Starting phenix.real_space_refine
on Thu Jan 18 20:52:36 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/01_2024/6wwz_21950.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/01_2024/6wwz_21950.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.34
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/01_2024/6wwz_21950.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/01_2024/6wwz_21950.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/01_2024/6wwz_21950.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wwz_21950/01_2024/6wwz_21950.pdb"
  }
  resolution = 3.34
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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      70      5.16       5
     C    6026      2.51       5
     N    1612      2.21       5
     O    1742      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ARG   48": "NH1" <-> "NH2"
    Residue "B ARG   52": "NH1" <-> "NH2"
    Residue "B PHE  180": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   13": "NH1" <-> "NH2"
    Residue "C ARG   61": "NH1" <-> "NH2"
    Residue "Y ARG   62": "NH1" <-> "NH2"
    Residue "A ARG  313": "NH1" <-> "NH2"
    Residue "A ARG  349": "NH1" <-> "NH2"
    Residue "S ARG   72": "NH1" <-> "NH2"
    Residue "R ARG   46": "NH1" <-> "NH2"
    Residue "R ARG  286": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib"
  Total number of atoms: 9450
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "C"
      Number of atoms: 530
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 66, 530
          Classifications: {'peptide': 66}
          Link IDs: {'PTRANS': 2, 'TRANS': 63}
    Chain: "Y"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1649
          Classifications: {'peptide': 210}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 4, 'TRANS': 205}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "S"
      Number of atoms: 1770
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1770
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 2468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 310, 2468
          Classifications: {'peptide': 310}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 8, 'TRANS': 301}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 5.71, per 1000 atoms: 0.60
  Number of scatterers: 9450
  At special positions: 0
  Unit cell: (116.58, 121.8, 157.47, 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      70     16.00
     O    1742      8.00
     N    1612      7.00
     C    6026      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C   6 " - pdb=" SG  CYS C  32 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  48 " distance=2.02
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.05
    Simple disulfide: pdb=" SG  CYS S 147 " - pdb=" SG  CYS S 217 " distance=2.05
    Simple disulfide: pdb=" SG  CYS R  36 " - pdb=" SG  CYS R 288 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 118 " - pdb=" SG  CYS R 197 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.46
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2270

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 14 sheets defined
      35.8% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'B' and resid 3 through 22
      removed outlier: 3.845A  pdb=" N   LEU B  14 " --> pdb=" O   GLU B  10 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.935A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 20
    Processing helix  chain 'C' and resid 53 through 63
      removed outlier: 3.628A  pdb=" N   LEU C  62 " --> pdb=" O   TYR C  58 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 9 through 22
    Processing helix  chain 'Y' and resid 29 through 45
      removed outlier: 3.635A  pdb=" N   ALA Y  33 " --> pdb=" O   LYS Y  29 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU Y  37 " --> pdb=" O   ALA Y  33 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA Y  43 " --> pdb=" O   ALA Y  39 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 46 through 48
      No H-bonds generated for 'chain 'Y' and resid 46 through 48'
    Processing helix  chain 'A' and resid 6 through 30
      removed outlier: 3.695A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A  24 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   GLU A  25 " --> pdb=" O   LYS A  21 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ASP A  26 " --> pdb=" O   ASN A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 51
      removed outlier: 3.536A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 214
      removed outlier: 3.877A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 256
      removed outlier: 3.544A  pdb=" N   ASN A 256 " --> pdb=" O   ASP A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 276
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 4.005A  pdb=" N   ILE A 286 " --> pdb=" O   PRO A 283 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   CYS A 287 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 283 through 287'
    Processing helix  chain 'A' and resid 296 through 299
      removed outlier: 4.179A  pdb=" N   ASP A 299 " --> pdb=" O   THR A 296 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 296 through 299'
    Processing helix  chain 'A' and resid 300 through 311
      removed outlier: 3.807A  pdb=" N   ILE A 304 " --> pdb=" O   ALA A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.677A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE A 342 " --> pdb=" O   ALA A 338 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ARG A 349 " --> pdb=" O   ALA A 345 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 39 through 73
      removed outlier: 3.943A  pdb=" N   LEU R  47 " --> pdb=" O   GLN R  43 " (cutoff:3.500A)
      Proline residue:  R  50  - end of helix
      removed outlier: 3.938A  pdb=" N   LEU R  66 " --> pdb=" O   LEU R  62 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   VAL R  67 " --> pdb=" O   GLY R  63 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 80 through 98
      removed outlier: 3.550A  pdb=" N   TYR R  84 " --> pdb=" O   MET R  80 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU R  94 " --> pdb=" O   ILE R  90 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   PHE R  95 " --> pdb=" O   ALA R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 99 through 109
      removed outlier: 4.290A  pdb=" N   ALA R 103 " --> pdb=" O   LEU R  99 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 114 through 149
      removed outlier: 3.564A  pdb=" N   CYS R 118 " --> pdb=" O   SER R 114 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LYS R 122 " --> pdb=" O   CYS R 118 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   GLY R 123 " --> pdb=" O   LYS R 119 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA R 126 " --> pdb=" O   LYS R 122 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ILE R 127 " --> pdb=" O   GLY R 123 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   MET R 133 " --> pdb=" O   PHE R 129 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LEU R 134 " --> pdb=" O   ASN R 130 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU R 135 " --> pdb=" O   CYS R 131 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   LEU R 136 " --> pdb=" O   GLY R 132 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLN R 149 " --> pdb=" O   ILE R 145 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 149 through 157
    Processing helix  chain 'R' and resid 160 through 185
      removed outlier: 4.288A  pdb=" N   SER R 164 " --> pdb=" O   THR R 160 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   LYS R 165 " --> pdb=" O   LEU R 161 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ILE R 166 " --> pdb=" O   PRO R 162 " (cutoff:3.500A)
      removed outlier: 4.575A  pdb=" N   SER R 181 " --> pdb=" O   ILE R 177 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   THR R 182 " --> pdb=" O   ILE R 178 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   PHE R 185 " --> pdb=" O   SER R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 206 through 242
      removed outlier: 3.930A  pdb=" N   TRP R 210 " --> pdb=" O   GLU R 206 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LYS R 211 " --> pdb=" O   PRO R 207 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLU R 218 " --> pdb=" O   MET R 214 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE R 221 " --> pdb=" O   LEU R 217 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ILE R 225 " --> pdb=" O   PHE R 221 " (cutoff:3.500A)
      Proline residue:  R 226  - end of helix
      removed outlier: 3.511A  pdb=" N   PHE R 229 " --> pdb=" O   ILE R 225 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   VAL R 238 " --> pdb=" O   TYR R 234 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   THR R 240 " --> pdb=" O   PHE R 236 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 248 through 280
      removed outlier: 3.812A  pdb=" N   ALA R 252 " --> pdb=" O   LYS R 248 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE R 253 " --> pdb=" O   ARG R 249 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ARG R 254 " --> pdb=" O   HIS R 250 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LEU R 264 " --> pdb=" O   VAL R 260 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE R 268 " --> pdb=" O   LEU R 264 " (cutoff:3.500A)
      Proline residue:  R 269  - end of helix
      removed outlier: 3.723A  pdb=" N   ALA R 278 " --> pdb=" O   LEU R 274 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASN R 280 " --> pdb=" O   VAL R 276 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 287 through 320
      removed outlier: 3.714A  pdb=" N   GLU R 291 " --> pdb=" O   SER R 287 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   THR R 297 " --> pdb=" O   LEU R 293 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   THR R 299 " --> pdb=" O   GLY R 295 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL R 300 " --> pdb=" O   TYR R 296 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL R 303 " --> pdb=" O   THR R 299 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   LEU R 304 " --> pdb=" O   VAL R 300 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   ALA R 305 " --> pdb=" O   THR R 301 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   PHE R 306 " --> pdb=" O   GLU R 302 " (cutoff:3.500A)
      Proline residue:  R 313  - end of helix
      removed outlier: 3.878A  pdb=" N   GLY R 320 " --> pdb=" O   TYR R 316 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 320 through 335
    Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.834A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.906A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.606A  pdb=" N   ALA B 113 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.130A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 153
      removed outlier: 5.711A  pdb=" N   CYS B 149 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   SER B 160 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.568A  pdb=" N   PHE B 151 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   VAL B 158 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.114A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.863A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.273A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.805A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.697A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.946A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 7.102A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 5.012A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 22 through 23
      removed outlier: 3.677A  pdb=" N   GLY C  22 " --> pdb=" O   HIS C  40 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 186 through 191
      removed outlier: 3.548A  pdb=" N   PHE A 190 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
      removed outlier: 9.346A  pdb=" N   ALA A 221 " --> pdb=" O   ASP A  33 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.812A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 7.280A  pdb=" N   ILE A 265 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   LEU A 267 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 3.557A  pdb=" N   THR S 115 " --> pdb=" O   TYR S  94 " (cutoff:3.500A)
      removed outlier: 7.191A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.864A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 128 through 129
      removed outlier: 3.575A  pdb=" N   CYS S 147 " --> pdb=" O   PHE S 200 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ALA S 199 " --> pdb=" O   SER S 196 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 134 through 135
      removed outlier: 6.826A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 186 through 189
      removed outlier: 3.537A  pdb=" N   GLN R 187 " --> pdb=" O   GLU R 198 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU R 198 " --> pdb=" O   GLN R 187 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   TYR R 189 " --> pdb=" O   VAL R 196 " (cutoff:3.500A)

    381 hydrogen bonds defined for protein.
    1092 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: 2.38

  Time building geometry restraints manager: 3.69 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: 1915
        1.34 -     1.46: 2249
        1.46 -     1.58: 5380
        1.58 -     1.70: 0
        1.70 -     1.82: 97
  Bond restraints: 9641
  Sorted by residual:
  bond pdb=" N   VAL B 276 "
       pdb=" CA  VAL B 276 "
    ideal  model  delta    sigma   weight residual
    1.456  1.499 -0.043 1.11e-02 8.12e+03 1.49e+01
  bond pdb=" N   VAL S 137 "
       pdb=" CA  VAL S 137 "
    ideal  model  delta    sigma   weight residual
    1.457  1.500 -0.043 1.11e-02 8.12e+03 1.48e+01
  bond pdb=" N   ASN R 312 "
       pdb=" CA  ASN R 312 "
    ideal  model  delta    sigma   weight residual
    1.462  1.491 -0.029 7.70e-03 1.69e+04 1.45e+01
  bond pdb=" N   ILE B 269 "
       pdb=" CA  ILE B 269 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.044 1.19e-02 7.06e+03 1.39e+01
  bond pdb=" N   LEU R  99 "
       pdb=" CA  LEU R  99 "
    ideal  model  delta    sigma   weight residual
    1.462  1.493 -0.031 8.50e-03 1.38e+04 1.33e+01
  ... (remaining 9636 not shown)

  Histogram of bond angle deviations from ideal:
       99.26 -   106.30: 194
      106.30 -   113.33: 5003
      113.33 -   120.37: 4373
      120.37 -   127.41: 3410
      127.41 -   134.45: 69
  Bond angle restraints: 13049
  Sorted by residual:
  angle pdb=" N   GLU A 217 "
        pdb=" CA  GLU A 217 "
        pdb=" C   GLU A 217 "
      ideal   model   delta    sigma   weight residual
     111.28  120.08   -8.80 1.09e+00 8.42e-01 6.51e+01
  angle pdb=" C   CYS A 287 "
        pdb=" N   PHE A 288 "
        pdb=" CA  PHE A 288 "
      ideal   model   delta    sigma   weight residual
     123.10  116.84    6.26 9.60e-01 1.09e+00 4.25e+01
  angle pdb=" N   VAL A 219 "
        pdb=" CA  VAL A 219 "
        pdb=" C   VAL A 219 "
      ideal   model   delta    sigma   weight residual
     108.35  100.25    8.10 1.32e+00 5.74e-01 3.77e+01
  angle pdb=" C   CYS B 114 "
        pdb=" N   GLY B 115 "
        pdb=" CA  GLY B 115 "
      ideal   model   delta    sigma   weight residual
     121.61  125.52   -3.91 7.70e-01 1.69e+00 2.58e+01
  angle pdb=" C   VAL A 202 "
        pdb=" N   GLY A 203 "
        pdb=" CA  GLY A 203 "
      ideal   model   delta    sigma   weight residual
     121.61  125.52   -3.91 7.70e-01 1.69e+00 2.58e+01
  ... (remaining 13044 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5284
       17.91 -    35.83: 374
       35.83 -    53.74: 75
       53.74 -    71.66: 15
       71.66 -    89.57: 2
  Dihedral angle restraints: 5750
    sinusoidal: 2236
      harmonic: 3514
  Sorted by residual:
  dihedral pdb=" CB  CYS R  36 "
           pdb=" SG  CYS R  36 "
           pdb=" SG  CYS R 288 "
           pdb=" CB  CYS R 288 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.57   89.57     1      1.00e+01 1.00e-02 9.53e+01
  dihedral pdb=" CB  CYS C   7 "
           pdb=" SG  CYS C   7 "
           pdb=" SG  CYS C  48 "
           pdb=" CB  CYS C  48 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  150.18  -57.18     1      1.00e+01 1.00e-02 4.40e+01
  dihedral pdb=" CA  THR A 296 "
           pdb=" C   THR A 296 "
           pdb=" N   TYR A 297 "
           pdb=" CA  TYR A 297 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.67  -20.33     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 5747 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 601
       0.060 -    0.120: 607
       0.120 -    0.179: 237
       0.179 -    0.239: 44
       0.239 -    0.299: 4
  Chirality restraints: 1493
  Sorted by residual:
  chirality pdb=" CA  VAL A 219 "
            pdb=" N   VAL A 219 "
            pdb=" C   VAL A 219 "
            pdb=" CB  VAL A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  ILE A 213 "
            pdb=" N   ILE A 213 "
            pdb=" C   ILE A 213 "
            pdb=" CB  ILE A 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.73   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CA  LEU C  15 "
            pdb=" N   LEU C  15 "
            pdb=" C   LEU C  15 "
            pdb=" CB  LEU C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1490 not shown)

  Planarity restraints: 1644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL S 135 "   -0.074 5.00e-02 4.00e+02   1.12e-01 2.00e+01
        pdb=" N   PRO S 136 "    0.193 5.00e-02 4.00e+02
        pdb=" CA  PRO S 136 "   -0.060 5.00e-02 4.00e+02
        pdb=" CD  PRO S 136 "   -0.059 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR R  74 "   -0.018 2.00e-02 2.50e+03   3.85e-02 1.48e+01
        pdb=" C   TYR R  74 "    0.066 2.00e-02 2.50e+03
        pdb=" O   TYR R  74 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   LYS R  75 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 210 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.96e+00
        pdb=" C   LYS A 210 "    0.038 2.00e-02 2.50e+03
        pdb=" O   LYS A 210 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LYS A 211 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1641 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 1551
        2.83 -     3.35: 8695
        3.35 -     3.87: 12654
        3.87 -     4.38: 15974
        4.38 -     4.90: 27265
  Nonbonded interactions: 66139
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 224 "
            pdb=" NH1 ARG B 251 "
     model   vdw
     2.318 2.520
  nonbonded pdb=" O   PHE R  71 "
            pdb=" NH2 ARG R  78 "
     model   vdw
     2.355 2.520
  nonbonded pdb=" OD2 ASP B  83 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.449 2.440
  nonbonded pdb=" N   VAL A 219 "
            pdb=" O   VAL A 219 "
     model   vdw
     2.513 2.496
  nonbonded pdb=" OG1 THR A 292 "
            pdb=" N   GLY A 293 "
     model   vdw
     2.528 2.520
  ... (remaining 66134 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             3.980
  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:             0.020
  Extract box with map and model:          12.500
  Check model and map are aligned:         0.150
  Set scattering table:                    0.100
  Process input model:                     27.460
  Find NCS groups from input model:        0.310
  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:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
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      :  0.014   0.054   9641  Z= 0.927
  Angle     :  1.768   8.796  13049  Z= 1.321
  Chirality :  0.091   0.299   1493
  Planarity :  0.004   0.112   1644
  Dihedral  : 13.132  82.851   3462
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 2.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  5.71 %
    Favored  : 94.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -3.33 (0.19), residues: 1193
  helix: -1.81 (0.21), residues: 368
  sheet: -1.52 (0.30), residues: 235
  loop : -2.78 (0.19), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  63 
 HIS   0.004   0.001   HIS S 220 
 PHE   0.013   0.002   PHE Y  61 
 TYR   0.020   0.002   TYR R 125 
 ARG   0.004   0.001   ARG S  67 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 1.116 
Fit side-chains
REVERT: B   23 LYS cc_start: 0.7082 (tptt) cc_final: 0.5837 (ttmm)
REVERT: B   66 ASP cc_start: 0.7820 (t0) cc_final: 0.7327 (p0)
REVERT: B  163 ASP cc_start: 0.8120 (t0) cc_final: 0.7813 (t0)
REVERT: B  197 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7379 (tpp-160)
REVERT: B  254 ASP cc_start: 0.8685 (m-30) cc_final: 0.7811 (p0)
REVERT: C   25 ARG cc_start: 0.8059 (mtp-110) cc_final: 0.7842 (mtp85)
REVERT: Y   42 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6526 (tt0)
REVERT: A  249 MET cc_start: 0.7301 (ttm) cc_final: 0.6688 (mmt)
REVERT: A  273 ASP cc_start: 0.6091 (t0) cc_final: 0.5836 (p0)
REVERT: A  280 LYS cc_start: 0.7967 (tttt) cc_final: 0.6845 (mptt)
REVERT: A  322 HIS cc_start: 0.6950 (t70) cc_final: 0.6660 (t-90)
REVERT: S   34 MET cc_start: 0.8621 (mmt) cc_final: 0.8243 (mmm)
REVERT: S   87 ARG cc_start: 0.7303 (mtp-110) cc_final: 0.6604 (mtm110)
REVERT: S   89 GLU cc_start: 0.7344 (pt0) cc_final: 0.6864 (pp20)
REVERT: S  206 ARG cc_start: 0.8409 (mtp180) cc_final: 0.7801 (ttp80)
REVERT: R  141 MET cc_start: 0.6807 (mmm) cc_final: 0.6534 (tpt)
REVERT: R  157 ARG cc_start: 0.6999 (tpt90) cc_final: 0.6714 (ttt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2279
  time to fit residues: 55.1184
Evaluate side-chains
  113 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 90 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
B 239 ASN
C   3 ASN
C  35 ASN
A 205 GLN
A 214 HIS
A 305 GLN
S  82 GLN
S 174 GLN
R  87 ASN
R 186 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9641  Z= 0.202
  Angle     :  0.608   8.965  13049  Z= 0.328
  Chirality :  0.042   0.144   1493
  Planarity :  0.004   0.060   1644
  Dihedral  :  5.044  63.114   1304
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 1.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 11.71 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.47 (0.22), residues: 1193
  helix:  0.88 (0.26), residues: 386
  sheet: -1.12 (0.28), residues: 297
  loop : -2.37 (0.21), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP S  47 
 HIS   0.005   0.001   HIS B 225 
 PHE   0.012   0.001   PHE B 235 
 TYR   0.021   0.002   TYR R 296 
 ARG   0.003   0.000   ARG B  96 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 129
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
REVERT: B   44 GLN cc_start: 0.7472 (pt0) cc_final: 0.6890 (tt0)
REVERT: B   99 TRP cc_start: 0.7182 (m-90) cc_final: 0.6833 (m100)
REVERT: B  228 ASP cc_start: 0.7553 (m-30) cc_final: 0.7305 (p0)
REVERT: B  254 ASP cc_start: 0.8628 (m-30) cc_final: 0.7945 (p0)
REVERT: A  249 MET cc_start: 0.7530 (ttm) cc_final: 0.6965 (mmt)
REVERT: A  273 ASP cc_start: 0.5854 (t0) cc_final: 0.5588 (p0)
REVERT: A  280 LYS cc_start: 0.7790 (tttt) cc_final: 0.6682 (mptt)
REVERT: A  322 HIS cc_start: 0.6836 (t70) cc_final: 0.6468 (t70)
REVERT: S   87 ARG cc_start: 0.7195 (mtp-110) cc_final: 0.6532 (mtm110)
REVERT: S   89 GLU cc_start: 0.7319 (pt0) cc_final: 0.6863 (pp20)
REVERT: S  206 ARG cc_start: 0.8313 (mtp180) cc_final: 0.7647 (ttp-110)
REVERT: S  211 ASP cc_start: 0.7662 (t0) cc_final: 0.7111 (t0)
REVERT: R  133 MET cc_start: 0.6472 (mmt) cc_final: 0.6091 (mmt)
REVERT: R  157 ARG cc_start: 0.6767 (tpt90) cc_final: 0.6529 (ttt-90)
  outliers start: 14
  outliers final: 10
  residues processed: 136
  average time/residue: 0.2356
  time to fit residues: 43.5456
Evaluate side-chains
  118 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  276 VAL
Chi-restraints excluded: chain R residue  314 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 108 optimal weight:    0.5980
   chunk 116 optimal weight:    6.9990
   chunk 96 optimal weight:    5.9990
   chunk 107 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
R 128 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9641  Z= 0.187
  Angle     :  0.561  12.589  13049  Z= 0.291
  Chirality :  0.042   0.135   1493
  Planarity :  0.004   0.040   1644
  Dihedral  :  4.702  58.481   1304
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 2.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 13.84 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.79 (0.23), residues: 1193
  helix:  1.64 (0.27), residues: 386
  sheet: -0.55 (0.29), residues: 291
  loop : -2.27 (0.22), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP S  47 
 HIS   0.006   0.001   HIS B 225 
 PHE   0.013   0.001   PHE B 199 
 TYR   0.015   0.001   TYR B 105 
 ARG   0.005   0.001   ARG B  42 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 121
  time to evaluate  : 1.252 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7345 (m-90) cc_final: 0.6989 (m100)
REVERT: B  228 ASP cc_start: 0.7531 (m-30) cc_final: 0.7259 (p0)
REVERT: B  254 ASP cc_start: 0.8606 (m-30) cc_final: 0.7827 (p0)
REVERT: A  249 MET cc_start: 0.7407 (ttm) cc_final: 0.6918 (mmt)
REVERT: A  273 ASP cc_start: 0.5863 (t0) cc_final: 0.5612 (p0)
REVERT: A  280 LYS cc_start: 0.7650 (tttt) cc_final: 0.6568 (mptt)
REVERT: S   19 LYS cc_start: 0.6817 (OUTLIER) cc_final: 0.6610 (ttpp)
REVERT: S   34 MET cc_start: 0.8645 (mmm) cc_final: 0.8408 (mmt)
REVERT: S   87 ARG cc_start: 0.7143 (mtp-110) cc_final: 0.6539 (mtm110)
REVERT: S   89 GLU cc_start: 0.7333 (pt0) cc_final: 0.6921 (pp20)
REVERT: S  206 ARG cc_start: 0.8351 (mtp180) cc_final: 0.7684 (ttp-110)
REVERT: S  211 ASP cc_start: 0.7868 (t0) cc_final: 0.7290 (t0)
REVERT: R   80 MET cc_start: 0.5810 (mmt) cc_final: 0.5469 (mmt)
REVERT: R  224 PHE cc_start: 0.6932 (m-80) cc_final: 0.6608 (m-10)
  outliers start: 20
  outliers final: 12
  residues processed: 136
  average time/residue: 0.2160
  time to fit residues: 41.5689
Evaluate side-chains
  118 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 1.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain R residue   54 SER
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  194 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0570
   chunk 51 optimal weight:    0.4980
   chunk 72 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 115 optimal weight:    4.9990
   chunk 102 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
C  16 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9641  Z= 0.158
  Angle     :  0.507   7.894  13049  Z= 0.266
  Chirality :  0.040   0.136   1493
  Planarity :  0.003   0.037   1644
  Dihedral  :  4.517  59.776   1304
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 2.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 14.71 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.44 (0.23), residues: 1193
  helix:  1.94 (0.27), residues: 386
  sheet: -0.26 (0.30), residues: 290
  loop : -2.13 (0.22), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.011   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.003   0.000   ARG A  15 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7371 (m-90) cc_final: 0.7087 (m100)
REVERT: B  234 PHE cc_start: 0.8598 (OUTLIER) cc_final: 0.8237 (m-80)
REVERT: B  254 ASP cc_start: 0.8519 (m-30) cc_final: 0.7761 (p0)
REVERT: C   16 HIS cc_start: 0.5510 (OUTLIER) cc_final: 0.4785 (t-90)
REVERT: A  249 MET cc_start: 0.7357 (ttm) cc_final: 0.6931 (mmt)
REVERT: A  273 ASP cc_start: 0.5856 (t0) cc_final: 0.5599 (p0)
REVERT: A  280 LYS cc_start: 0.7676 (tttt) cc_final: 0.7417 (ptmm)
REVERT: S   87 ARG cc_start: 0.7178 (mtp-110) cc_final: 0.6391 (mtm-85)
REVERT: S   89 GLU cc_start: 0.7332 (pt0) cc_final: 0.6947 (pp20)
REVERT: S  206 ARG cc_start: 0.8374 (mtp180) cc_final: 0.7709 (ttp-110)
REVERT: S  211 ASP cc_start: 0.7909 (t0) cc_final: 0.7343 (t0)
REVERT: R  224 PHE cc_start: 0.7076 (m-80) cc_final: 0.6726 (m-10)
  outliers start: 27
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2150
  time to fit residues: 38.4259
Evaluate side-chains
  122 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 1.071 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   16 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain R residue   54 SER
Chi-restraints excluded: chain R residue   71 PHE
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  194 SER
Chi-restraints excluded: chain R residue  242 VAL
Chi-restraints excluded: chain R residue  276 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0370
   chunk 85 optimal weight:    6.9990
   chunk 47 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 0 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 103 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
B 239 ASN
C  16 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   9641  Z= 0.132
  Angle     :  0.485   8.694  13049  Z= 0.253
  Chirality :  0.039   0.130   1493
  Planarity :  0.003   0.035   1644
  Dihedral  :  4.388  60.055   1304
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.68 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.21 (0.24), residues: 1193
  helix:  2.12 (0.27), residues: 386
  sheet: -0.09 (0.30), residues: 294
  loop : -2.05 (0.23), residues: 513

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP S  47 
 HIS   0.011   0.001   HIS C  16 
 PHE   0.012   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.002   0.000   ARG S  18 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7368 (m-90) cc_final: 0.7105 (m100)
REVERT: B  197 ARG cc_start: 0.7042 (tpp-160) cc_final: 0.6739 (ttm-80)
REVERT: B  234 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.8194 (m-80)
REVERT: B  254 ASP cc_start: 0.8485 (m-30) cc_final: 0.7738 (p0)
REVERT: C   16 HIS cc_start: 0.5563 (OUTLIER) cc_final: 0.4727 (t-90)
REVERT: A  249 MET cc_start: 0.7330 (ttm) cc_final: 0.6944 (mmt)
REVERT: A  273 ASP cc_start: 0.5883 (t0) cc_final: 0.5636 (p0)
REVERT: A  280 LYS cc_start: 0.7658 (tttt) cc_final: 0.7394 (ptmm)
REVERT: S   87 ARG cc_start: 0.7132 (mtp-110) cc_final: 0.6366 (mtm-85)
REVERT: S   89 GLU cc_start: 0.7348 (pt0) cc_final: 0.6972 (pp20)
REVERT: S  206 ARG cc_start: 0.8353 (mtp180) cc_final: 0.7681 (ttp-110)
REVERT: S  211 ASP cc_start: 0.7941 (t0) cc_final: 0.7348 (t0)
REVERT: R  224 PHE cc_start: 0.7103 (m-80) cc_final: 0.6748 (m-10)
  outliers start: 25
  outliers final: 19
  residues processed: 125
  average time/residue: 0.2241
  time to fit residues: 39.7491
Evaluate side-chains
  126 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   70 LEU
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   16 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  219 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  207 LEU
Chi-restraints excluded: chain R residue   71 PHE
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 115 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C  16 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7227
moved from start:          0.3300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9641  Z= 0.184
  Angle     :  0.510   7.807  13049  Z= 0.266
  Chirality :  0.040   0.135   1493
  Planarity :  0.003   0.035   1644
  Dihedral  :  4.433  60.341   1304
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.59 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.15 (0.24), residues: 1193
  helix:  2.15 (0.27), residues: 385
  sheet:  0.04 (0.30), residues: 299
  loop : -2.05 (0.23), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP S  47 
 HIS   0.008   0.001   HIS C  16 
 PHE   0.015   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.002   0.000   ARG R 159 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7378 (m-90) cc_final: 0.7103 (m100)
REVERT: B  197 ARG cc_start: 0.7041 (tpp-160) cc_final: 0.6781 (ttm-80)
REVERT: B  254 ASP cc_start: 0.8524 (m-30) cc_final: 0.7753 (p0)
REVERT: C   16 HIS cc_start: 0.5617 (OUTLIER) cc_final: 0.4701 (t-90)
REVERT: A  249 MET cc_start: 0.7208 (ttm) cc_final: 0.6836 (mmt)
REVERT: A  273 ASP cc_start: 0.5880 (t0) cc_final: 0.5602 (p0)
REVERT: S   19 LYS cc_start: 0.6778 (OUTLIER) cc_final: 0.6567 (ttpp)
REVERT: S   87 ARG cc_start: 0.7125 (mtp-110) cc_final: 0.6332 (mtm-85)
REVERT: S   89 GLU cc_start: 0.7401 (pt0) cc_final: 0.7007 (pp20)
REVERT: S  206 ARG cc_start: 0.8354 (mtp180) cc_final: 0.7702 (ttp-110)
REVERT: S  211 ASP cc_start: 0.7962 (t0) cc_final: 0.7416 (t0)
  outliers start: 30
  outliers final: 19
  residues processed: 126
  average time/residue: 0.2261
  time to fit residues: 39.8881
Evaluate side-chains
  117 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   16 HIS
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  207 LEU
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  194 SER
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 12 optimal weight:    0.1980
   chunk 65 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9980
   chunk 96 optimal weight:    4.9990
   chunk 64 optimal weight:    0.4980
   chunk 114 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
C  16 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.3413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9641  Z= 0.143
  Angle     :  0.486   7.489  13049  Z= 0.254
  Chirality :  0.039   0.131   1493
  Planarity :  0.003   0.035   1644
  Dihedral  :  4.380  61.146   1304
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.88 %
    Favored  : 81.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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: -0.05 (0.24), residues: 1193
  helix:  2.26 (0.27), residues: 385
  sheet:  0.04 (0.31), residues: 294
  loop : -1.97 (0.23), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.011   0.001   HIS C  16 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.002   0.000   ARG R 159 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7371 (m-90) cc_final: 0.7121 (m100)
REVERT: B  197 ARG cc_start: 0.7055 (tpp-160) cc_final: 0.6783 (ttm-80)
REVERT: B  254 ASP cc_start: 0.8485 (m-30) cc_final: 0.7732 (p0)
REVERT: A  249 MET cc_start: 0.7196 (ttm) cc_final: 0.6872 (mmt)
REVERT: A  273 ASP cc_start: 0.5864 (t0) cc_final: 0.5596 (p0)
REVERT: S   19 LYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6553 (ttpp)
REVERT: S   87 ARG cc_start: 0.7088 (mtp-110) cc_final: 0.6310 (mtm-85)
REVERT: S   89 GLU cc_start: 0.7427 (pt0) cc_final: 0.7032 (pp20)
REVERT: S  206 ARG cc_start: 0.8358 (mtp180) cc_final: 0.7680 (ttp-110)
REVERT: S  211 ASP cc_start: 0.8000 (t0) cc_final: 0.7500 (t0)
  outliers start: 32
  outliers final: 26
  residues processed: 124
  average time/residue: 0.2101
  time to fit residues: 37.3327
Evaluate side-chains
  125 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain S residue   19 LYS
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  207 LEU
Chi-restraints excluded: chain R residue   71 PHE
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 10 optimal weight:    0.1980
   chunk 90 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   chunk 109 optimal weight:    0.1980
   chunk 100 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN
C  16 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7201
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9641  Z= 0.139
  Angle     :  0.486   9.410  13049  Z= 0.251
  Chirality :  0.039   0.131   1493
  Planarity :  0.003   0.034   1644
  Dihedral  :  4.305  62.007   1304
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 16.17 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.07 (0.24), residues: 1193
  helix:  2.27 (0.27), residues: 386
  sheet:  0.19 (0.31), residues: 299
  loop : -1.90 (0.23), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.013   0.001   TYR R 125 
 ARG   0.002   0.000   ARG A  15 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7363 (m-90) cc_final: 0.7146 (m100)
REVERT: B  254 ASP cc_start: 0.8457 (m-30) cc_final: 0.7733 (p0)
REVERT: A  249 MET cc_start: 0.7107 (ttm) cc_final: 0.6826 (mmt)
REVERT: A  273 ASP cc_start: 0.5843 (t0) cc_final: 0.5612 (p0)
REVERT: S   87 ARG cc_start: 0.7061 (mtp-110) cc_final: 0.6447 (mtm-85)
REVERT: S   89 GLU cc_start: 0.7446 (pt0) cc_final: 0.7041 (pp20)
REVERT: S  206 ARG cc_start: 0.8363 (mtp180) cc_final: 0.7680 (ttp-110)
REVERT: S  211 ASP cc_start: 0.8026 (t0) cc_final: 0.7545 (t0)
REVERT: R   74 TYR cc_start: 0.4342 (p90) cc_final: 0.3767 (p90)
REVERT: R   80 MET cc_start: 0.5739 (mmt) cc_final: 0.5519 (mmt)
  outliers start: 28
  outliers final: 26
  residues processed: 123
  average time/residue: 0.2118
  time to fit residues: 36.8809
Evaluate side-chains
  126 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 100
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain A residue  287 CYS
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  207 LEU
Chi-restraints excluded: chain R residue   71 PHE
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  191 THR
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 109 optimal weight:    0.2980
   chunk 64 optimal weight:    0.9980
   chunk 46 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 101 optimal weight:    0.0570
   chunk 70 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.6700

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9641  Z= 0.155
  Angle     :  0.501   9.366  13049  Z= 0.260
  Chirality :  0.040   0.168   1493
  Planarity :  0.003   0.034   1644
  Dihedral  :  4.318  62.156   1304
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 16.26 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.06 (0.24), residues: 1193
  helix:  2.25 (0.27), residues: 386
  sheet:  0.19 (0.31), residues: 298
  loop : -1.90 (0.23), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.014   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.002   0.000   ARG R 159 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 1.136 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 TRP cc_start: 0.7346 (m-90) cc_final: 0.7142 (m100)
REVERT: B  254 ASP cc_start: 0.8452 (m-30) cc_final: 0.7727 (p0)
REVERT: A  249 MET cc_start: 0.7112 (ttm) cc_final: 0.6827 (mmt)
REVERT: A  273 ASP cc_start: 0.5826 (t0) cc_final: 0.5599 (p0)
REVERT: S   89 GLU cc_start: 0.7468 (pt0) cc_final: 0.7046 (pp20)
REVERT: S  206 ARG cc_start: 0.8375 (mtp180) cc_final: 0.7698 (ttp-110)
REVERT: S  211 ASP cc_start: 0.8035 (t0) cc_final: 0.7559 (t0)
REVERT: R   74 TYR cc_start: 0.4179 (p90) cc_final: 0.3618 (p90)
REVERT: R   80 MET cc_start: 0.5746 (mmt) cc_final: 0.5512 (mmt)
  outliers start: 30
  outliers final: 25
  residues processed: 127
  average time/residue: 0.2100
  time to fit residues: 38.3272
Evaluate side-chains
  128 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  114 CYS
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  187 VAL
Chi-restraints excluded: chain S residue  207 LEU
Chi-restraints excluded: chain R residue   71 PHE
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    0.2980
   chunk 78 optimal weight:    0.9990
   chunk 118 optimal weight:    1.9990
   chunk 109 optimal weight:    0.0770
   chunk 94 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
B 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   9641  Z= 0.138
  Angle     :  0.488   9.416  13049  Z= 0.253
  Chirality :  0.039   0.144   1493
  Planarity :  0.003   0.034   1644
  Dihedral  :  4.257  62.504   1304
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 17.13 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.13 (0.24), residues: 1193
  helix:  2.27 (0.27), residues: 387
  sheet:  0.25 (0.31), residues: 296
  loop : -1.85 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.013   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.004   0.000   ARG B 304 

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 1.174 
Fit side-chains
   revert: symmetry clash
REVERT: B  254 ASP cc_start: 0.8416 (m-30) cc_final: 0.7730 (p0)
REVERT: A  249 MET cc_start: 0.7044 (ttm) cc_final: 0.6785 (mmt)
REVERT: A  273 ASP cc_start: 0.5793 (t0) cc_final: 0.5565 (p0)
REVERT: S   89 GLU cc_start: 0.7471 (pt0) cc_final: 0.7051 (pp20)
REVERT: S  206 ARG cc_start: 0.8383 (mtp180) cc_final: 0.7707 (ttp-110)
REVERT: S  211 ASP cc_start: 0.8044 (t0) cc_final: 0.7558 (t0)
REVERT: R   74 TYR cc_start: 0.4046 (p90) cc_final: 0.3426 (p90)
REVERT: R   80 MET cc_start: 0.5813 (mmt) cc_final: 0.5530 (mmt)
  outliers start: 23
  outliers final: 23
  residues processed: 117
  average time/residue: 0.2041
  time to fit residues: 34.2630
Evaluate side-chains
  123 residues out of total 1044 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 1.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  118 ASP
Chi-restraints excluded: chain B residue  189 SER
Chi-restraints excluded: chain B residue  228 ASP
Chi-restraints excluded: chain B residue  323 ASP
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   60 VAL
Chi-restraints excluded: chain Y residue   19 LEU
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  262 ASP
Chi-restraints excluded: chain S residue   78 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  143 VAL
Chi-restraints excluded: chain S residue  144 SER
Chi-restraints excluded: chain S residue  154 LEU
Chi-restraints excluded: chain S residue  181 SER
Chi-restraints excluded: chain S residue  183 LEU
Chi-restraints excluded: chain S residue  207 LEU
Chi-restraints excluded: chain R residue   71 PHE
Chi-restraints excluded: chain R residue  151 THR
Chi-restraints excluded: chain R residue  161 LEU
Chi-restraints excluded: chain R residue  183 PHE
Chi-restraints excluded: chain R residue  242 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 87 optimal weight:    0.0980
   chunk 13 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0870
   chunk 5 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8362

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

Flipped N/Q/H residues before XYZ refinement:
R 192 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.142808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.119623 restraints weight = 13476.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3397 rms_B_bonded: 2.22
r_work: 0.3201 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9641  Z= 0.181
  Angle     :  0.530   9.126  13049  Z= 0.273
  Chirality :  0.040   0.170   1493
  Planarity :  0.003   0.034   1644
  Dihedral  :  4.383  62.334   1304
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 16.65 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    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:  0.03 (0.24), residues: 1193
  helix:  2.18 (0.27), residues: 387
  sheet:  0.19 (0.31), residues: 296
  loop : -1.89 (0.23), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP S  47 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.016   0.001   PHE B 292 
 TYR   0.014   0.001   TYR R 125 
 ARG   0.002   0.000   ARG R 159 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2396.01 seconds
wall clock time: 44 minutes 25.24 seconds (2665.24 seconds total)