Starting phenix.real_space_refine
on Mon Mar 11 10:20:41 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/03_2024/8id9_35360_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/03_2024/8id9_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_35360/03_2024/8id9_35360.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/03_2024/8id9_35360.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/03_2024/8id9_35360_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8id9_35360/03_2024/8id9_35360_updated.pdb"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 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: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 4.83, per 1000 atoms: 0.60
  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: 3.28
  Conformation dependent library (CDL) restraints added in 1.8 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: 1.62
  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: 2.19

  Time building geometry restraints manager: 3.37 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:                  0.000
  Normalize map: mean=0, sd=1:             0.310
  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:          1.950
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     25.600
  Find NCS groups from input model:        0.220
  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:12.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.760
-------------------------------------------------------------------------------
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 %
    Allowed  :  6.12 %
    Favored  : 93.75 %
  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

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP R 104 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.019   0.001   PHE R 263 
 TYR   0.008   0.001   TYR S 191 
 ARG   0.005   0.001   ARG S  18 

*********************** 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  : 0.867 
Fit side-chains
REVERT: A   53 MET cc_start: 0.5715 (mmm) cc_final: 0.5334 (mmm)
REVERT: R  290 GLN cc_start: 0.8340 (pp30) cc_final: 0.8099 (pp30)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 1.2793
  time to fit residues: 179.9734
Evaluate side-chains
  115 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
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:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8159  Z= 0.183
  Angle     :  0.538   7.201  11114  Z= 0.284
  Chirality :  0.041   0.139   1331
  Planarity :  0.005   0.070   1393
  Dihedral  :  5.080  50.953   1169
  Min Nonbonded Distance : 2.152

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.59 %
    Favored  : 86.98 %
  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:  0.13 (0.26), residues: 1063
  helix:  1.12 (0.29), residues: 351
  sheet:  0.46 (0.31), residues: 280
  loop : -1.00 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 104 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.015   0.001   PHE R 176 
 TYR   0.009   0.001   TYR A 302 
 ARG   0.005   0.000   ARG A 208 

*********************** 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  : 0.977 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.7813 (mmmm) cc_final: 0.7550 (mmmm)
REVERT: A   53 MET cc_start: 0.5671 (mmm) cc_final: 0.5338 (mmm)
REVERT: A  243 MET cc_start: 0.8566 (tpp) cc_final: 0.8159 (mpp)
REVERT: R  290 GLN cc_start: 0.8505 (pp30) cc_final: 0.8165 (pp30)
  outliers start: 11
  outliers final: 4
  residues processed: 126
  average time/residue: 1.2854
  time to fit residues: 171.4173
Evaluate side-chains
  120 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 116
  time to evaluate  : 0.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    7.9990
   chunk 80 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   chunk 97 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9990
   chunk 86 optimal weight:   10.0000
   chunk 96 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.9186

-------------------------------------------------------------------------------
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: 0.8111
moved from start:          0.1359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8159  Z= 0.163
  Angle     :  0.496   7.805  11114  Z= 0.261
  Chirality :  0.040   0.137   1331
  Planarity :  0.005   0.057   1393
  Dihedral  :  4.858  48.962   1169
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.67 %
    Favored  : 84.90 %
  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:  0.26 (0.26), residues: 1063
  helix:  1.34 (0.29), residues: 352
  sheet:  0.40 (0.31), residues: 282
  loop : -0.94 (0.29), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 104 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.018   0.001   PHE R  25 
 TYR   0.008   0.001   TYR S 191 
 ARG   0.007   0.000   ARG A 208 

*********************** 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
  132 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 0.787 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.7858 (mmmm) cc_final: 0.7578 (mmmm)
REVERT: A   53 MET cc_start: 0.5660 (mmm) cc_final: 0.5236 (mmm)
REVERT: A  243 MET cc_start: 0.8625 (tpp) cc_final: 0.8065 (mpp)
REVERT: R  290 GLN cc_start: 0.8550 (pp30) cc_final: 0.8216 (pp30)
  outliers start: 11
  outliers final: 5
  residues processed: 127
  average time/residue: 1.2561
  time to fit residues: 168.7743
Evaluate side-chains
  120 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 96 optimal weight:    0.0000
   chunk 73 optimal weight:    3.9990
   chunk 50 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 51 optimal weight:    8.9990
   chunk 92 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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: 0.8090
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8159  Z= 0.128
  Angle     :  0.471   7.928  11114  Z= 0.247
  Chirality :  0.040   0.134   1331
  Planarity :  0.004   0.057   1393
  Dihedral  :  4.631  47.237   1169
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 15.10 %
    Favored  : 83.33 %
  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:  1.57 (0.29), residues: 350
  sheet:  0.39 (0.31), residues: 281
  loop : -0.88 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP R 104 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.010   0.001   PHE R  88 
 TYR   0.011   0.001   TYR A 302 
 ARG   0.007   0.000   ARG R 254 

*********************** 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
  132 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.7822 (mmmm) cc_final: 0.7606 (mmmm)
REVERT: A  304 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: R  290 GLN cc_start: 0.8557 (pp30) cc_final: 0.8202 (pp30)
REVERT: R  291 ASN cc_start: 0.8751 (t0) cc_final: 0.8531 (t160)
  outliers start: 12
  outliers final: 6
  residues processed: 127
  average time/residue: 1.2279
  time to fit residues: 165.1225
Evaluate side-chains
  125 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 119
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  302 LEU
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:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 42 optimal weight:    5.9990
   chunk 88 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 92 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
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
A 255 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1752

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= 0.292
  Angle     :  0.542   7.967  11114  Z= 0.284
  Chirality :  0.042   0.144   1331
  Planarity :  0.005   0.067   1393
  Dihedral  :  4.793  45.949   1169
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.80 %
    Favored  : 80.86 %
  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:  1.38 (0.29), residues: 352
  sheet:  0.32 (0.31), residues: 278
  loop : -0.85 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 104 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.022   0.002   PHE R  25 
 TYR   0.009   0.001   TYR R 116 
 ARG   0.010   0.001   ARG R 238 

*********************** 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
  138 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 120
  time to evaluate  : 0.972 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8141 (m-80) cc_final: 0.7747 (m-80)
REVERT: B  280 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8038 (ttpp)
REVERT: A   35 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7713 (mmtm)
REVERT: A  243 MET cc_start: 0.8745 (tpp) cc_final: 0.8138 (mpp)
REVERT: A  304 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8721 (tm-30)
REVERT: R  270 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7248 (mtt)
REVERT: R  290 GLN cc_start: 0.8632 (pp30) cc_final: 0.8231 (pp30)
  outliers start: 18
  outliers final: 7
  residues processed: 130
  average time/residue: 1.2386
  time to fit residues: 170.5439
Evaluate side-chains
  125 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   46 ARG
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue  241 ASN
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  270 MET
Chi-restraints excluded: chain R residue  271 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 93 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 103 optimal weight:    0.5980
   chunk 85 optimal weight:    0.4980
   chunk 47 optimal weight:    4.9990
   chunk 8 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 99 optimal weight:    4.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
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: 0.8122
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8159  Z= 0.165
  Angle     :  0.492   8.361  11114  Z= 0.256
  Chirality :  0.040   0.136   1331
  Planarity :  0.005   0.060   1393
  Dihedral  :  4.626  44.710   1169
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 18.49 %
    Favored  : 79.30 %
  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:  0.44 (0.26), residues: 1063
  helix:  1.61 (0.29), residues: 348
  sheet:  0.35 (0.31), residues: 276
  loop : -0.79 (0.29), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 104 
 HIS   0.002   0.001   HIS S  35 
 PHE   0.009   0.001   PHE A 189 
 TYR   0.010   0.001   TYR A 302 
 ARG   0.011   0.000   ARG A 208 

*********************** 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
  139 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.7895 (mmmm) cc_final: 0.7663 (mmtm)
REVERT: A  186 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7671 (mm-30)
REVERT: A  243 MET cc_start: 0.8738 (tpp) cc_final: 0.8037 (mpp)
REVERT: A  304 GLN cc_start: 0.9134 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: R  290 GLN cc_start: 0.8642 (pp30) cc_final: 0.8229 (pp30)
  outliers start: 17
  outliers final: 10
  residues processed: 134
  average time/residue: 1.2491
  time to fit residues: 177.3482
Evaluate side-chains
  128 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  319 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0980
   chunk 87 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   chunk 103 optimal weight:    0.5980
   chunk 64 optimal weight:    0.0010
   chunk 62 optimal weight:    4.9990
   chunk 47 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.4988

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 0.8099
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8159  Z= 0.133
  Angle     :  0.501   8.576  11114  Z= 0.257
  Chirality :  0.040   0.133   1331
  Planarity :  0.004   0.057   1393
  Dihedral  :  4.468  43.539   1169
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 6.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 19.27 %
    Favored  : 79.04 %
  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:  0.54 (0.26), residues: 1063
  helix:  1.71 (0.29), residues: 350
  sheet:  0.40 (0.31), residues: 275
  loop : -0.75 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP R 104 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.024   0.001   PHE R  25 
 TYR   0.007   0.001   TYR S 191 
 ARG   0.012   0.000   ARG A 208 

*********************** 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
  133 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.904 
Fit side-chains
REVERT: A   35 LYS cc_start: 0.7835 (mmmm) cc_final: 0.7620 (mmtm)
REVERT: A  242 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.7818 (mpp-170)
REVERT: A  243 MET cc_start: 0.8747 (tpp) cc_final: 0.8090 (mpp)
REVERT: A  304 GLN cc_start: 0.9111 (tm-30) cc_final: 0.8709 (tm-30)
REVERT: R  290 GLN cc_start: 0.8650 (pp30) cc_final: 0.8182 (pp30)
REVERT: R  291 ASN cc_start: 0.8746 (t0) cc_final: 0.8511 (t160)
  outliers start: 13
  outliers final: 9
  residues processed: 129
  average time/residue: 1.3250
  time to fit residues: 180.9306
Evaluate side-chains
  125 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 116
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain A residue  348 LEU
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  302 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 31 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 19 optimal weight:    5.9990
   chunk 65 optimal weight:    6.9990
   chunk 70 optimal weight:    6.9990
   chunk 50 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8159  Z= 0.364
  Angle     :  0.608   8.408  11114  Z= 0.315
  Chirality :  0.044   0.161   1331
  Planarity :  0.005   0.073   1393
  Dihedral  :  4.845  43.486   1169
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 19.92 %
    Favored  : 78.26 %
  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:  1.32 (0.28), residues: 352
  sheet:  0.32 (0.31), residues: 285
  loop : -0.89 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP R 104 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.015   0.002   PHE R  27 
 TYR   0.013   0.002   TYR B  59 
 ARG   0.010   0.001   ARG R 238 

*********************** 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
  136 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.360 
Fit side-chains
REVERT: B  280 LYS cc_start: 0.8738 (OUTLIER) cc_final: 0.8219 (ttpp)
REVERT: Y   62 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7663 (mtt90)
REVERT: A  243 MET cc_start: 0.8764 (tpp) cc_final: 0.8033 (mpp)
REVERT: A  304 GLN cc_start: 0.9128 (tm-30) cc_final: 0.8699 (tm-30)
REVERT: R  290 GLN cc_start: 0.8738 (pp30) cc_final: 0.8249 (pp30)
REVERT: R  291 ASN cc_start: 0.8775 (t0) cc_final: 0.8526 (t160)
  outliers start: 14
  outliers final: 6
  residues processed: 132
  average time/residue: 1.4071
  time to fit residues: 196.7055
Evaluate side-chains
  126 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain R residue   55 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  195 THR
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  302 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 90 optimal weight:    0.9980
   chunk 96 optimal weight:    0.0170
   chunk 98 optimal weight:    2.9990
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0770
   chunk 29 optimal weight:    0.4980
   chunk 86 optimal weight:   10.0000
   chunk 95 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 101 optimal weight:    0.7980
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
A 255 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8159  Z= 0.136
  Angle     :  0.519   9.061  11114  Z= 0.265
  Chirality :  0.040   0.175   1331
  Planarity :  0.005   0.060   1393
  Dihedral  :  4.555  42.780   1169
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 21.61 %
    Favored  : 77.47 %
  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:  1.74 (0.29), residues: 348
  sheet:  0.40 (0.31), residues: 281
  loop : -0.90 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP R 104 
 HIS   0.002   0.000   HIS S  35 
 PHE   0.027   0.001   PHE R  25 
 TYR   0.007   0.001   TYR S  60 
 ARG   0.016   0.001   ARG R 238 

*********************** 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
  127 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 120
  time to evaluate  : 0.935 
Fit side-chains
REVERT: B  280 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.7921 (ttpp)
REVERT: Y   62 ARG cc_start: 0.7807 (mtm180) cc_final: 0.7574 (mtt90)
REVERT: A  243 MET cc_start: 0.8737 (tpp) cc_final: 0.8040 (mpp)
REVERT: A  304 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8665 (tm-30)
REVERT: R  239 LYS cc_start: 0.8356 (tptp) cc_final: 0.8155 (tptm)
  outliers start: 7
  outliers final: 4
  residues processed: 125
  average time/residue: 1.2928
  time to fit residues: 170.8881
Evaluate side-chains
  121 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 116
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  302 LEU
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:    9.9990
   chunk 106 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0870
   chunk 65 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    0.0170
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.7398

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
R 291 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8159  Z= 0.160
  Angle     :  0.540  10.762  11114  Z= 0.272
  Chirality :  0.040   0.163   1331
  Planarity :  0.005   0.063   1393
  Dihedral  :  4.434  42.510   1169
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 22.27 %
    Favored  : 76.95 %
  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:  0.53 (0.26), residues: 1063
  helix:  1.79 (0.29), residues: 351
  sheet:  0.47 (0.31), residues: 278
  loop : -0.91 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP R 104 
 HIS   0.003   0.001   HIS S  35 
 PHE   0.010   0.001   PHE A 189 
 TYR   0.014   0.001   TYR A 302 
 ARG   0.009   0.000   ARG R 238 

********************** 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
  126 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.853 
Fit side-chains
REVERT: Y   62 ARG cc_start: 0.7848 (mtm180) cc_final: 0.7619 (mtt90)
REVERT: A  208 ARG cc_start: 0.8606 (mtm110) cc_final: 0.8362 (mtm110)
REVERT: A  243 MET cc_start: 0.8737 (tpp) cc_final: 0.8062 (mpp)
REVERT: A  304 GLN cc_start: 0.9057 (tm-30) cc_final: 0.8669 (tm-30)
REVERT: R  290 GLN cc_start: 0.8790 (pp30) cc_final: 0.8407 (pp30)
  outliers start: 6
  outliers final: 7
  residues processed: 125
  average time/residue: 1.2400
  time to fit residues: 164.0449
Evaluate side-chains
  126 residues out of total 939 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  280 LYS
Chi-restraints excluded: chain B residue  284 LEU
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain R residue  135 GLU
Chi-restraints excluded: chain R residue  233 ILE
Chi-restraints excluded: chain R residue  302 LEU
Chi-restraints excluded: chain R residue  319 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0970
   chunk 10 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 74 optimal weight:    4.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.5782

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 176 GLN
B 220 GLN
A 255 ASN
R 291 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.100485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.076362 restraints weight = 15189.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.55
r_work: 0.2984 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   8159  Z= 0.244
  Angle     :  0.563  10.461  11114  Z= 0.288
  Chirality :  0.042   0.149   1331
  Planarity :  0.005   0.076   1393
  Dihedral  :  4.527  42.290   1169
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 22.27 %
    Favored  : 76.56 %
  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:  0.46 (0.26), residues: 1063
  helix:  1.63 (0.29), residues: 353
  sheet:  0.44 (0.31), residues: 279
  loop : -0.88 (0.30), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP R 104 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.026   0.001   PHE R  25 
 TYR   0.008   0.001   TYR B  59 
 ARG   0.017   0.001   ARG R 238 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3392.74 seconds
wall clock time: 60 minutes 48.97 seconds (3648.97 seconds total)