Starting phenix.real_space_refine (version: dev)
on Fri Feb 17 05:01:36 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/02_2023/7u12_26275.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/02_2023/7u12_26275.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/02_2023/7u12_26275.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/02_2023/7u12_26275.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/02_2023/7u12_26275.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u12_26275/02_2023/7u12_26275.pdb"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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
-------------------------------------------------------------------------------
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=   0.002
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
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  211": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 3456
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "B"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "C"
      Number of atoms: 1096
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
      Conformer: "B"
        Number of residues, atoms: 135, 1087
          Classifications: {'peptide': 135}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 132}
          bond proxies already assigned to first conformer: 1094
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.86, per 1000 atoms: 1.12
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (98.808, 118.14, 32.22, 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      21     16.00
     O     702      8.00
     N     531      7.00
     C    2202      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 214 " - pdb=" SG  CYS A 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 214 " - pdb=" SG  CYS B 253 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " 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
  Links applied
    NAG-ASN
      " NAG A 301 " - " ASN A 183 "
      " NAG A 302 " - " ASN A 151 "
      " NAG A 303 " - " ASN A 145 "
      " NAG A 304 " - " ASN A 164 "
      " NAG B 301 " - " ASN B 183 "
      " NAG B 302 " - " ASN B 151 "
      " NAG B 303 " - " ASN B 145 "
      " NAG B 304 " - " ASN B 164 "
      " NAG C 301 " - " ASN C 183 "
      " NAG C 302 " - " ASN C 151 "
      " NAG C 303 " - " ASN C 145 "
      " NAG C 304 " - " ASN C 164 "
  Time building additional restraints: 1.39
  Conformation dependent library (CDL) restraints added in 880.6 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  786

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 12 sheets defined
      0.0% alpha, 64.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.22
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125
      removed outlier: 6.633A  pdb=" N   VAL A 123 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL B 123 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 137
      removed outlier: 9.036A  pdb=" N   SER A 130 " --> pdb=" O   ALA B 131 " (cutoff:3.500A)
      removed outlier: 9.415A  pdb=" N   VAL B 133 " --> pdb=" O   SER A 130 " (cutoff:3.500A)
      removed outlier: 5.743A  pdb=" N   TYR A 132 " --> pdb=" O   VAL B 133 " (cutoff:3.500A)
      removed outlier: 8.246A  pdb=" N   TYR B 135 " --> pdb=" O   TYR A 132 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   SER A 134 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 7.179A  pdb=" N   VAL B 137 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 6.462A  pdb=" N   ASP A 136 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
      removed outlier: 9.051A  pdb=" N   SER B 130 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
      removed outlier: 9.429A  pdb=" N   VAL C 133 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 5.751A  pdb=" N   TYR B 132 " --> pdb=" O   VAL C 133 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   TYR C 135 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   SER B 134 " --> pdb=" O   TYR C 135 " (cutoff:3.500A)
      removed outlier: 7.168A  pdb=" N   VAL C 137 " --> pdb=" O   SER B 134 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   ASP B 136 " --> pdb=" O   VAL C 137 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 165
      removed outlier: 5.950A  pdb=" N   ILE A 142 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   ASN B 145 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   LEU A 144 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   THR B 147 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
      removed outlier: 8.959A  pdb=" N   ILE A 146 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 10.049A  pdb=" N   THR B 149 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   ASN A 148 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 10.327A  pdb=" N   ASN B 151 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 9.030A  pdb=" N   LEU A 150 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 10.440A  pdb=" N   THR B 153 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
      removed outlier: 9.238A  pdb=" N   ILE A 152 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 9.988A  pdb=" N   ASN B 155 " --> pdb=" O   ILE A 152 " (cutoff:3.500A)
      removed outlier: 8.994A  pdb=" N   ASN A 154 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 10.600A  pdb=" N   TYR B 157 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
      removed outlier: 9.047A  pdb=" N   ASN A 156 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 9.896A  pdb=" N   SER B 159 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
      removed outlier: 9.371A  pdb=" N   TYR A 158 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 10.388A  pdb=" N   GLU B 161 " --> pdb=" O   TYR A 158 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL A 160 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 8.863A  pdb=" N   GLU B 163 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.603A  pdb=" N   VAL A 162 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 7.865A  pdb=" N   ILE B 165 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   ASN A 164 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   ILE B 142 " --> pdb=" O   TYR C 143 " (cutoff:3.500A)
      removed outlier: 7.466A  pdb=" N   ASN C 145 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 8.854A  pdb=" N   LEU B 144 " --> pdb=" O   ASN C 145 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   THR C 147 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 8.955A  pdb=" N   ILE B 146 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
      removed outlier: 10.033A  pdb=" N   THR C 149 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 9.073A  pdb=" N   ASN B 148 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 10.295A  pdb=" N   ASN C 151 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 8.990A  pdb=" N   LEU B 150 " --> pdb=" O   ASN C 151 " (cutoff:3.500A)
      removed outlier: 10.398A  pdb=" N   THR C 153 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 9.193A  pdb=" N   ILE B 152 " --> pdb=" O   THR C 153 " (cutoff:3.500A)
      removed outlier: 9.935A  pdb=" N   ASN C 155 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   ASN B 154 " --> pdb=" O   ASN C 155 " (cutoff:3.500A)
      removed outlier: 10.542A  pdb=" N   TYR C 157 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 8.981A  pdb=" N   ASN B 156 " --> pdb=" O   TYR C 157 " (cutoff:3.500A)
      removed outlier: 9.830A  pdb=" N   SER C 159 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 9.306A  pdb=" N   TYR B 158 " --> pdb=" O   SER C 159 " (cutoff:3.500A)
      removed outlier: 10.323A  pdb=" N   GLU C 161 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   VAL B 160 " --> pdb=" O   GLU C 161 " (cutoff:3.500A)
      removed outlier: 8.808A  pdb=" N   GLU C 163 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   VAL B 162 " --> pdb=" O   GLU C 163 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ILE C 165 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   ASN B 164 " --> pdb=" O   ILE C 165 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 168 through 177
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.575A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   ARG B 180 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 187
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 8.946A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 8.856A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 7.754A  pdb=" N   TYR B 197 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ASP A 196 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 8.938A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 8.865A  pdb=" N   ILE C 195 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   GLN B 194 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   TYR C 197 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   ASP B 196 " --> pdb=" O   TYR C 197 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 201 through 203
      removed outlier: 6.452A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   VAL B 202 " --> pdb=" O   ILE C 203 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 209 through 219
      removed outlier: 6.952A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.051A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.049A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.059A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   PHE C 213 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 222 through 228
      removed outlier: 6.991A  pdb=" N   HIS A 222 " --> pdb=" O   ASN B 223 " (cutoff:3.500A)
      removed outlier: 8.988A  pdb=" N   VAL B 225 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   ILE A 224 " --> pdb=" O   VAL B 225 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   MET B 227 " --> pdb=" O   ILE A 224 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   LEU A 226 " --> pdb=" O   MET B 227 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   HIS B 222 " --> pdb=" O   ASN C 223 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   VAL C 225 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
      removed outlier: 6.487A  pdb=" N   ILE B 224 " --> pdb=" O   VAL C 225 " (cutoff:3.500A)
      removed outlier: 7.729A  pdb=" N   MET C 227 " --> pdb=" O   ILE B 224 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   LEU B 226 " --> pdb=" O   MET C 227 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.422A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 8.240A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.355A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.148A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.023A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   THR B 234 " --> pdb=" O   THR C 235 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   PHE C 237 " --> pdb=" O   THR B 234 " (cutoff:3.500A)
      removed outlier: 6.780A  pdb=" N   TYR B 236 " --> pdb=" O   PHE C 237 " (cutoff:3.500A)
      removed outlier: 8.243A  pdb=" N   HIS C 239 " --> pdb=" O   TYR B 236 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   GLY B 238 " --> pdb=" O   HIS C 239 " (cutoff:3.500A)
      removed outlier: 8.339A  pdb=" N   GLU C 241 " --> pdb=" O   GLY B 238 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   SER B 240 " --> pdb=" O   GLU C 241 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ILE C 243 " --> pdb=" O   SER B 240 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   GLN B 242 " --> pdb=" O   ILE C 243 " (cutoff:3.500A)
      removed outlier: 8.022A  pdb=" N   GLN C 245 " --> pdb=" O   GLN B 242 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   SER B 244 " --> pdb=" O   GLN C 245 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'A' and resid 251 through 253
      removed outlier: 6.309A  pdb=" N   VAL A 251 " --> pdb=" O   ASP B 252 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   VAL B 251 " --> pdb=" O   ASP C 252 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    36 hydrogen bonds defined for protein.
    108 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: 0.84

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1051
        1.34 -     1.46: 685
        1.46 -     1.57: 1741
        1.57 -     1.69: 3
        1.69 -     1.81: 36
  Bond restraints: 3516
  Sorted by residual:
  bond pdb=" CG  PRO C 189 "
       pdb=" CD  PRO C 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.253  0.250 3.40e-02 8.65e+02 5.40e+01
  bond pdb=" CG  PRO A 189 "
       pdb=" CD  PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.253  0.250 3.40e-02 8.65e+02 5.39e+01
  bond pdb=" CG  PRO B 189 "
       pdb=" CD  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.255  0.248 3.40e-02 8.65e+02 5.34e+01
  bond pdb=" CB  PRO B 189 "
       pdb=" CG  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.669 -0.177 5.00e-02 4.00e+02 1.26e+01
  bond pdb=" CB  PRO C 189 "
       pdb=" CG  PRO C 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.669 -0.177 5.00e-02 4.00e+02 1.25e+01
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
       89.32 -    97.76: 6
       97.76 -   106.19: 56
      106.19 -   114.63: 2146
      114.63 -   123.07: 2200
      123.07 -   131.51: 380
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" N   PRO C 189 "
        pdb=" CD  PRO C 189 "
        pdb=" CG  PRO C 189 "
      ideal   model   delta    sigma   weight residual
     103.20   89.32   13.88 1.50e+00 4.44e-01 8.56e+01
  angle pdb=" N   PRO A 189 "
        pdb=" CD  PRO A 189 "
        pdb=" CG  PRO A 189 "
      ideal   model   delta    sigma   weight residual
     103.20   89.34   13.86 1.50e+00 4.44e-01 8.53e+01
  angle pdb=" N   PRO B 189 "
        pdb=" CD  PRO B 189 "
        pdb=" CG  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     103.20   89.37   13.83 1.50e+00 4.44e-01 8.50e+01
  angle pdb=" N   PHE A 171 "
        pdb=" CA  PHE A 171 "
        pdb=" C   PHE A 171 "
      ideal   model   delta    sigma   weight residual
     108.96  115.81   -6.85 1.49e+00 4.50e-01 2.12e+01
  angle pdb=" N   PHE B 171 "
        pdb=" CA  PHE B 171 "
        pdb=" C   PHE B 171 "
      ideal   model   delta    sigma   weight residual
     108.96  115.78   -6.82 1.49e+00 4.50e-01 2.10e+01
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 1821
       16.69 -    33.37: 171
       33.37 -    50.06: 73
       50.06 -    66.74: 17
       66.74 -    83.43: 9
  Dihedral angle restraints: 2091
    sinusoidal: 858
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" CB  CYS B 214 "
           pdb=" SG  CYS B 214 "
           pdb=" SG  CYS B 253 "
           pdb=" CB  CYS B 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   30.37   62.63     1      1.00e+01 1.00e-02 5.19e+01
  dihedral pdb=" CB  CYS C 214 "
           pdb=" SG  CYS C 214 "
           pdb=" SG  CYS C 253 "
           pdb=" CB  CYS C 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   30.37   62.63     1      1.00e+01 1.00e-02 5.19e+01
  dihedral pdb=" CB  CYS A 214 "
           pdb=" SG  CYS A 214 "
           pdb=" SG  CYS A 253 "
           pdb=" CB  CYS A 253 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   30.42   62.58     1      1.00e+01 1.00e-02 5.18e+01
  ... (remaining 2088 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 486
       0.081 -    0.162: 99
       0.162 -    0.243: 15
       0.243 -    0.324: 3
       0.324 -    0.405: 3
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CG  LEU A 226 "
            pdb=" CB  LEU A 226 "
            pdb=" CD1 LEU A 226 "
            pdb=" CD2 LEU A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.18   -0.41 2.00e-01 2.50e+01 4.11e+00
  chirality pdb=" CG  LEU B 226 "
            pdb=" CB  LEU B 226 "
            pdb=" CD1 LEU B 226 "
            pdb=" CD2 LEU B 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.40 2.00e-01 2.50e+01 4.06e+00
  chirality pdb=" CG  LEU C 226 "
            pdb=" CB  LEU C 226 "
            pdb=" CD1 LEU C 226 "
            pdb=" CD2 LEU C 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.19   -0.39 2.00e-01 2.50e+01 3.90e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 125 "   -0.004 2.00e-02 2.50e+03   2.41e-02 1.16e+01
        pdb=" CG  TYR A 125 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 125 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 125 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 125 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 125 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 125 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 125 "   -0.005 2.00e-02 2.50e+03   2.41e-02 1.16e+01
        pdb=" CG  TYR C 125 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 125 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 125 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 125 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 125 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 125 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 125 "   -0.004 2.00e-02 2.50e+03   2.39e-02 1.15e+01
        pdb=" CG  TYR B 125 "    0.049 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 125 "   -0.040 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 125 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 125 "    0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 125 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 125 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 125 "    0.007 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 86
        2.71 -     3.26: 3290
        3.26 -     3.80: 5387
        3.80 -     4.35: 6630
        4.35 -     4.90: 12470
  Nonbonded interactions: 27863
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 215 "
            pdb=" OD1 ASP B 212 "
     model   vdw
     2.160 2.440
  nonbonded pdb=" OG1 THR B 215 "
            pdb=" OD1 ASP C 212 "
     model   vdw
     2.214 2.440
  nonbonded pdb=" NZ  LYS A 129 "
            pdb=" OD2 ASP A 136 "
     model   vdw
     2.277 2.520
  nonbonded pdb=" NZ  LYS C 129 "
            pdb=" OD2 ASP C 136 "
     model   vdw
     2.279 2.520
  nonbonded pdb=" NZ  LYS B 129 "
            pdb=" OD2 ASP B 136 "
     model   vdw
     2.279 2.520
  ... (remaining 27858 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'B' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
  selection = (chain 'C' and (resid 120 through 210 or resid 212 through 254 or resid 301 thro \ 
ugh 304))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    2202      2.51       5
     N     531      2.21       5
     O     702      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             0.800
  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:          4.180
  Check model and map are aligned:         0.050
  Process input model:                     16.060
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Set scattering table:                    0.040
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4488
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      :  0.011   0.250   3516  Z= 0.729
  Angle     :  1.019  13.880   4788  Z= 0.600
  Chirality :  0.071   0.405    606
  Planarity :  0.008   0.081    579
  Dihedral  : 16.791  83.426   1296
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer Outliers :  5.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.37), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.28 (0.28), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 109
  time to evaluate  : 0.412 
Fit side-chains
  outliers start: 21
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1539
  time to fit residues: 21.2946
Evaluate side-chains
  71 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.404 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5582
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 19 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    6.9990
   chunk 22 optimal weight:    9.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 222 HIS
A 245 GLN
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5092
moved from start:          0.5594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.059   3516  Z= 0.315
  Angle     :  0.817   8.506   4788  Z= 0.441
  Chirality :  0.060   0.410    606
  Planarity :  0.005   0.037    579
  Dihedral  :  6.514  25.761    531
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer Outliers :  3.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.34), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.26), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 101
  time to evaluate  : 0.348 
Fit side-chains
  outliers start: 13
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1104
  time to fit residues: 14.9040
Evaluate side-chains
  86 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 76
  time to evaluate  : 0.352 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0770
  time to fit residues: 1.4999
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 28 optimal weight:    5.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    2.8988

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5227
moved from start:          0.6662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3516  Z= 0.255
  Angle     :  0.713   6.895   4788  Z= 0.383
  Chirality :  0.057   0.355    606
  Planarity :  0.003   0.027    579
  Dihedral  :  5.834  20.154    531
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer Outliers :  2.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.53 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.380 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 91
  average time/residue: 0.0937
  time to fit residues: 11.7065
Evaluate side-chains
  85 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 78
  time to evaluate  : 0.381 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0371
  time to fit residues: 1.0532
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 18 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 33 optimal weight:    9.9990
   chunk 10 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 21 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 222 HIS
C 222 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5363
moved from start:          0.7889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3516  Z= 0.280
  Angle     :  0.742   7.179   4788  Z= 0.405
  Chirality :  0.060   0.410    606
  Planarity :  0.003   0.022    579
  Dihedral  :  6.121  20.230    531
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 15.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer Outliers :  2.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.45 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.62 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.369 
Fit side-chains
  outliers start: 11
  outliers final: 8
  residues processed: 88
  average time/residue: 0.0895
  time to fit residues: 10.8461
Evaluate side-chains
  85 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.417 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.0350
  time to fit residues: 1.0821
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 15 optimal weight:    5.9990
   chunk 32 optimal weight:    6.9990
   chunk 26 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 9 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5350
moved from start:          0.8658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3516  Z= 0.251
  Angle     :  0.696   7.625   4788  Z= 0.376
  Chirality :  0.058   0.390    606
  Planarity :  0.003   0.021    579
  Dihedral  :  5.903  19.450    531
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 15.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer Outliers :  1.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.49 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.65 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.394 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 89
  average time/residue: 0.0941
  time to fit residues: 11.3933
Evaluate side-chains
  80 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 78
  time to evaluate  : 0.398 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0419
  time to fit residues: 0.6859
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    9.9990
   chunk 31 optimal weight:   20.0000
   chunk 17 optimal weight:    0.9990
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    3.9990
   chunk 19 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 21 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   overall best weight:    3.1588

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5373
moved from start:          0.9181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3516  Z= 0.257
  Angle     :  0.705   6.815   4788  Z= 0.382
  Chirality :  0.058   0.395    606
  Planarity :  0.003   0.021    579
  Dihedral  :  5.855  18.365    531
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer Outliers :  2.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.58 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.72 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.321 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 89
  average time/residue: 0.0937
  time to fit residues: 11.4197
Evaluate side-chains
  85 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.425 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0375
  time to fit residues: 0.9790
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 37 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 15 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 25 optimal weight:    0.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5330
moved from start:          0.9502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3516  Z= 0.227
  Angle     :  0.680   6.390   4788  Z= 0.367
  Chirality :  0.057   0.347    606
  Planarity :  0.003   0.020    579
  Dihedral  :  5.608  16.922    531
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer Outliers :  1.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.74 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.379 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 87
  average time/residue: 0.0944
  time to fit residues: 11.2168
Evaluate side-chains
  82 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.406 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0350
  time to fit residues: 0.8738
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9990
   chunk 34 optimal weight:    7.9990
   chunk 36 optimal weight:    7.9990
   chunk 32 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:   20.0000
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:   20.0000
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5387
moved from start:          0.9978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3516  Z= 0.257
  Angle     :  0.727   6.976   4788  Z= 0.389
  Chirality :  0.058   0.374    606
  Planarity :  0.003   0.019    579
  Dihedral  :  5.742  17.265    531
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer Outliers :  1.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.74 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.85 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.450 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 2
  residues processed: 86
  average time/residue: 0.0923
  time to fit residues: 10.8622
Evaluate side-chains
  84 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.375 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0358
  time to fit residues: 0.6441
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 34 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 22 optimal weight:    7.9990
   chunk 17 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5440
moved from start:          1.0633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3516  Z= 0.269
  Angle     :  0.760  10.533   4788  Z= 0.404
  Chirality :  0.059   0.387    606
  Planarity :  0.003   0.019    579
  Dihedral  :  5.920  18.121    531
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.77 %
    Favored  : 90.23 %
  Rotamer Outliers :  0.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.95 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.397 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 81
  average time/residue: 0.1023
  time to fit residues: 11.1078
Evaluate side-chains
  79 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.366 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0415
  time to fit residues: 0.6753
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 28 optimal weight:    0.0470
   chunk 4 optimal weight:    0.9990
   chunk 8 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   overall best weight:    1.0284

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5314
moved from start:          1.0599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3516  Z= 0.198
  Angle     :  0.714  13.508   4788  Z= 0.371
  Chirality :  0.057   0.307    606
  Planarity :  0.003   0.020    579
  Dihedral  :  5.542  16.126    531
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer Outliers :  0.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.90 (0.27), residues: 402

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 91
  time to evaluate  : 0.411 
Fit side-chains
  outliers start: 2
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1124
  time to fit residues: 13.3940
Evaluate side-chains
  81 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.542 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.5849
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:   20.0000
   chunk 1 optimal weight:   20.0000
   chunk 22 optimal weight:    0.3980
   chunk 35 optimal weight:    7.9990
   chunk 20 optimal weight:    9.9990
   chunk 26 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    6.9990
   overall best weight:    4.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** 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 = 0.5378 r_free = 0.5378 target = 0.300273 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.5623 r_free = 0.5623 target = 0.261053 restraints weight = 21172.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.5588 r_free = 0.5588 target = 0.264102 restraints weight = 8762.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.5594 r_free = 0.5594 target = 0.264756 restraints weight = 5236.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.5304
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5378
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5378 r_free = 0.5378    target_work(ls_wunit_k1) = 0.300         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5368 r_free = 0.5368    target_work(ls_wunit_k1) = 0.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.5368
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5704
moved from start:          1.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.042   3516  Z= 0.302
  Angle     :  0.845  12.208   4788  Z= 0.442
  Chirality :  0.060   0.371    606
  Planarity :  0.003   0.021    579
  Dihedral  :  5.787  17.387    531
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer Outliers :  0.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.89 (0.35), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.96 (0.27), residues: 402

===============================================================================
Job complete
usr+sys time: 1076.91 seconds
wall clock time: 20 minutes 21.56 seconds (1221.56 seconds total)