Starting phenix.real_space_refine (version: dev)
on Mon Apr  4 21:23:14 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346_ligands.cif

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew3_31346/04_2022/7ew3_31346_updated.pdb"
  }
  resolution = 3.1
  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=   0.002 sd=   0.131
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   14": "OE1" <-> "OE2"
    Residue "A ARG   15": "NH1" <-> "NH2"
    Residue "A GLU   25": "OE1" <-> "OE2"
    Residue "A GLU   43": "OE1" <-> "OE2"
    Residue "A ARG  205": "NH1" <-> "NH2"
    Residue "A GLU  275": "OE1" <-> "OE2"
    Residue "A GLU  297": "OE1" <-> "OE2"
    Residue "B ARG    8": "NH1" <-> "NH2"
    Residue "B ARG   46": "NH1" <-> "NH2"
    Residue "B ARG   96": "NH1" <-> "NH2"
    Residue "B ARG  137": "NH1" <-> "NH2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "B ARG  219": "NH1" <-> "NH2"
    Residue "B GLU  226": "OE1" <-> "OE2"
    Residue "B ARG  256": "NH1" <-> "NH2"
    Residue "B GLU  260": "OE1" <-> "OE2"
    Residue "C GLU   58": "OE1" <-> "OE2"
    Residue "C ARG   62": "NH1" <-> "NH2"
    Residue "R GLU   20": "OE1" <-> "OE2"
    Residue "R GLU   56": "OE1" <-> "OE2"
    Residue "R ARG   73": "NH1" <-> "NH2"
    Residue "R ARG  114": "NH1" <-> "NH2"
    Residue "R GLU  115": "OE1" <-> "OE2"
    Residue "R ARG  144": "NH1" <-> "NH2"
    Residue "R ARG  217": "NH1" <-> "NH2"
    Residue "R ARG  237": "NH1" <-> "NH2"
    Residue "R ARG  243": "NH1" <-> "NH2"
    Residue "R ARG  307": "NH1" <-> "NH2"
    Residue "S GLU  153": "OE1" <-> "OE2"
    Residue "S ARG  160": "NH1" <-> "NH2"
    Residue "S ARG  218": "NH1" <-> "NH2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib"
  Total number of atoms: 9072
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1813
          Classifications: {'peptide': 226}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 223}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 340, 2611
          Classifications: {'peptide': 340}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 334}
    Chain: "C"
      Number of atoms: 474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 61, 474
          Classifications: {'peptide': 61}
          Link IDs: {'PTRANS': 4, 'TRANS': 56}
    Chain: "R"
      Number of atoms: 2294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 290, 2294
          Classifications: {'peptide': 290}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 8, 'TRANS': 281}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "S"
      Number of atoms: 1783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1783
          Classifications: {'peptide': 232}
          Link IDs: {'PTRANS': 9, 'TRANS': 221, 'PCIS': 1}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 97
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 97
          Unusual residues: {'PLM': 4, 'S1P': 1}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 6.01, per 1000 atoms: 0.66
  Number of scatterers: 9072
  At special positions: 0
  Unit cell: (94.76, 124.2, 134.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      68     16.00
     P       1     15.00
     O    1678      8.00
     N    1531      7.00
     C    5794      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 178 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 269 " - pdb=" SG  CYS R 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " 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
  Time building additional restraints: 3.69
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      24 helices and 13 sheets defined
      33.2% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.82
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 27
      removed outlier: 3.983A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 32
      No H-bonds generated for 'chain 'A' and resid 30 through 32'
    Processing helix  chain 'A' and resid 48 through 52
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 272 through 280
      removed outlier: 4.321A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
      removed outlier: 3.778A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 2 through 25
      removed outlier: 3.857A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 35
    Processing helix  chain 'C' and resid 8 through 22
      removed outlier: 3.608A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 47
      removed outlier: 4.918A  pdb=" N   LYS C  46 " --> pdb=" O   GLU C  42 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   GLU C  47 " --> pdb=" O   ALA C  43 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 17 through 25
    Processing helix  chain 'R' and resid 41 through 66
    Processing helix  chain 'R' and resid 74 through 98
    Processing helix  chain 'R' and resid 108 through 141
      removed outlier: 3.545A  pdb=" N   MET R 118 " --> pdb=" O   ARG R 114 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER R 128 " --> pdb=" O   ALA R 124 " (cutoff:3.500A)
      removed outlier: 4.860A  pdb=" N   LEU R 129 " --> pdb=" O   SER R 125 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   LEU R 130 " --> pdb=" O   THR R 126 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 174
      Proline residue:  R 172  - end of helix
    Processing helix  chain 'R' and resid 194 through 228
      removed outlier: 4.122A  pdb=" N   ILE R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   TYR R 219 " --> pdb=" O   TYR R 215 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   PHE R 220 " --> pdb=" O   ALA R 216 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   LEU R 221 " --> pdb=" O   ARG R 217 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LYS R 228 " --> pdb=" O   SER R 224 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 232 through 268
      removed outlier: 3.763A  pdb=" N   CYS R 255 " --> pdb=" O   VAL R 251 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   TRP R 256 " --> pdb=" O   PHE R 252 " (cutoff:3.500A)
      Proline residue:  R 258  - end of helix
    Processing helix  chain 'R' and resid 276 through 278
      No H-bonds generated for 'chain 'R' and resid 276 through 278'
    Processing helix  chain 'R' and resid 280 through 297
      removed outlier: 4.299A  pdb=" N   VAL R 285 " --> pdb=" O   TRP R 282 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ASN R 294 " --> pdb=" O   SER R 291 " (cutoff:3.500A)
      Proline residue:  R 295  - end of helix
    Processing helix  chain 'R' and resid 303 through 311
    Processing helix  chain 'S' and resid 29 through 31
      No H-bonds generated for 'chain 'S' and resid 29 through 31'
    Processing helix  chain 'S' and resid 88 through 90
      No H-bonds generated for 'chain 'S' and resid 88 through 90'
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.834A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 8.276A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.678A  pdb=" N   HIS A 195 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.786A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.325A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.456A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 6.506A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   GLY A  40 " --> pdb=" O   PHE A 199 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 7.032A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.028A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 102 through 105
      removed outlier: 3.722A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.903A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.341A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.056A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.923A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.522A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 262 through 264
      removed outlier: 3.814A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.406A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 46 through 52
      removed outlier: 6.951A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.704A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   PHE B 335 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER B 331 " --> pdb=" O   PHE B 335 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'S' and resid 115 through 117
      removed outlier: 3.741A  pdb=" N   ALA S  49 " --> pdb=" O   TRP S  36 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 146 through 148
      removed outlier: 7.242A  pdb=" N   LYS S 244 " --> pdb=" O   VAL S 147 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=  M, first strand: chain 'S' and resid 226 through 231
      removed outlier: 3.502A  pdb=" N   PHE S 177 " --> pdb=" O   TYR S 228 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 5.384A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)

    395 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.43

  Time building geometry restraints manager: 3.93 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2904
        1.35 -     1.46: 2234
        1.46 -     1.58: 4010
        1.58 -     1.70: 1
        1.70 -     1.82: 99
  Bond restraints: 9248
  Sorted by residual:
  bond pdb=" C14 S1P R 401 "
       pdb=" C15 S1P R 401 "
    ideal  model  delta    sigma   weight residual
    1.557  1.443  0.114 2.00e-02 2.50e+03 3.24e+01
  bond pdb=" C12 S1P R 401 "
       pdb=" C13 S1P R 401 "
    ideal  model  delta    sigma   weight residual
    1.562  1.458  0.104 2.00e-02 2.50e+03 2.69e+01
  bond pdb=" C8  S1P R 401 "
       pdb=" C9  S1P R 401 "
    ideal  model  delta    sigma   weight residual
    1.554  1.452  0.102 2.00e-02 2.50e+03 2.61e+01
  bond pdb=" C13 S1P R 401 "
       pdb=" C14 S1P R 401 "
    ideal  model  delta    sigma   weight residual
    1.553  1.451  0.102 2.00e-02 2.50e+03 2.60e+01
  bond pdb=" C15 S1P R 401 "
       pdb=" C16 S1P R 401 "
    ideal  model  delta    sigma   weight residual
    1.549  1.455  0.094 2.00e-02 2.50e+03 2.22e+01
  ... (remaining 9243 not shown)

  Histogram of bond angle deviations from ideal:
       99.05 -   106.05: 147
      106.05 -   113.04: 4998
      113.04 -   120.03: 3107
      120.03 -   127.02: 4134
      127.02 -   134.01: 98
  Bond angle restraints: 12484
  Sorted by residual:
  angle pdb=" O1  S1P R 401 "
        pdb=" P22 S1P R 401 "
        pdb=" O24 S1P R 401 "
      ideal   model   delta    sigma   weight residual
     109.49   99.05   10.44 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" C3  S1P R 401 "
        pdb=" C2  S1P R 401 "
        pdb=" N2  S1P R 401 "
      ideal   model   delta    sigma   weight residual
     109.47   99.16   10.31 3.00e+00 1.11e-01 1.18e+01
  angle pdb=" C1  S1P R 401 "
        pdb=" O1  S1P R 401 "
        pdb=" P22 S1P R 401 "
      ideal   model   delta    sigma   weight residual
     118.45  127.34   -8.89 3.00e+00 1.11e-01 8.79e+00
  angle pdb=" N   THR R 103 "
        pdb=" CA  THR R 103 "
        pdb=" C   THR R 103 "
      ideal   model   delta    sigma   weight residual
     111.28  114.12   -2.84 1.09e+00 8.42e-01 6.77e+00
  angle pdb=" O1  S1P R 401 "
        pdb=" P22 S1P R 401 "
        pdb=" O23 S1P R 401 "
      ideal   model   delta    sigma   weight residual
     109.47  116.69   -7.22 3.00e+00 1.11e-01 5.80e+00
  ... (remaining 12479 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 4979
       17.99 -    35.98: 442
       35.98 -    53.98: 81
       53.98 -    71.97: 9
       71.97 -    89.96: 11
  Dihedral angle restraints: 5522
    sinusoidal: 2190
      harmonic: 3332
  Sorted by residual:
  dihedral pdb=" CB  CYS R 178 "
           pdb=" SG  CYS R 178 "
           pdb=" SG  CYS R 185 "
           pdb=" CB  CYS R 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.01   42.99     1      1.00e+01 1.00e-02 2.58e+01
  dihedral pdb=" CB  CYS R 269 "
           pdb=" SG  CYS R 269 "
           pdb=" SG  CYS R 274 "
           pdb=" CB  CYS R 274 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  121.11  -28.11     1      1.00e+01 1.00e-02 1.13e+01
  dihedral pdb=" CB  GLU R  56 "
           pdb=" CG  GLU R  56 "
           pdb=" CD  GLU R  56 "
           pdb=" OE1 GLU R  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.96  -89.96     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 5519 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 879
       0.027 -    0.054: 313
       0.054 -    0.081: 136
       0.081 -    0.108: 52
       0.108 -    0.134: 33
  Chirality restraints: 1413
  Sorted by residual:
  chirality pdb=" CB  VAL A 201 "
            pdb=" CA  VAL A 201 "
            pdb=" CG1 VAL A 201 "
            pdb=" CG2 VAL A 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.49   -0.13 2.00e-01 2.50e+01 4.51e-01
  chirality pdb=" C2  S1P R 401 "
            pdb=" C1  S1P R 401 "
            pdb=" C3  S1P R 401 "
            pdb=" N2  S1P R 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.74    0.13 2.00e-01 2.50e+01 4.31e-01
  chirality pdb=" CA  PRO R 172 "
            pdb=" N   PRO R 172 "
            pdb=" C   PRO R 172 "
            pdb=" CB  PRO R 172 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.80e-01
  ... (remaining 1410 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG S 180 "   -0.025 5.00e-02 4.00e+02   3.78e-02 2.28e+00
        pdb=" N   PRO S 181 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO S 181 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO S 181 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.023 5.00e-02 4.00e+02   3.48e-02 1.94e+00
        pdb=" N   PRO B 236 "    0.060 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 246 "   -0.007 2.00e-02 2.50e+03   1.31e-02 1.71e+00
        pdb=" C   ASP B 246 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ASP B 246 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ASP B 247 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 2174
        2.80 -     3.32: 7900
        3.32 -     3.85: 13947
        3.85 -     4.37: 15856
        4.37 -     4.90: 29216
  Nonbonded interactions: 69093
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 168 "
            pdb=" OH  TYR R 196 "
     model   vdw
     2.274 2.440
  nonbonded pdb=" NH1 ARG S  67 "
            pdb=" O   SER S  85 "
     model   vdw
     2.309 2.520
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.320 2.440
  nonbonded pdb=" O   PHE S  32 "
            pdb=" NH2 ARG S  72 "
     model   vdw
     2.330 2.520
  nonbonded pdb=" NH1 ARG S  87 "
            pdb=" OE2 GLU S  89 "
     model   vdw
     2.340 2.520
  ... (remaining 69088 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      68      5.16       5
     C    5794      2.51       5
     N    1531      2.21       5
     O    1678      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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          4.380
  Check model and map are aligned:         0.140
  Convert atoms to be neutral:             0.080
  Process input model:                     27.720
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
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      :  0.004   0.114   9248  Z= 0.273
  Angle     :  0.500  10.435  12484  Z= 0.262
  Chirality :  0.039   0.134   1413
  Planarity :  0.003   0.038   1566
  Dihedral  : 14.174  89.960   3361
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.25), residues: 1133
  helix:  2.58 (0.26), residues: 385
  sheet:  1.16 (0.32), residues: 270
  loop : -0.70 (0.26), residues: 478

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.114 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2180
  time to fit residues: 39.5929
Evaluate side-chains
  109 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 1.091 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.5097
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 103 optimal weight:    7.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9248  Z= 0.194
  Angle     :  0.492   6.644  12484  Z= 0.258
  Chirality :  0.041   0.156   1413
  Planarity :  0.004   0.101   1566
  Dihedral  :  5.985  74.080   1310
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer Outliers :  0.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.25), residues: 1133
  helix:  3.01 (0.27), residues: 375
  sheet:  0.99 (0.32), residues: 270
  loop : -0.78 (0.26), residues: 488

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 1.136 
Fit side-chains
  outliers start: 7
  outliers final: 5
  residues processed: 105
  average time/residue: 0.2513
  time to fit residues: 35.9991
Evaluate side-chains
  102 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 1.080 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0905
  time to fit residues: 2.3411
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 28 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 112 optimal weight:    7.9990
   chunk 92 optimal weight:    7.9990
   chunk 102 optimal weight:    6.9990
   chunk 35 optimal weight:    0.7980
   chunk 83 optimal weight:    2.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.097   9248  Z= 0.339
  Angle     :  0.586  10.232  12484  Z= 0.306
  Chirality :  0.043   0.150   1413
  Planarity :  0.004   0.051   1566
  Dihedral  :  6.340  61.640   1310
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  1.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1133
  helix:  2.79 (0.27), residues: 380
  sheet:  0.76 (0.31), residues: 276
  loop : -0.95 (0.26), residues: 477

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.146 
Fit side-chains
  outliers start: 11
  outliers final: 6
  residues processed: 104
  average time/residue: 0.2503
  time to fit residues: 35.1619
Evaluate side-chains
  92 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 1.160 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0853
  time to fit residues: 2.4439
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 53 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:   40.0000
   chunk 110 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R  21 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.089   9248  Z= 0.196
  Angle     :  0.483   7.463  12484  Z= 0.256
  Chirality :  0.040   0.147   1413
  Planarity :  0.004   0.056   1566
  Dihedral  :  5.956  60.606   1310
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer Outliers :  0.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.25), residues: 1133
  helix:  2.98 (0.27), residues: 379
  sheet:  0.86 (0.32), residues: 267
  loop : -0.98 (0.25), residues: 487

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.965 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 100
  average time/residue: 0.2461
  time to fit residues: 33.8934
Evaluate side-chains
  93 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 89
  time to evaluate  : 1.117 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0868
  time to fit residues: 2.2298
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 62 optimal weight:    5.9990
   chunk 1 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 94 optimal weight:    9.9990
   chunk 76 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.081   9248  Z= 0.400
  Angle     :  0.612  10.920  12484  Z= 0.321
  Chirality :  0.045   0.152   1413
  Planarity :  0.005   0.065   1566
  Dihedral  :  6.557  61.291   1310
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer Outliers :  1.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.25), residues: 1133
  helix:  2.62 (0.27), residues: 382
  sheet:  0.56 (0.31), residues: 274
  loop : -1.15 (0.25), residues: 477

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 1.106 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 99
  average time/residue: 0.2569
  time to fit residues: 34.2898
Evaluate side-chains
  92 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.083 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0895
  time to fit residues: 2.7342
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 99 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 64 optimal weight:   10.0000
   chunk 27 optimal weight:    0.6980
   chunk 110 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9248  Z= 0.154
  Angle     :  0.465   6.439  12484  Z= 0.246
  Chirality :  0.041   0.147   1413
  Planarity :  0.004   0.061   1566
  Dihedral  :  5.984  58.624   1310
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer Outliers :  0.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.25), residues: 1133
  helix:  2.94 (0.27), residues: 380
  sheet:  0.54 (0.31), residues: 273
  loop : -1.11 (0.25), residues: 480

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 1.101 
Fit side-chains
  outliers start: 9
  outliers final: 3
  residues processed: 101
  average time/residue: 0.2392
  time to fit residues: 33.2009
Evaluate side-chains
  86 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 83
  time to evaluate  : 1.071 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0835
  time to fit residues: 1.9416
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 62 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 68 optimal weight:    6.9990
   chunk 66 optimal weight:    7.9990
   chunk 50 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.117   9248  Z= 0.234
  Angle     :  0.514   8.829  12484  Z= 0.272
  Chirality :  0.041   0.163   1413
  Planarity :  0.004   0.071   1566
  Dihedral  :  5.956  58.230   1310
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer Outliers :  0.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.05 (0.25), residues: 1133
  helix:  2.90 (0.27), residues: 381
  sheet:  0.58 (0.31), residues: 272
  loop : -1.12 (0.25), residues: 480

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.069 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 100
  average time/residue: 0.2628
  time to fit residues: 35.2854
Evaluate side-chains
  95 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 1.074 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0901
  time to fit residues: 1.9676
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 69 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 86 optimal weight:    4.9990
   chunk 99 optimal weight:    9.9990
   chunk 105 optimal weight:    8.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.144   9248  Z= 0.383
  Angle     :  0.618  10.995  12484  Z= 0.325
  Chirality :  0.045   0.186   1413
  Planarity :  0.005   0.078   1566
  Dihedral  :  6.455  59.982   1310
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.25), residues: 1133
  helix:  2.61 (0.27), residues: 386
  sheet:  0.41 (0.30), residues: 282
  loop : -1.13 (0.25), residues: 465

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 1.030 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2732
  time to fit residues: 37.0564
Evaluate side-chains
  91 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 1.095 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0846
  time to fit residues: 1.6677
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   chunk 105 optimal weight:    9.9990
   chunk 61 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 92 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 108 optimal weight:    2.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.2754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.116   9248  Z= 0.278
  Angle     :  0.568  12.162  12484  Z= 0.297
  Chirality :  0.043   0.220   1413
  Planarity :  0.004   0.077   1566
  Dihedral  :  6.348  59.664   1310
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.25), residues: 1133
  helix:  2.80 (0.27), residues: 380
  sheet:  0.40 (0.30), residues: 278
  loop : -1.14 (0.25), residues: 475

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.145 
Fit side-chains
  outliers start: 6
  outliers final: 2
  residues processed: 99
  average time/residue: 0.2745
  time to fit residues: 36.1059
Evaluate side-chains
  95 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 93
  time to evaluate  : 1.147 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1005
  time to fit residues: 1.9146
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 113 optimal weight:    0.8980
   chunk 104 optimal weight:   20.0000
   chunk 90 optimal weight:    7.9990
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.155   9248  Z= 0.245
  Angle     :  0.555  14.008  12484  Z= 0.292
  Chirality :  0.042   0.206   1413
  Planarity :  0.005   0.093   1566
  Dihedral  :  6.082  59.871   1310
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer Outliers :  0.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.25), residues: 1133
  helix:  2.91 (0.27), residues: 378
  sheet:  0.45 (0.31), residues: 277
  loop : -1.12 (0.25), residues: 478

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

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

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2266 Ramachandran restraints generated.
    1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 1.137 
Fit side-chains
  outliers start: 5
  outliers final: 3
  residues processed: 99
  average time/residue: 0.2734
  time to fit residues: 36.0693
Evaluate side-chains
  97 residues out of total 984 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 1.069 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0921
  time to fit residues: 1.9728
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 90 optimal weight:    7.9990
   chunk 37 optimal weight:    0.6980
   chunk 93 optimal weight:    0.8980
   chunk 11 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.170500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.127087 restraints weight = 10528.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 2.55
r_work: 0.3413 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3395 rms_B_bonded: 2.28 restraints_weight: 0.2500
r_work: 0.3377 rms_B_bonded: 2.32 restraints_weight: 0.1250
r_work: 0.3358 rms_B_bonded: 2.41 restraints_weight: 0.0625
r_work: 0.3339 rms_B_bonded: 2.56 restraints_weight: 0.0312
r_work: 0.3317 rms_B_bonded: 2.75 restraints_weight: 0.0156
r_work: 0.3293 rms_B_bonded: 2.99 restraints_weight: 0.0078
r_work: 0.3268 rms_B_bonded: 3.29 restraints_weight: 0.0039
r_work: 0.3239 rms_B_bonded: 3.66 restraints_weight: 0.0020
r_work: 0.3207 rms_B_bonded: 4.10 restraints_weight: 0.0010
r_work: 0.3170 rms_B_bonded: 4.63 restraints_weight: 0.0005
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.163   9248  Z= 0.201
  Angle     :  0.520  15.743  12484  Z= 0.276
  Chirality :  0.041   0.200   1413
  Planarity :  0.005   0.109   1566
  Dihedral  :  5.705  58.674   1310
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer Outliers :  0.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.25), residues: 1133
  helix:  3.08 (0.27), residues: 378
  sheet:  0.47 (0.31), residues: 279
  loop : -1.05 (0.26), residues: 476

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Job complete
usr+sys time: 1778.46 seconds
wall clock time: 33 minutes 16.57 seconds (1996.57 seconds total)