Starting phenix.real_space_refine (version: 1.21rc1)
on Thu Apr 20 17:35:09 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/04_2023/8id9_35360_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/04_2023/8id9_35360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/04_2023/8id9_35360.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/04_2023/8id9_35360.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/04_2023/8id9_35360_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/04_2023/8id9_35360_updated.pdb"
  }
  resolution = 3.0
  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=   0.007 sd=   0.072
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      46      5.16       5
     C    5148      2.51       5
     N    1364      2.21       5
     O    1438      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  124": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 7996
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "B"
      Number of atoms: 2448
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2448
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 33}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Unresolved non-hydrogen bonds: 119
          Unresolved non-hydrogen angles: 146
          Unresolved non-hydrogen dihedrals: 92
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 3, 'ASP:plan': 10}
          Unresolved non-hydrogen planarities: 91
    Chain: "Y"
      Number of atoms: 372
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 372
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 52
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 45
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "S"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1661
          Classifications: {'peptide': 227}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 216}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 64
    Chain: "A"
      Number of atoms: 1429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1429
          Classifications: {'peptide': 197}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 48}
          Link IDs: {'TRANS': 196}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 165
          Unresolved non-hydrogen angles: 197
          Unresolved non-hydrogen dihedrals: 133
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 10, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 11}
          Unresolved non-hydrogen planarities: 98
    Chain: "R"
      Number of atoms: 2086
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 283, 2086
          Unusual residues: {'EPA': 1}
          Classifications: {'peptide': 282, 'undetermined': 1}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PTRANS': 11, 'TRANS': 270, None: 1}
            Not linked:
              pdbres="ARG R 327 "
              pdbres="EPA R 401 "
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 185
          Unresolved non-hydrogen angles: 240
          Unresolved non-hydrogen dihedrals: 142
          Unresolved non-hydrogen chiralities: 29
          Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 2, 'GLU:plan': 3, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 88
  Time building chain proxies: 4.95, per 1000 atoms: 0.62
  Number of scatterers: 7996
  At special positions: 0
  Unit cell: (103.428, 126.75, 111.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      46     16.00
     O    1438      8.00
     N    1364      7.00
     C    5148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 160 " - pdb=" SG  CYS S 230 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.02
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2052

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      22 helices and 12 sheets defined
      32.3% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'B' and resid 9 through 23
      removed outlier: 3.501A  pdb=" N   ARG B  19 " --> pdb=" O   LYS B  15 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 9 through 24
    Processing helix  chain 'Y' and resid 30 through 42
      removed outlier: 3.565A  pdb=" N   CYS Y  41 " --> pdb=" O   LEU Y  37 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 56 through 58
      No H-bonds generated for 'chain 'Y' and resid 56 through 58'
    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 helix  chain 'A' and resid 7 through 30
      removed outlier: 3.718A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 52
      removed outlier: 4.108A  pdb=" N   GLN A  52 " --> pdb=" O   THR A  48 " (cutoff:3.500A)
    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 275
      No H-bonds generated for 'chain 'A' and resid 272 through 275'
    Processing helix  chain 'A' and resid 297 through 308
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.534A  pdb=" N   VAL A 335 " --> pdb=" O   ASN A 331 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 36 through 70
      removed outlier: 3.585A  pdb=" N   GLU R  43 " --> pdb=" O   LEU R  39 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU R  64 " --> pdb=" O   CYS R  60 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   VAL R  65 " --> pdb=" O   ALA R  61 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG R  67 " --> pdb=" O   VAL R  63 " (cutoff:3.500A)
      removed outlier: 4.546A  pdb=" N   ARG R  68 " --> pdb=" O   LEU R  64 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 99
      removed outlier: 3.920A  pdb=" N   LEU R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ALA R  91 " --> pdb=" O   LEU R  87 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   ILE R  92 " --> pdb=" O   PHE R  88 " (cutoff:3.500A)
      Proline residue:  R  93  - end of helix
    Processing helix  chain 'R' and resid 108 through 140
      removed outlier: 3.874A  pdb=" N   LEU R 113 " --> pdb=" O   VAL R 109 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   PHE R 115 " --> pdb=" O   CYS R 111 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TYR R 116 " --> pdb=" O   HIS R 112 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   MET R 118 " --> pdb=" O   LEU R 114 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER R 123 " --> pdb=" O   THR R 119 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE R 140 " --> pdb=" O   ARG R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 152 through 169
      removed outlier: 3.579A  pdb=" N   VAL R 168 " --> pdb=" O   GLY R 164 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 175
    Processing helix  chain 'R' and resid 201 through 242
      removed outlier: 3.513A  pdb=" N   TRP R 207 " --> pdb=" O   GLY R 203 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP R 208 " --> pdb=" O   GLU R 204 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU R 214 " --> pdb=" O   SER R 210 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ASN R 215 " --> pdb=" O   PHE R 211 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   VAL R 218 " --> pdb=" O   LEU R 214 " (cutoff:3.500A)
      Proline residue:  R 219  - end of helix
    Processing helix  chain 'R' and resid 250 through 275
      removed outlier: 4.001A  pdb=" N   ILE R 253 " --> pdb=" O   SER R 250 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLN R 257 " --> pdb=" O   ARG R 254 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU R 266 " --> pdb=" O   PHE R 263 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   SER R 272 " --> pdb=" O   LEU R 269 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   ILE R 275 " --> pdb=" O   SER R 272 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 278 through 292
    Processing helix  chain 'R' and resid 302 through 321
      removed outlier: 4.178A  pdb=" N   ASN R 313 " --> pdb=" O   PHE R 309 " (cutoff:3.500A)
      removed outlier: 4.530A  pdb=" N   SER R 314 " --> pdb=" O   THR R 310 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ALA R 315 " --> pdb=" O   PHE R 311 " (cutoff:3.500A)
      Proline residue:  R 318  - end of helix
    Processing sheet with id=  A, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.735A  pdb=" N   TYR B  59 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.887A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.355A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.761A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.396A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.768A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.728A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.277A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.680A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.618A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.792A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 273 through 277
      removed outlier: 6.594A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.362A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.642A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=  I, first strand: chain 'S' and resid 115 through 117
      removed outlier: 6.118A  pdb=" N   ARG S  38 " --> pdb=" O   TRP S  47 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   TRP S  47 " --> pdb=" O   ARG S  38 " (cutoff:3.500A)
    Processing sheet with id=  J, first strand: chain 'S' and resid 156 through 160
      removed outlier: 3.686A  pdb=" N   ALA S 212 " --> pdb=" O   SER S 209 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'S' and resid 227 through 232
      removed outlier: 3.643A  pdb=" N   ILE S 190 " --> pdb=" O   TRP S 177 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU S 179 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)
      removed outlier: 5.685A  pdb=" N   LEU S 188 " --> pdb=" O   LEU S 179 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'A' and resid 319 through 322
      removed outlier: 6.576A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.897A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   HIS A 195 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 195 " (cutoff:3.500A)
      removed outlier: 6.038A  pdb=" N   LYS A 197 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
      removed outlier: 5.949A  pdb=" N   PHE A 199 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    963 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: 2.36

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1254
        1.29 -     1.42: 2211
        1.42 -     1.55: 4623
        1.55 -     1.68: 5
        1.68 -     1.81: 66
  Bond restraints: 8159
  Sorted by residual:
  bond pdb=" CA  ASN R 322 "
       pdb=" C   ASN R 322 "
    ideal  model  delta    sigma   weight residual
    1.523  1.426  0.097 1.34e-02 5.57e+03 5.21e+01
  bond pdb=" CA  ARG R  70 "
       pdb=" CB  ARG R  70 "
    ideal  model  delta    sigma   weight residual
    1.531  1.434  0.097 1.56e-02 4.11e+03 3.86e+01
  bond pdb=" C   ARG R 238 "
       pdb=" O   ARG R 238 "
    ideal  model  delta    sigma   weight residual
    1.236  1.159  0.077 1.29e-02 6.01e+03 3.59e+01
  bond pdb=" C   ARG R  70 "
       pdb=" O   ARG R  70 "
    ideal  model  delta    sigma   weight residual
    1.237  1.163  0.074 1.31e-02 5.83e+03 3.19e+01
  bond pdb=" N   ASN R 322 "
       pdb=" CA  ASN R 322 "
    ideal  model  delta    sigma   weight residual
    1.457  1.388  0.070 1.29e-02 6.01e+03 2.90e+01
  ... (remaining 8154 not shown)

  Histogram of bond angle deviations from ideal:
       99.99 -   106.83: 184
      106.83 -   113.67: 4565
      113.67 -   120.51: 3066
      120.51 -   127.35: 3220
      127.35 -   134.19: 79
  Bond angle restraints: 11114
  Sorted by residual:
  angle pdb=" N   LEU R 316 "
        pdb=" CA  LEU R 316 "
        pdb=" C   LEU R 316 "
      ideal   model   delta    sigma   weight residual
     111.36  120.65   -9.29 1.09e+00 8.42e-01 7.26e+01
  angle pdb=" N   VAL R 175 "
        pdb=" CA  VAL R 175 "
        pdb=" C   VAL R 175 "
      ideal   model   delta    sigma   weight residual
     110.62  118.42   -7.80 1.02e+00 9.61e-01 5.85e+01
  angle pdb=" N   VAL R 141 "
        pdb=" CA  VAL R 141 "
        pdb=" C   VAL R 141 "
      ideal   model   delta    sigma   weight residual
     113.53  106.06    7.47 9.80e-01 1.04e+00 5.80e+01
  angle pdb=" N   VAL R  65 "
        pdb=" CA  VAL R  65 "
        pdb=" C   VAL R  65 "
      ideal   model   delta    sigma   weight residual
     113.53  107.27    6.26 9.80e-01 1.04e+00 4.08e+01
  angle pdb=" C   LEU R 171 "
        pdb=" N   PRO R 172 "
        pdb=" CA  PRO R 172 "
      ideal   model   delta    sigma   weight residual
     119.84  114.13    5.71 1.25e+00 6.40e-01 2.09e+01
  ... (remaining 11109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 4300
       18.00 -    36.00: 343
       36.00 -    54.00: 72
       54.00 -    72.00: 7
       72.00 -    89.99: 6
  Dihedral angle restraints: 4728
    sinusoidal: 1566
      harmonic: 3162
  Sorted by residual:
  dihedral pdb=" CD  ARG R 238 "
           pdb=" NE  ARG R 238 "
           pdb=" CZ  ARG R 238 "
           pdb=" NH1 ARG R 238 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   68.48  -68.48     1      1.00e+01 1.00e-02 6.08e+01
  dihedral pdb=" CD  ARG R 254 "
           pdb=" NE  ARG R 254 "
           pdb=" CZ  ARG R 254 "
           pdb=" NH1 ARG R 254 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -53.39   53.39     1      1.00e+01 1.00e-02 3.87e+01
  dihedral pdb=" CB  CYS S 160 "
           pdb=" SG  CYS S 160 "
           pdb=" SG  CYS S 230 "
           pdb=" CB  CYS S 230 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  130.52  -37.52     1      1.00e+01 1.00e-02 1.99e+01
  ... (remaining 4725 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 1192
       0.076 -    0.152: 128
       0.152 -    0.228: 8
       0.228 -    0.304: 2
       0.304 -    0.380: 1
  Chirality restraints: 1331
  Sorted by residual:
  chirality pdb=" CA  LEU R 171 "
            pdb=" N   LEU R 171 "
            pdb=" C   LEU R 171 "
            pdb=" CB  LEU R 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.62e+00
  chirality pdb=" CA  LEU R 316 "
            pdb=" N   LEU R 316 "
            pdb=" C   LEU R 316 "
            pdb=" CB  LEU R 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  ARG R 238 "
            pdb=" N   ARG R 238 "
            pdb=" C   ARG R 238 "
            pdb=" CB  ARG R 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.63e+00
  ... (remaining 1328 not shown)

  Planarity restraints: 1393
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 238 "    1.011 9.50e-02 1.11e+02   4.53e-01 1.24e+02
        pdb=" NE  ARG R 238 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 238 "   -0.009 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 238 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 238 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG R 254 "    0.865 9.50e-02 1.11e+02   3.88e-01 9.13e+01
        pdb=" NE  ARG R 254 "   -0.053 2.00e-02 2.50e+03
        pdb=" CZ  ARG R 254 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG R 254 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG R 254 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP S  74 "   -0.074 5.00e-02 4.00e+02   1.10e-01 1.92e+01
        pdb=" N   PRO S  75 "    0.189 5.00e-02 4.00e+02
        pdb=" CA  PRO S  75 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO S  75 "   -0.059 5.00e-02 4.00e+02
  ... (remaining 1390 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 416
        2.73 -     3.27: 7783
        3.27 -     3.81: 13009
        3.81 -     4.36: 15308
        4.36 -     4.90: 27175
  Nonbonded interactions: 63691
  Sorted by model distance:
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.182 2.440
  nonbonded pdb=" O   LEU R  87 "
            pdb=" OG  SER R  90 "
     model   vdw
     2.213 2.440
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.228 2.440
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.230 2.440
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.234 2.440
  ... (remaining 63686 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          2.200
  Check model and map are aligned:         0.130
  Set scattering table:                    0.070
  Process input model:                     24.020
  Find NCS groups from input model:        0.230
  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:12.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.097   8159  Z= 0.343
  Angle     :  0.732  10.014  11114  Z= 0.424
  Chirality :  0.047   0.380   1331
  Planarity :  0.017   0.453   1393
  Dihedral  : 13.948  89.995   2673
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer Outliers :  0.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.26), residues: 1063
  helix:  0.70 (0.28), residues: 356
  sheet:  0.30 (0.32), residues: 282
  loop : -1.10 (0.28), residues: 425

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.860 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 1.1332
  time to fit residues: 160.3921
Evaluate side-chains
  115 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3097
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 45 optimal weight:    7.9990
   chunk 27 optimal weight:    5.9990
   chunk 54 optimal weight:    0.4980
   chunk 43 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 32 optimal weight:    0.4980
   chunk 50 optimal weight:    6.9990
   chunk 62 optimal weight:    0.9980
   chunk 97 optimal weight:    1.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 340 ASN
A 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.1036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8159  Z= 0.184
  Angle     :  0.547   7.645  11114  Z= 0.287
  Chirality :  0.041   0.139   1331
  Planarity :  0.005   0.070   1393
  Dihedral  :  5.086  50.967   1169
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer Outliers :  1.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.12 (0.26), residues: 1063
  helix:  1.11 (0.29), residues: 351
  sheet:  0.46 (0.31), residues: 280
  loop : -1.01 (0.29), residues: 432

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 1.033 
Fit side-chains
  outliers start: 11
  outliers final: 4
  residues processed: 126
  average time/residue: 1.3077
  time to fit residues: 174.0558
Evaluate side-chains
  120 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.934 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 3
  residues processed: 2
  average time/residue: 0.6680
  time to fit residues: 2.6967
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 80 optimal weight:   20.0000
   chunk 66 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 97 optimal weight:    0.6980
   chunk 105 optimal weight:    4.9990
   chunk 86 optimal weight:   10.0000
   chunk 96 optimal weight:    0.4980
   chunk 33 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8159  Z= 0.345
  Angle     :  0.586   7.210  11114  Z= 0.309
  Chirality :  0.044   0.157   1331
  Planarity :  0.005   0.074   1393
  Dihedral  :  5.257  49.244   1169
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer Outliers :  2.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.26), residues: 1063
  helix:  0.92 (0.29), residues: 354
  sheet:  0.21 (0.31), residues: 280
  loop : -0.95 (0.29), residues: 429

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.947 
Fit side-chains
  outliers start: 16
  outliers final: 5
  residues processed: 128
  average time/residue: 1.2771
  time to fit residues: 172.9735
Evaluate side-chains
  120 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.965 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 4
  residues processed: 1
  average time/residue: 1.4471
  time to fit residues: 2.8065
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 73 optimal weight:    0.6980
   chunk 50 optimal weight:    0.3980
   chunk 10 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9980
   chunk 103 optimal weight:    0.0050
   chunk 51 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 220 GLN
A 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.1701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8159  Z= 0.138
  Angle     :  0.499   8.623  11114  Z= 0.259
  Chirality :  0.040   0.135   1331
  Planarity :  0.005   0.059   1393
  Dihedral  :  4.883  48.592   1169
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer Outliers :  2.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.24 (0.26), residues: 1063
  helix:  1.31 (0.29), residues: 353
  sheet:  0.34 (0.31), residues: 282
  loop : -0.90 (0.29), residues: 428

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.993 
Fit side-chains
  outliers start: 18
  outliers final: 7
  residues processed: 131
  average time/residue: 1.2855
  time to fit residues: 178.2513
Evaluate side-chains
  123 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 0.864 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 5
  residues processed: 2
  average time/residue: 0.5801
  time to fit residues: 2.4775
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 58 optimal weight:    3.9990
   chunk 1 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 92 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 220 GLN
A 204 GLN
A 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8159  Z= 0.286
  Angle     :  0.559   8.669  11114  Z= 0.293
  Chirality :  0.042   0.145   1331
  Planarity :  0.005   0.071   1393
  Dihedral  :  4.984  47.218   1169
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer Outliers :  2.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.19 (0.26), residues: 1063
  helix:  1.24 (0.29), residues: 351
  sheet:  0.24 (0.31), residues: 278
  loop : -0.82 (0.29), residues: 434

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.939 
Fit side-chains
  outliers start: 16
  outliers final: 8
  residues processed: 128
  average time/residue: 1.2499
  time to fit residues: 169.4452
Evaluate side-chains
  122 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 114
  time to evaluate  : 0.933 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 7
  residues processed: 1
  average time/residue: 0.0716
  time to fit residues: 1.3232
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 93 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0070
   chunk 25 optimal weight:    5.9990
   chunk 103 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.6600

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 220 GLN
A 255 ASN
R 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8159  Z= 0.142
  Angle     :  0.515   8.898  11114  Z= 0.265
  Chirality :  0.040   0.136   1331
  Planarity :  0.005   0.060   1393
  Dihedral  :  4.744  45.903   1169
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer Outliers :  2.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.40 (0.26), residues: 1063
  helix:  1.49 (0.29), residues: 348
  sheet:  0.37 (0.31), residues: 280
  loop : -0.76 (0.30), residues: 435

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.963 
Fit side-chains
  outliers start: 17
  outliers final: 12
  residues processed: 134
  average time/residue: 1.2151
  time to fit residues: 172.6845
Evaluate side-chains
  129 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 117
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 10
  residues processed: 3
  average time/residue: 0.9572
  time to fit residues: 4.3182
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 58 optimal weight:    4.9990
   chunk 75 optimal weight:    0.0270
   chunk 87 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 64 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    2.2046

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
A 255 ASN
R 291 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8174
moved from start:          0.2114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8159  Z= 0.316
  Angle     :  0.578   8.183  11114  Z= 0.302
  Chirality :  0.043   0.150   1331
  Planarity :  0.005   0.072   1393
  Dihedral  :  4.939  44.988   1169
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer Outliers :  1.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.20 (0.26), residues: 1063
  helix:  1.23 (0.28), residues: 351
  sheet:  0.25 (0.31), residues: 283
  loop : -0.80 (0.30), residues: 429

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 123
  time to evaluate  : 0.869 
Fit side-chains
  outliers start: 14
  outliers final: 8
  residues processed: 134
  average time/residue: 1.2332
  time to fit residues: 174.9483
Evaluate side-chains
  127 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.887 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 8
  residues processed: 0
  time to fit residues: 1.2279
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 31 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 19 optimal weight:    6.9990
   chunk 65 optimal weight:    4.9990
   chunk 70 optimal weight:   20.0000
   chunk 50 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0470
   chunk 81 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    1.5084

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
B 220 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.2199

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8159  Z= 0.232
  Angle     :  0.565   8.647  11114  Z= 0.295
  Chirality :  0.042   0.142   1331
  Planarity :  0.005   0.068   1393
  Dihedral  :  4.885  45.609   1169
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer Outliers :  1.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.26), residues: 1063
  helix:  1.27 (0.28), residues: 355
  sheet:  0.31 (0.31), residues: 281
  loop : -0.88 (0.30), residues: 427

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.924 
Fit side-chains
  outliers start: 15
  outliers final: 9
  residues processed: 133
  average time/residue: 1.3123
  time to fit residues: 184.8212
Evaluate side-chains
  128 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.965 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 8
  residues processed: 1
  average time/residue: 1.1537
  time to fit residues: 2.4978
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 98 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    4.9990
   chunk 75 optimal weight:    0.3980
   chunk 29 optimal weight:    5.9990
   chunk 86 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
A 255 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8159  Z= 0.159
  Angle     :  0.551   9.225  11114  Z= 0.285
  Chirality :  0.041   0.155   1331
  Planarity :  0.005   0.063   1393
  Dihedral  :  4.723  45.618   1169
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer Outliers :  1.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.35 (0.26), residues: 1063
  helix:  1.52 (0.29), residues: 348
  sheet:  0.38 (0.31), residues: 279
  loop : -0.90 (0.30), residues: 436

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 0.920 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 135
  average time/residue: 1.2452
  time to fit residues: 177.9085
Evaluate side-chains
  129 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 121
  time to evaluate  : 0.943 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 8
  residues processed: 0
  time to fit residues: 1.1565
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 62 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 84 optimal weight:    0.0470
   chunk 8 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0040
   chunk 67 optimal weight:    7.9990
   chunk 90 optimal weight:    5.9990
   overall best weight:    0.5090

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 220 GLN
R 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8159  Z= 0.143
  Angle     :  0.547  10.228  11114  Z= 0.280
  Chirality :  0.040   0.170   1331
  Planarity :  0.004   0.063   1393
  Dihedral  :  4.604  45.421   1169
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer Outliers :  1.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1063
  helix:  1.69 (0.29), residues: 348
  sheet:  0.42 (0.30), residues: 284
  loop : -0.87 (0.30), residues: 431

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

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

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2126 Ramachandran restraints generated.
    1063 Oldfield, 0 Emsley, 1063 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.898 
Fit side-chains
  outliers start: 12
  outliers final: 10
  residues processed: 127
  average time/residue: 1.3162
  time to fit residues: 176.7420
Evaluate side-chains
  124 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.929 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 10
  residues processed: 1
  average time/residue: 0.2040
  time to fit residues: 1.4371
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 23 optimal weight:    5.9990
   chunk 85 optimal weight:    0.3980
   chunk 35 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 4 optimal weight:    0.0370
   overall best weight:    2.2262

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 176 GLN
B 220 GLN
B 230 ASN
A 255 ASN
R 291 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.098790 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.075111 restraints weight = 15350.221|
|-----------------------------------------------------------------------------|
r_work (start): 0.3100 rms_B_bonded: 2.51
r_work: 0.2966 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.2313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.044   8159  Z= 0.320
  Angle     :  0.612   9.456  11114  Z= 0.317
  Chirality :  0.043   0.162   1331
  Planarity :  0.005   0.070   1393
  Dihedral  :  4.849  45.444   1169
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer Outliers :  1.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    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:  0.29 (0.26), residues: 1063
  helix:  1.40 (0.28), residues: 348
  sheet:  0.34 (0.31), residues: 281
  loop : -0.88 (0.30), residues: 434

===============================================================================
Job complete
usr+sys time: 3318.43 seconds
wall clock time: 59 minutes 27.93 seconds (3567.93 seconds total)