Starting phenix.real_space_refine
on Thu Dec  7 18:27:09 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/12_2023/7u13_26276.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/12_2023/7u13_26276.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/12_2023/7u13_26276.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/12_2023/7u13_26276.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/12_2023/7u13_26276.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u13_26276/12_2023/7u13_26276.pdb"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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      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.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU  241": "OE1" <-> "OE2"
    Residue "B GLU  241": "OE1" <-> "OE2"
    Residue "C GLU  241": "OE1" <-> "OE2"
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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 dihedrals: 12
          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 dihedrals: 12
          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 dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.90, per 1000 atoms: 1.13
  Number of scatterers: 3456
  At special positions: 0
  Unit cell: (97.734, 117.066, 31.146, 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=2.03
    Simple disulfide: pdb=" SG  CYS C 214 " - pdb=" SG  CYS C 253 " distance=2.03

  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: 1.36
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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, 68.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 122 through 125
    Processing sheet with id=AA2, first strand: chain 'A' and resid 129 through 131
      removed outlier: 6.322A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 129 through 131
      removed outlier: 6.322A  pdb=" N   LYS A 129 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TYR B 132 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 9.062A  pdb=" N   ALA A 131 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 6.166A  pdb=" N   SER B 134 " --> pdb=" O   ALA A 131 " (cutoff:3.500A)
      removed outlier: 6.990A  pdb=" N   SER B 130 " --> pdb=" O   LYS C 129 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ALA C 131 " --> pdb=" O   SER B 130 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   TYR B 132 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 177
      removed outlier: 9.050A  pdb=" N   THR A 141 " --> pdb=" O   ILE B 142 " (cutoff:3.500A)
      removed outlier: 9.031A  pdb=" N   LEU B 144 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   TYR A 143 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
      removed outlier: 9.078A  pdb=" N   ILE B 146 " --> pdb=" O   TYR A 143 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ASN A 145 " --> pdb=" O   ILE B 146 " (cutoff:3.500A)
      removed outlier: 7.892A  pdb=" N   ASN B 148 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   THR A 147 " --> pdb=" O   ASN B 148 " (cutoff:3.500A)
      removed outlier: 7.891A  pdb=" N   LEU B 150 " --> pdb=" O   THR A 147 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   THR A 149 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)
      removed outlier: 8.170A  pdb=" N   ILE B 152 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   ASN A 151 " --> pdb=" O   ILE B 152 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ASN B 154 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   THR A 153 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      removed outlier: 7.627A  pdb=" N   ASN B 156 " --> pdb=" O   THR A 153 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ASN A 155 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   TYR B 158 " --> pdb=" O   ASN A 155 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   TYR A 157 " --> pdb=" O   TYR B 158 " (cutoff:3.500A)
      removed outlier: 7.718A  pdb=" N   VAL B 160 " --> pdb=" O   TYR A 157 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   SER A 159 " --> pdb=" O   VAL B 160 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   VAL B 162 " --> pdb=" O   SER A 159 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   GLU A 161 " --> pdb=" O   VAL B 162 " (cutoff:3.500A)
      removed outlier: 9.930A  pdb=" N   ASN B 164 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
      removed outlier: 9.474A  pdb=" N   GLU A 163 " --> pdb=" O   ASN B 164 " (cutoff:3.500A)
      removed outlier: 10.042A  pdb=" N   THR B 166 " --> pdb=" O   GLU A 163 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ILE A 165 " --> pdb=" O   THR B 166 " (cutoff:3.500A)
      removed outlier: 8.407A  pdb=" N   GLN B 168 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ALA A 167 " --> pdb=" O   GLN B 168 " (cutoff:3.500A)
      removed outlier: 7.917A  pdb=" N   GLN B 170 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   VAL A 169 " --> pdb=" O   GLN B 170 " (cutoff:3.500A)
      removed outlier: 7.997A  pdb=" N   SER B 172 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   PHE A 171 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 8.292A  pdb=" N   THR B 174 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   LYS A 173 " --> pdb=" O   THR B 174 " (cutoff:3.500A)
      removed outlier: 8.266A  pdb=" N   ILE B 176 " --> pdb=" O   LYS A 173 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   VAL A 175 " --> pdb=" O   ILE B 176 " (cutoff:3.500A)
      removed outlier: 9.093A  pdb=" N   THR B 141 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 9.071A  pdb=" N   LEU C 144 " --> pdb=" O   THR B 141 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   TYR B 143 " --> pdb=" O   LEU C 144 " (cutoff:3.500A)
      removed outlier: 9.097A  pdb=" N   ILE C 146 " --> pdb=" O   TYR B 143 " (cutoff:3.500A)
      removed outlier: 6.729A  pdb=" N   ASN B 145 " --> pdb=" O   ILE C 146 " (cutoff:3.500A)
      removed outlier: 7.889A  pdb=" N   ASN C 148 " --> pdb=" O   ASN B 145 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR B 147 " --> pdb=" O   ASN C 148 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   LEU C 150 " --> pdb=" O   THR B 147 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   THR B 149 " --> pdb=" O   LEU C 150 " (cutoff:3.500A)
      removed outlier: 8.145A  pdb=" N   ILE C 152 " --> pdb=" O   THR B 149 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   ASN B 151 " --> pdb=" O   ILE C 152 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   ASN C 154 " --> pdb=" O   ASN B 151 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   THR B 153 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   ASN C 156 " --> pdb=" O   THR B 153 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ASN B 155 " --> pdb=" O   ASN C 156 " (cutoff:3.500A)
      removed outlier: 7.944A  pdb=" N   TYR C 158 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TYR B 157 " --> pdb=" O   TYR C 158 " (cutoff:3.500A)
      removed outlier: 7.666A  pdb=" N   VAL C 160 " --> pdb=" O   TYR B 157 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   SER B 159 " --> pdb=" O   VAL C 160 " (cutoff:3.500A)
      removed outlier: 5.971A  pdb=" N   VAL C 162 " --> pdb=" O   SER B 159 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   GLU B 161 " --> pdb=" O   VAL C 162 " (cutoff:3.500A)
      removed outlier: 9.877A  pdb=" N   ASN C 164 " --> pdb=" O   GLU B 161 " (cutoff:3.500A)
      removed outlier: 9.408A  pdb=" N   GLU B 163 " --> pdb=" O   ASN C 164 " (cutoff:3.500A)
      removed outlier: 9.975A  pdb=" N   THR C 166 " --> pdb=" O   GLU B 163 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ILE B 165 " --> pdb=" O   THR C 166 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   GLN C 168 " --> pdb=" O   ILE B 165 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   ALA B 167 " --> pdb=" O   GLN C 168 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   GLN C 170 " --> pdb=" O   ALA B 167 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   VAL B 169 " --> pdb=" O   GLN C 170 " (cutoff:3.500A)
      removed outlier: 7.950A  pdb=" N   SER C 172 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   PHE B 171 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 8.242A  pdb=" N   THR C 174 " --> pdb=" O   PHE B 171 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   LYS B 173 " --> pdb=" O   THR C 174 " (cutoff:3.500A)
      removed outlier: 8.215A  pdb=" N   ILE C 176 " --> pdb=" O   LYS B 173 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   VAL B 175 " --> pdb=" O   ILE C 176 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 181
      removed outlier: 6.630A  pdb=" N   ARG A 180 " --> pdb=" O   LEU B 181 " (cutoff:3.500A)
      removed outlier: 6.626A  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
      removed outlier: 6.458A  pdb=" N   THR A 185 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   THR B 185 " --> pdb=" O   ILE C 186 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 198
      removed outlier: 8.929A  pdb=" N   MET A 192 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
      removed outlier: 9.771A  pdb=" N   ILE B 195 " --> pdb=" O   MET A 192 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   GLN A 194 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
      removed outlier: 8.430A  pdb=" N   TYR B 197 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   ASP A 196 " --> pdb=" O   TYR B 197 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   MET B 192 " --> pdb=" O   LYS C 193 " (cutoff:3.500A)
      removed outlier: 9.784A  pdb=" N   ILE C 195 " --> pdb=" O   MET B 192 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   GLN B 194 " --> pdb=" O   ILE C 195 " (cutoff:3.500A)
      removed outlier: 8.464A  pdb=" N   TYR C 197 " --> pdb=" O   GLN B 194 " (cutoff:3.500A)
      removed outlier: 6.397A  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: 6.278A  pdb=" N   VAL A 202 " --> pdb=" O   ILE B 203 " (cutoff:3.500A)
      removed outlier: 6.327A  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: 6.960A  pdb=" N   MET A 210 " --> pdb=" O   TYR B 209 " (cutoff:3.500A)
      removed outlier: 6.954A  pdb=" N   TYR B 211 " --> pdb=" O   MET A 210 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   ASP A 212 " --> pdb=" O   TYR B 211 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   PHE B 213 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   MET B 210 " --> pdb=" O   TYR C 209 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   TYR C 211 " --> pdb=" O   MET B 210 " (cutoff:3.500A)
      removed outlier: 7.052A  pdb=" N   ASP B 212 " --> pdb=" O   TYR C 211 " (cutoff:3.500A)
      removed outlier: 7.018A  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: 6.853A  pdb=" N   ASN B 223 " --> pdb=" O   HIS A 222 " (cutoff:3.500A)
      removed outlier: 6.873A  pdb=" N   ASN C 223 " --> pdb=" O   HIS B 222 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 233 through 245
      removed outlier: 6.470A  pdb=" N   THR A 234 " --> pdb=" O   THR B 235 " (cutoff:3.500A)
      removed outlier: 8.461A  pdb=" N   PHE B 237 " --> pdb=" O   THR A 234 " (cutoff:3.500A)
      removed outlier: 6.808A  pdb=" N   TYR A 236 " --> pdb=" O   PHE B 237 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   HIS B 239 " --> pdb=" O   TYR A 236 " (cutoff:3.500A)
      removed outlier: 6.643A  pdb=" N   GLY A 238 " --> pdb=" O   HIS B 239 " (cutoff:3.500A)
      removed outlier: 8.398A  pdb=" N   GLU B 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   SER A 240 " --> pdb=" O   GLU B 241 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   ILE B 243 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   GLN A 242 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   GLN B 245 " --> pdb=" O   GLN A 242 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   SER A 244 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 249 through 253
      removed outlier: 6.871A  pdb=" N   TYR B 250 " --> pdb=" O   GLN A 249 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   TYR C 250 " --> pdb=" O   GLN B 249 " (cutoff:3.500A)

    53 hydrogen bonds defined for protein.
    156 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: 0.85

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.06 -     1.21: 9
        1.21 -     1.36: 1059
        1.36 -     1.51: 1090
        1.51 -     1.66: 1322
        1.66 -     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  1.173  0.330 3.40e-02 8.65e+02 9.43e+01
  bond pdb=" CG  PRO B 189 "
       pdb=" CD  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.173  0.330 3.40e-02 8.65e+02 9.40e+01
  bond pdb=" CG  PRO A 189 "
       pdb=" CD  PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.503  1.174  0.329 3.40e-02 8.65e+02 9.35e+01
  bond pdb=" CB  PRO A 189 "
       pdb=" CG  PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.063  0.429 5.00e-02 4.00e+02 7.38e+01
  bond pdb=" CB  PRO B 189 "
       pdb=" CG  PRO B 189 "
    ideal  model  delta    sigma   weight residual
    1.492  1.063  0.429 5.00e-02 4.00e+02 7.38e+01
  ... (remaining 3511 not shown)

  Histogram of bond angle deviations from ideal:
       73.84 -    95.06: 6
       95.06 -   116.29: 2463
      116.29 -   137.51: 2316
      137.51 -   158.73: 0
      158.73 -   179.96: 3
  Bond angle restraints: 4788
  Sorted by residual:
  angle pdb=" CB  PRO A 189 "
        pdb=" CG  PRO A 189 "
        pdb=" CD  PRO A 189 "
      ideal   model   delta    sigma   weight residual
     106.10  179.96  -73.86 3.20e+00 9.77e-02 5.33e+02
  angle pdb=" CB  PRO B 189 "
        pdb=" CG  PRO B 189 "
        pdb=" CD  PRO B 189 "
      ideal   model   delta    sigma   weight residual
     106.10  179.92  -73.82 3.20e+00 9.77e-02 5.32e+02
  angle pdb=" CB  PRO C 189 "
        pdb=" CG  PRO C 189 "
        pdb=" CD  PRO C 189 "
      ideal   model   delta    sigma   weight residual
     106.10  179.89  -73.79 3.20e+00 9.77e-02 5.32e+02
  angle pdb=" N   PRO A 189 "
        pdb=" CD  PRO A 189 "
        pdb=" CG  PRO A 189 "
      ideal   model   delta    sigma   weight residual
     103.20   73.84   29.36 1.50e+00 4.44e-01 3.83e+02
  angle pdb=" N   PRO C 189 "
        pdb=" CD  PRO C 189 "
        pdb=" CG  PRO C 189 "
      ideal   model   delta    sigma   weight residual
     103.20   73.95   29.25 1.50e+00 4.44e-01 3.80e+02
  ... (remaining 4783 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.07: 2068
       26.07 -    52.13: 171
       52.13 -    78.20: 18
       78.20 -   104.27: 10
      104.27 -   130.33: 4
  Dihedral angle restraints: 2271
    sinusoidal: 1038
      harmonic: 1233
  Sorted by residual:
  dihedral pdb=" N   PRO A 189 "
           pdb=" CG  PRO A 189 "
           pdb=" CD  PRO A 189 "
           pdb=" CB  PRO A 189 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -160.33  130.33     1      1.50e+01 4.44e-03 7.03e+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   33.46   59.54     1      1.00e+01 1.00e-02 4.73e+01
  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   33.48   59.52     1      1.00e+01 1.00e-02 4.73e+01
  ... (remaining 2268 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 438
       0.072 -    0.143: 139
       0.143 -    0.215: 26
       0.215 -    0.286: 0
       0.286 -    0.358: 3
  Chirality restraints: 606
  Sorted by residual:
  chirality pdb=" CB  ILE C 203 "
            pdb=" CA  ILE C 203 "
            pdb=" CG1 ILE C 203 "
            pdb=" CG2 ILE C 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" CB  ILE A 203 "
            pdb=" CA  ILE A 203 "
            pdb=" CG1 ILE A 203 "
            pdb=" CG2 ILE A 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" CB  ILE B 203 "
            pdb=" CA  ILE B 203 "
            pdb=" CG1 ILE B 203 "
            pdb=" CG2 ILE B 203 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.29    0.36 2.00e-01 2.50e+01 3.16e+00
  ... (remaining 603 not shown)

  Planarity restraints: 591
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 157 "    0.008 2.00e-02 2.50e+03   1.44e-02 4.15e+00
        pdb=" CG  TYR A 157 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 157 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 157 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 157 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 157 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 157 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 157 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 157 "    0.009 2.00e-02 2.50e+03   1.43e-02 4.11e+00
        pdb=" CG  TYR B 157 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 157 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 157 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 157 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 157 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 157 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 157 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 157 "    0.009 2.00e-02 2.50e+03   1.43e-02 4.09e+00
        pdb=" CG  TYR C 157 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 157 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 157 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 157 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 157 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 157 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 157 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 588 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 82
        2.68 -     3.23: 3267
        3.23 -     3.79: 5409
        3.79 -     4.34: 6959
        4.34 -     4.90: 12721
  Nonbonded interactions: 28438
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 197 "
            pdb=" NZ  LYS B 220 "
     model   vdw
     2.120 2.520
  nonbonded pdb=" NE2 GLN C 229 "
            pdb=" OG1 THR C 234 "
     model   vdw
     2.139 2.520
  nonbonded pdb=" NE2 GLN B 229 "
            pdb=" OG1 THR B 234 "
     model   vdw
     2.139 2.520
  nonbonded pdb=" NE2 GLN A 229 "
            pdb=" OG1 THR A 234 "
     model   vdw
     2.140 2.520
  nonbonded pdb=" OH  TYR B 197 "
            pdb=" NZ  LYS C 220 "
     model   vdw
     2.168 2.520
  ... (remaining 28433 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
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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          4.100
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     16.140
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.600
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4696
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      :  0.018   0.429   3516  Z= 1.157
  Angle     :  2.431  73.856   4788  Z= 1.083
  Chirality :  0.071   0.358    606
  Planarity :  0.006   0.049    579
  Dihedral  : 19.232 130.333   1476
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 29.95
  Ramachandran Plot:
    Outliers :  0.75 %
    Allowed  : 11.28 %
    Favored  : 87.97 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  :  3.15 %
    Favored  : 90.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.75 %

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: -3.06 (0.36), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.33 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.003   0.002   HIS A 222 
   PHE   0.016   0.004   PHE A 171 
   TYR   0.033   0.005   TYR A 157 
   ARG   0.004   0.001   ARG C 247 

*********************** 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
  145 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 9
  residues processed: 136
  average time/residue: 0.8931
  time to fit residues: 125.6630
Evaluate side-chains
  74 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.373 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 8
  residues processed: 1
  average time/residue: 1.1119
  time to fit residues: 1.6419
-------------------------------------------------------------------------------
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:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 10 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 15 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   overall best weight:    4.1188

-------------------------------------------------------------------------------
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 249 GLN
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
C 170 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5333
moved from start:          0.6808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   3516  Z= 0.367
  Angle     :  0.965   9.023   4788  Z= 0.510
  Chirality :  0.063   0.299    606
  Planarity :  0.006   0.062    579
  Dihedral  : 15.023 108.255    711
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.03 %
    Favored  : 89.97 %
  Rotamer:
    Outliers :  7.09 %
    Allowed  : 19.69 %
    Favored  : 73.23 %
  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: -3.54 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.69 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.010   0.004   HIS A 239 
   PHE   0.013   0.002   PHE A 171 
   TYR   0.020   0.003   TYR C 248 
   ARG   0.002   0.000   ARG A 140 

*********************** 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: 27
    poor density    : 87
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 8
  residues processed: 102
  average time/residue: 0.6872
  time to fit residues: 73.3441
Evaluate side-chains
  79 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.406 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 4
  residues processed: 4
  average time/residue: 0.3888
  time to fit residues: 2.2121
-------------------------------------------------------------------------------
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:   10.0000
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 24 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 12 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 26 optimal weight:    6.9990
   overall best weight:    4.5988

-------------------------------------------------------------------------------
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**
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5462
moved from start:          0.8800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   3516  Z= 0.367
  Angle     :  1.003   9.988   4788  Z= 0.527
  Chirality :  0.062   0.347    606
  Planarity :  0.005   0.037    579
  Dihedral  : 14.825 107.780    711
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 20.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.28 %
    Favored  : 89.72 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 27.30 %
    Favored  : 65.09 %
  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: -3.84 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.008   0.003   HIS C 239 
   PHE   0.018   0.002   PHE B 171 
   TYR   0.017   0.003   TYR A 125 
   ARG   0.003   0.001   ARG C 140 

*********************** 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
  110 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 81
  time to evaluate  : 0.392 
Fit side-chains
  outliers start: 29
  outliers final: 9
  residues processed: 98
  average time/residue: 0.7066
  time to fit residues: 72.4557
Evaluate side-chains
  79 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.411 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 3
  residues processed: 6
  average time/residue: 0.2259
  time to fit residues: 2.0952
-------------------------------------------------------------------------------
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:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 16 optimal weight:    6.9990
   chunk 23 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 37 optimal weight:    7.9990
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 31 optimal weight:    8.9990
   chunk 21 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 249 GLN
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5499
moved from start:          0.9758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3516  Z= 0.328
  Angle     :  0.978  10.698   4788  Z= 0.505
  Chirality :  0.063   0.306    606
  Planarity :  0.004   0.026    579
  Dihedral  : 14.509 106.471    711
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 29.66 %
    Favored  : 64.04 %
  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: -4.03 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.07 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS C 239 
   PHE   0.017   0.002   PHE A 237 
   TYR   0.021   0.003   TYR B 125 
   ARG   0.001   0.000   ARG A 140 

*********************** 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
  95 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 71
  time to evaluate  : 0.461 
Fit side-chains
  outliers start: 24
  outliers final: 8
  residues processed: 86
  average time/residue: 0.7753
  time to fit residues: 69.5409
Evaluate side-chains
  72 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.387 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 4
  residues processed: 4
  average time/residue: 0.0436
  time to fit residues: 0.8032
-------------------------------------------------------------------------------
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:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0070
   chunk 0 optimal weight:   10.0000
   chunk 19 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 9 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.6006

-------------------------------------------------------------------------------
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 249 GLN
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5524
moved from start:          1.0286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   3516  Z= 0.304
  Angle     :  0.928   9.053   4788  Z= 0.485
  Chirality :  0.061   0.288    606
  Planarity :  0.004   0.022    579
  Dihedral  : 14.217 105.188    711
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 19.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.53 %
    Favored  : 87.47 %
  Rotamer:
    Outliers :  7.61 %
    Allowed  : 28.61 %
    Favored  : 63.78 %
  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: -4.22 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.21 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS C 239 
   PHE   0.016   0.002   PHE A 237 
   TYR   0.016   0.002   TYR B 236 
   ARG   0.001   0.000   ARG C 247 

*********************** 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
  99 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 70
  time to evaluate  : 0.362 
Fit side-chains
  outliers start: 29
  outliers final: 14
  residues processed: 87
  average time/residue: 0.7552
  time to fit residues: 68.5871
Evaluate side-chains
  78 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.389 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 8
  residues processed: 6
  average time/residue: 0.0469
  time to fit residues: 0.9634
-------------------------------------------------------------------------------
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:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 31 optimal weight:   10.0000
   chunk 17 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 19 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 4 optimal weight:    0.0470
   chunk 21 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   overall best weight:    2.8282

-------------------------------------------------------------------------------
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**
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 194 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5508
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      :  0.004   0.038   3516  Z= 0.279
  Angle     :  0.935  11.573   4788  Z= 0.476
  Chirality :  0.059   0.258    606
  Planarity :  0.004   0.018    579
  Dihedral  : 13.702 101.493    711
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 31.23 %
    Favored  : 62.99 %
  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: -4.21 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.20 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 239 
   PHE   0.020   0.003   PHE C 237 
   TYR   0.019   0.002   TYR B 236 
   ARG   0.001   0.000   ARG C 247 

*********************** 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
  93 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 71
  time to evaluate  : 0.399 
Fit side-chains
  outliers start: 22
  outliers final: 15
  residues processed: 85
  average time/residue: 0.7964
  time to fit residues: 70.5147
Evaluate side-chains
  82 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.368 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 8
  residues processed: 7
  average time/residue: 0.1797
  time to fit residues: 1.9532
-------------------------------------------------------------------------------
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:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 37 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 17 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 11 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   overall best weight:    5.1990

-------------------------------------------------------------------------------
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 249 GLN
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 148 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5635
moved from start:          1.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   3516  Z= 0.382
  Angle     :  1.030  10.586   4788  Z= 0.529
  Chirality :  0.062   0.302    606
  Planarity :  0.004   0.021    579
  Dihedral  : 14.020 100.154    711
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 22.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.29 %
    Favored  : 85.71 %
  Rotamer:
    Outliers :  6.30 %
    Allowed  : 32.55 %
    Favored  : 61.15 %
  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: -4.48 (0.31), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.23), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.005   0.002   HIS A 239 
   PHE   0.018   0.003   PHE C 171 
   TYR   0.024   0.003   TYR C 250 
   ARG   0.001   0.000   ARG C 247 

*********************** 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
  96 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.339 
Fit side-chains
  outliers start: 24
  outliers final: 15
  residues processed: 88
  average time/residue: 0.7544
  time to fit residues: 69.3159
Evaluate side-chains
  81 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 66
  time to evaluate  : 0.387 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 9
  residues processed: 6
  average time/residue: 0.0416
  time to fit residues: 0.9340
-------------------------------------------------------------------------------
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:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 34 optimal weight:    0.5980
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 21 optimal weight:    6.9990
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0870
   chunk 31 optimal weight:    6.9990
   overall best weight:    1.9160

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

Flipped N/Q/H residues before XYZ refinement:
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5494
moved from start:          1.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3516  Z= 0.266
  Angle     :  0.941  12.826   4788  Z= 0.475
  Chirality :  0.059   0.240    606
  Planarity :  0.004   0.026    579
  Dihedral  : 12.992  97.700    711
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 17.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.53 %
    Favored  : 88.47 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 33.07 %
    Favored  : 62.20 %
  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: -4.28 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.003   HIS A 239 
   PHE   0.018   0.002   PHE C 237 
   TYR   0.022   0.002   TYR B 236 
   ARG   0.001   0.000   ARG B 180 

*********************** 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
  87 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.402 
Fit side-chains
  outliers start: 18
  outliers final: 13
  residues processed: 82
  average time/residue: 0.8717
  time to fit residues: 74.3189
Evaluate side-chains
  78 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 0.357 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 8
  residues processed: 5
  average time/residue: 0.2411
  time to fit residues: 1.8564
-------------------------------------------------------------------------------
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:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 17 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   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 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 249 GLN
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN
C 242 GLN
C 249 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5577
moved from start:          1.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054   3516  Z= 0.334
  Angle     :  1.004  11.877   4788  Z= 0.505
  Chirality :  0.060   0.270    606
  Planarity :  0.004   0.028    579
  Dihedral  : 12.796  93.989    711
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.54 %
    Favored  : 85.46 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 34.91 %
    Favored  : 60.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.33 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.29 (0.24), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.006   0.002   HIS A 239 
   PHE   0.016   0.003   PHE A 237 
   TYR   0.022   0.002   TYR B 125 
   ARG   0.002   0.000   ARG C 247 

*********************** 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
  87 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.412 
Fit side-chains
  outliers start: 18
  outliers final: 14
  residues processed: 82
  average time/residue: 0.8447
  time to fit residues: 72.1105
Evaluate side-chains
  77 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.360 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 11
  residues processed: 3
  average time/residue: 0.0333
  time to fit residues: 0.7394
-------------------------------------------------------------------------------
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:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 9 optimal weight:    8.9990
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0570
   chunk 12 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN
C 249 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5496
moved from start:          1.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3516  Z= 0.274
  Angle     :  0.942  12.229   4788  Z= 0.475
  Chirality :  0.058   0.231    606
  Planarity :  0.004   0.034    579
  Dihedral  : 12.268  92.089    711
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 16.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 35.43 %
    Favored  : 60.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.15 (0.32), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 239 
   PHE   0.021   0.003   PHE C 237 
   TYR   0.024   0.002   TYR B 125 
   ARG   0.001   0.000   ARG B 180 

********************** 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
  80 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.368 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 77
  average time/residue: 0.7592
  time to fit residues: 61.1572
Evaluate side-chains
  76 residues out of total 375 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.415 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 11
  residues processed: 2
  average time/residue: 0.0589
  time to fit residues: 0.7165
-------------------------------------------------------------------------------
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:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:    9.9990
   chunk 22 optimal weight:    8.9990
   chunk 35 optimal weight:    6.9990
   chunk 20 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 23 optimal weight:    0.0030
   chunk 15 optimal weight:    0.6980
   overall best weight:    2.7396

-------------------------------------------------------------------------------
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**
** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 249 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5620 r_free = 0.5620 target = 0.311916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.6065 r_free = 0.6065 target = 0.277312 restraints weight = 21381.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.5540 rms_B_bonded: 4.18
r_work: 0.5915 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.5857 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.5857
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.5465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.5465 r_free = 0.5465    target_work(ls_wunit_k1) = 0.291         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.5463 r_free = 0.5463    target_work(ls_wunit_k1) = 0.291         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
r_final: 0.5463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5626
moved from start:          1.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3516  Z= 0.290
  Angle     :  0.977  11.798   4788  Z= 0.487
  Chirality :  0.059   0.242    606
  Planarity :  0.004   0.036    579
  Dihedral  : 11.980  89.362    711
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 17.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.78 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 36.22 %
    Favored  : 59.32 %
  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: -4.15 (0.33), residues: 402
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.15 (0.25), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   HIS   0.007   0.002   HIS A 239 
   PHE   0.018   0.003   PHE C 237 
   TYR   0.022   0.002   TYR B 125 
   ARG   0.001   0.000   ARG A 247 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1824.82 seconds
wall clock time: 33 minutes 27.24 seconds (2007.24 seconds total)