TYR   0.028   0.001   TYR A 230 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03666 (  429)
  hydrogen bonds       : angle       4.73553 ( 1221)
  SS BOND              : bond        0.00262 (    3)
  SS BOND              : angle       1.30197 (    6)
  covalent geometry    : bond        0.00334 ( 8705)
  covalent geometry    : angle       0.55989 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 157
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.8614 (tt0)
REVERT: A   20 ASP cc_start: 0.8470 (t0) cc_final: 0.8187 (m-30)
REVERT: A   33 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7213 (tt0)
REVERT: A  242 ARG cc_start: 0.7338 (mmp-170) cc_final: 0.7056 (mmp-170)
REVERT: A  245 GLU cc_start: 0.7755 (mp0) cc_final: 0.7067 (mp0)
REVERT: A  308 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8062 (mt-10)
REVERT: A  337 ASP cc_start: 0.8381 (m-30) cc_final: 0.8066 (m-30)
REVERT: B  156 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8418 (mt0)
REVERT: B  161 SER cc_start: 0.9343 (OUTLIER) cc_final: 0.8964 (t)
REVERT: E   38 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.7790 (ptp90)
REVERT: E   83 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8140 (mtp)
REVERT: R   65 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7136 (tt)
REVERT: R   87 PHE cc_start: 0.8250 (m-10) cc_final: 0.7746 (m-80)
REVERT: R  124 GLN cc_start: 0.7579 (mp10) cc_final: 0.7019 (mp10)
REVERT: R  258 ARG cc_start: 0.8063 (tmt170) cc_final: 0.7784 (tmt170)
  outliers start: 28
  outliers final: 13
  residues processed: 170
  average time/residue: 1.2359
  time to fit residues: 222.8462
Evaluate side-chains
  166 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain A residue  341 ASP
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue  156 GLN
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 88 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   chunk 106 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.104728 restraints weight = 11797.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.47
r_work: 0.3146 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.1801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8708  Z= 0.138
  Angle     :  0.554   9.749  11832  Z= 0.289
  Chirality :  0.042   0.154   1372
  Planarity :  0.003   0.047   1485
  Dihedral  :  5.605  75.602   1221
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.50 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.26), residues: 1103
  helix:  1.51 (0.28), residues: 361
  sheet: -0.11 (0.30), residues: 285
  loop : -0.47 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.011   0.001   PHE A 189 
 TYR   0.027   0.001   TYR A 230 
 ARG   0.003   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03580 (  429)
  hydrogen bonds       : angle       4.68327 ( 1221)
  SS BOND              : bond        0.00228 (    3)
  SS BOND              : angle       1.24864 (    6)
  covalent geometry    : bond        0.00321 ( 8705)
  covalent geometry    : angle       0.55375 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8602 (tt0)
REVERT: A   20 ASP cc_start: 0.8451 (t0) cc_final: 0.8183 (m-30)
REVERT: A   33 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7058 (tt0)
REVERT: A  188 HIS cc_start: 0.8244 (m90) cc_final: 0.7725 (t70)
REVERT: A  245 GLU cc_start: 0.7790 (mp0) cc_final: 0.7097 (mp0)
REVERT: A  308 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8090 (mt-10)
REVERT: A  337 ASP cc_start: 0.8368 (m-30) cc_final: 0.8063 (m-30)
REVERT: B  161 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.8961 (t)
REVERT: E   38 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.7761 (ptp90)
REVERT: R   65 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7118 (tt)
REVERT: R   87 PHE cc_start: 0.8259 (m-10) cc_final: 0.7812 (m-80)
REVERT: R  124 GLN cc_start: 0.7562 (mp10) cc_final: 0.7029 (mp10)
REVERT: R  258 ARG cc_start: 0.8081 (tmt170) cc_final: 0.7822 (tmt170)
REVERT: R  344 LYS cc_start: 0.7367 (mmmm) cc_final: 0.7148 (mmmm)
  outliers start: 31
  outliers final: 15
  residues processed: 175
  average time/residue: 1.2193
  time to fit residues: 226.9130
Evaluate side-chains
  169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.138749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.102133 restraints weight = 11892.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.49
r_work: 0.3108 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   8708  Z= 0.200
  Angle     :  0.603  10.997  11832  Z= 0.314
  Chirality :  0.044   0.145   1372
  Planarity :  0.004   0.048   1485
  Dihedral  :  5.652  72.342   1221
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.29 %
    Favored  : 74.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.26), residues: 1103
  helix:  1.46 (0.28), residues: 359
  sheet: -0.18 (0.29), residues: 298
  loop : -0.44 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.010   0.001   PHE A 196 
 TYR   0.013   0.002   TYR E 178 
 ARG   0.002   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03814 (  429)
  hydrogen bonds       : angle       4.79865 ( 1221)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       1.46960 (    6)
  covalent geometry    : bond        0.00475 ( 8705)
  covalent geometry    : angle       0.60189 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 148
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8644 (tt0)
REVERT: A   20 ASP cc_start: 0.8545 (t0) cc_final: 0.8271 (m-30)
REVERT: A   33 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7406 (tt0)
REVERT: A  242 ARG cc_start: 0.7463 (mmp-170) cc_final: 0.7107 (mmp-170)
REVERT: A  245 GLU cc_start: 0.7744 (mp0) cc_final: 0.7010 (mp0)
REVERT: A  308 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8096 (mt-10)
REVERT: A  337 ASP cc_start: 0.8409 (m-30) cc_final: 0.8079 (m-30)
REVERT: B  161 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.8980 (t)
REVERT: E   38 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.7783 (ptp90)
REVERT: R   65 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.7129 (tt)
REVERT: R   87 PHE cc_start: 0.8256 (m-10) cc_final: 0.7854 (m-80)
REVERT: R  124 GLN cc_start: 0.7568 (mp10) cc_final: 0.7016 (mp10)
REVERT: R  186 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7197 (mp)
REVERT: R  258 ARG cc_start: 0.8020 (tmt170) cc_final: 0.7712 (tmt170)
  outliers start: 34
  outliers final: 18
  residues processed: 169
  average time/residue: 1.2559
  time to fit residues: 226.5157
Evaluate side-chains
  168 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 144
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   37 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  270 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   38 ARG
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  130 MET
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0970
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 65 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 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 = 0.3816 r_free = 0.3816 target = 0.141738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.105738 restraints weight = 11962.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 2.48
r_work: 0.3165 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3024 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8708  Z= 0.120
  Angle     :  0.559   9.660  11832  Z= 0.290
  Chirality :  0.042   0.132   1372
  Planarity :  0.003   0.046   1485
  Dihedral  :  5.334  66.517   1221
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 22.20 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.26), residues: 1103
  helix:  1.48 (0.28), residues: 367
  sheet: -0.10 (0.30), residues: 280
  loop : -0.38 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 226 
 HIS   0.002   0.000   HIS E  35 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.026   0.001   TYR A 230 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03378 (  429)
  hydrogen bonds       : angle       4.59235 ( 1221)
  SS BOND              : bond        0.00297 (    3)
  SS BOND              : angle       1.07667 (    6)
  covalent geometry    : bond        0.00273 ( 8705)
  covalent geometry    : angle       0.55899 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 157
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8575 (tt0)
REVERT: A   20 ASP cc_start: 0.8402 (t0) cc_final: 0.8123 (m-30)
REVERT: A  242 ARG cc_start: 0.7468 (mmp-170) cc_final: 0.7019 (mmp-170)
REVERT: A  245 GLU cc_start: 0.7842 (mp0) cc_final: 0.7132 (mp0)
REVERT: A  308 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8083 (mt-10)
REVERT: A  337 ASP cc_start: 0.8330 (m-30) cc_final: 0.8070 (m-30)
REVERT: B   42 ARG cc_start: 0.7598 (tpt170) cc_final: 0.7326 (tpp-160)
REVERT: B  161 SER cc_start: 0.9347 (OUTLIER) cc_final: 0.8937 (t)
REVERT: E   83 MET cc_start: 0.8675 (OUTLIER) cc_final: 0.8111 (mtp)
REVERT: R   65 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7083 (tt)
REVERT: R   87 PHE cc_start: 0.8247 (m-10) cc_final: 0.7833 (m-80)
REVERT: R  124 GLN cc_start: 0.7480 (mp10) cc_final: 0.6906 (mp10)
REVERT: R  258 ARG cc_start: 0.8088 (tmt170) cc_final: 0.7846 (tmt170)
REVERT: R  344 LYS cc_start: 0.7341 (mmmm) cc_final: 0.7135 (mmmm)
  outliers start: 30
  outliers final: 16
  residues processed: 174
  average time/residue: 1.1832
  time to fit residues: 219.2895
Evaluate side-chains
  163 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 143
  time to evaluate  : 0.933 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  222 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 102 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 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 = 0.3817 r_free = 0.3817 target = 0.141890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.105717 restraints weight = 11886.436|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 2.50
r_work: 0.3169 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8708  Z= 0.126
  Angle     :  0.579  11.568  11832  Z= 0.299
  Chirality :  0.042   0.137   1372
  Planarity :  0.003   0.045   1485
  Dihedral  :  5.167  60.611   1221
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 23.56 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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 (0.26), residues: 1103
  helix:  1.59 (0.28), residues: 362
  sheet: -0.04 (0.30), residues: 280
  loop : -0.40 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.009   0.001   PHE A 189 
 TYR   0.022   0.001   TYR A 296 
 ARG   0.004   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03357 (  429)
  hydrogen bonds       : angle       4.55611 ( 1221)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       1.86415 (    6)
  covalent geometry    : bond        0.00289 ( 8705)
  covalent geometry    : angle       0.57784 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 145
  time to evaluate  : 0.905 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8580 (tt0)
REVERT: A   20 ASP cc_start: 0.8497 (t0) cc_final: 0.8212 (m-30)
REVERT: A  242 ARG cc_start: 0.7407 (mmp-170) cc_final: 0.6916 (mmp-170)
REVERT: A  245 GLU cc_start: 0.7857 (mp0) cc_final: 0.7125 (mp0)
REVERT: A  308 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8099 (mt-10)
REVERT: A  337 ASP cc_start: 0.8322 (m-30) cc_final: 0.8053 (m-30)
REVERT: B   42 ARG cc_start: 0.7587 (tpt170) cc_final: 0.7278 (tpp-160)
REVERT: B  161 SER cc_start: 0.9352 (OUTLIER) cc_final: 0.8945 (t)
REVERT: B  325 MET cc_start: 0.9259 (mmt) cc_final: 0.8931 (mmm)
REVERT: E   83 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8206 (mtm)
REVERT: R   65 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7098 (tt)
REVERT: R   87 PHE cc_start: 0.8241 (m-10) cc_final: 0.7824 (m-80)
REVERT: R  124 GLN cc_start: 0.7473 (mp10) cc_final: 0.6932 (mp10)
REVERT: R  258 ARG cc_start: 0.8070 (tmt170) cc_final: 0.7844 (tmt170)
  outliers start: 26
  outliers final: 18
  residues processed: 162
  average time/residue: 1.2037
  time to fit residues: 207.6294
Evaluate side-chains
  165 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 143
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  276 GLU
Chi-restraints excluded: chain A residue  284 THR
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  222 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0970
   chunk 16 optimal weight:    0.8980
   chunk 72 optimal weight:    5.9990
   chunk 101 optimal weight:    0.8980
   chunk 70 optimal weight:    0.3980
   chunk 21 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.142318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.106228 restraints weight = 11844.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 2.49
r_work: 0.3178 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8708  Z= 0.122
  Angle     :  0.580  11.101  11832  Z= 0.299
  Chirality :  0.042   0.138   1372
  Planarity :  0.003   0.045   1485
  Dihedral  :  5.033  56.177   1221
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  : 23.44 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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:  0.49 (0.26), residues: 1103
  helix:  1.60 (0.28), residues: 362
  sheet: -0.06 (0.30), residues: 281
  loop : -0.36 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.002   0.000   HIS E  35 
 PHE   0.012   0.001   PHE A 274 
 TYR   0.024   0.001   TYR A 230 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03314 (  429)
  hydrogen bonds       : angle       4.52219 ( 1221)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       1.75129 (    6)
  covalent geometry    : bond        0.00279 ( 8705)
  covalent geometry    : angle       0.57898 (11826)

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

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

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2206 Ramachandran restraints generated.
    1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 148
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8580 (tt0)
REVERT: A   20 ASP cc_start: 0.8530 (t0) cc_final: 0.8251 (m-30)
REVERT: A  242 ARG cc_start: 0.7469 (mmp-170) cc_final: 0.6977 (mmp-170)
REVERT: A  245 GLU cc_start: 0.7828 (mp0) cc_final: 0.7107 (mp0)
REVERT: A  308 GLU cc_start: 0.8483 (mt-10) cc_final: 0.8056 (mt-10)
REVERT: A  337 ASP cc_start: 0.8318 (m-30) cc_final: 0.8042 (m-30)
REVERT: B   42 ARG cc_start: 0.7614 (tpt170) cc_final: 0.7309 (tpp-160)
REVERT: B  172 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8527 (tp30)
REVERT: B  325 MET cc_start: 0.9260 (mmt) cc_final: 0.8933 (mmm)
REVERT: E   83 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8209 (mtm)
REVERT: E  167 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8781 (tp40)
REVERT: R   65 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7072 (tt)
REVERT: R   87 PHE cc_start: 0.8228 (m-10) cc_final: 0.7773 (m-80)
REVERT: R  124 GLN cc_start: 0.7480 (mp10) cc_final: 0.6900 (mp10)
REVERT: R  186 ILE cc_start: 0.7797 (OUTLIER) cc_final: 0.7248 (mp)
REVERT: R  205 MET cc_start: 0.6910 (ttt) cc_final: 0.6709 (ttt)
REVERT: R  258 ARG cc_start: 0.8094 (tmt170) cc_final: 0.7877 (tmt170)
REVERT: R  338 PHE cc_start: 0.7856 (m-80) cc_final: 0.7623 (m-80)
  outliers start: 26
  outliers final: 17
  residues processed: 162
  average time/residue: 1.1643
  time to fit residues: 201.0506
Evaluate side-chains
  169 residues out of total 965 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 147
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   14 GLU
Chi-restraints excluded: chain A residue   25 GLU
Chi-restraints excluded: chain A residue  218 VAL
Chi-restraints excluded: chain A residue  316 THR
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue  147 SER
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain E residue   83 MET
Chi-restraints excluded: chain E residue   91 THR
Chi-restraints excluded: chain E residue  135 VAL
Chi-restraints excluded: chain E residue  167 GLN
Chi-restraints excluded: chain R residue   65 LEU
Chi-restraints excluded: chain R residue   72 THR
Chi-restraints excluded: chain R residue  145 SER
Chi-restraints excluded: chain R residue  146 ILE
Chi-restraints excluded: chain R residue  186 ILE
Chi-restraints excluded: chain R residue  222 SER
Chi-restraints excluded: chain R residue  236 VAL
Chi-restraints excluded: chain R residue  306 ILE
Chi-restraints excluded: chain R residue  330 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 76 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 97 optimal weight:    7.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 294 ASN
A 306 GLN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.141676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.105329 restraints weight = 11956.279|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 2.51
r_work: 0.3161 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8708  Z= 0.138
  Angle     :  0.594  11.736  11832  Z= 0.306
  Chirality :  0.043   0.146   1372
  Planarity :  0.003   0.046   1485
  Dihedral  :  4.944  50.307   1221
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.88 %
    Favored  : 73.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: 1103
  helix:  1.57 (0.28), residues: 362
  sheet: -0.06 (0.30), residues: 281
  loop : -0.37 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.009   0.001   PHE A 189 
 TYR   0.022   0.001   TYR A 296 
 ARG   0.005   0.000   ARG B  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  429)
  hydrogen bonds       : angle       4.56294 ( 1221)
  SS BOND              : bond        0.00234 (    3)
  SS BOND              : angle       1.73164 (    6)
  covalent geometry    : bond        0.00322 ( 8705)
  covalent geometry    : angle       0.59312 (11826)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7115.06 seconds
wall clock time: 121 minutes 43.57 seconds (7303.57 seconds total)