Starting phenix.real_space_refine
on Mon Jul 28 09:47:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v69_31739/07_2025/7v69_31739.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v69_31739/07_2025/7v69_31739.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v69_31739/07_2025/7v69_31739.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v69_31739/07_2025/7v69_31739.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v69_31739/07_2025/7v69_31739.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v69_31739/07_2025/7v69_31739.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2134 atoms to isotropic.
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      65      5.16       5
     C    5468      2.51       5
     N    1446      2.21       5
     O    1560      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8539
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1649
          Classifications: {'peptide': 218}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 2, 'TRANS': 215}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 107
          Unresolved non-hydrogen angles: 127
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 10, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 69
    Chain: "B"
      Number of atoms: 2553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2553
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 61
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 4, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 46
    Chain: "C"
      Number of atoms: 435
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 435
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "S"
      Number of atoms: 1746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1746
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 29
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 27
    Chain: "R"
      Number of atoms: 2156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2156
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 266}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 31
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 19
  Time building chain proxies: 5.12, per 1000 atoms: 0.60
  Number of scatterers: 8539
  At special positions: 0
  Unit cell: (90.48, 121.68, 122.72, 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      65     16.00
     O    1560      8.00
     N    1446      7.00
     C    5468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 105 " - pdb=" SG  CYS R 185 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 426 " - pdb=" SG  CYS R 429 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 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: 2.46
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 13 sheets defined
      39.1% alpha, 16.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 33
      removed outlier: 3.964A  pdb=" N   LYS A  29 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.620A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 204
      removed outlier: 4.207A  pdb=" N   GLY A 203 " --> pdb=" O   ASP A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.726A  pdb=" N   TRP A 211 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 270 through 281
    Processing helix  chain 'A' and resid 282 through 286
      removed outlier: 4.138A  pdb=" N   ILE A 285 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.536A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
      removed outlier: 3.616A  pdb=" N   GLN B   9 " --> pdb=" O   ASP B   5 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   GLU B  10 " --> pdb=" O   GLN B   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'B' and resid 280 through 282
      No H-bonds generated for 'chain 'B' and resid 280 through 282'
    Processing helix  chain 'C' and resid 9 through 24
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 34 through 43
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.565A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 53 through 56
    Processing helix  chain 'S' and resid 87 through 91
      removed outlier: 3.833A  pdb=" N   THR S  91 " --> pdb=" O   SER S  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 60
      removed outlier: 3.707A  pdb=" N   THR R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   VAL R  38 " --> pdb=" O   PHE R  34 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   LEU R  52 " --> pdb=" O   VAL R  48 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   VAL R  53 " --> pdb=" O   GLY R  49 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LEU R  55 " --> pdb=" O   ILE R  51 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS R  58 " --> pdb=" O   MET R  54 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ASN R  60 " --> pdb=" O   SER R  56 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 61 through 64
    Processing helix  chain 'R' and resid 65 through 66
      No H-bonds generated for 'chain 'R' and resid 65 through 66'
    Processing helix  chain 'R' and resid 67 through 95
      removed outlier: 4.206A  pdb=" N   LEU R  71 " --> pdb=" O   ASN R  67 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   PHE R  84 " --> pdb=" O   ILE R  80 " (cutoff:3.500A)
      removed outlier: 4.614A  pdb=" N   MET R  86 " --> pdb=" O   GLY R  82 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   ASN R  87 " --> pdb=" O   ALA R  83 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   LYS R  95 " --> pdb=" O   VAL R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 101 through 136
      removed outlier: 3.594A  pdb=" N   CYS R 105 " --> pdb=" O   GLY R 101 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   ALA R 110 " --> pdb=" O   ASP R 106 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   TYR R 113 " --> pdb=" O   LEU R 109 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   VAL R 115 " --> pdb=" O   LEU R 111 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL R 120 " --> pdb=" O   SER R 116 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 139 through 144
    Processing helix  chain 'R' and resid 145 through 170
      removed outlier: 3.805A  pdb=" N   MET R 152 " --> pdb=" O   MET R 148 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA R 155 " --> pdb=" O   LEU R 151 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   TRP R 157 " --> pdb=" O   ILE R 153 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER R 160 " --> pdb=" O   ALA R 156 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   PHE R 161 " --> pdb=" O   TRP R 157 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA R 165 " --> pdb=" O   PHE R 161 " (cutoff:3.500A)
      Proline residue:  R 166  - end of helix
      removed outlier: 3.638A  pdb=" N   LEU R 169 " --> pdb=" O   ALA R 165 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 170 through 176
      removed outlier: 3.745A  pdb=" N   VAL R 175 " --> pdb=" O   TRP R 171 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 192 through 202
      removed outlier: 3.734A  pdb=" N   GLY R 198 " --> pdb=" O   ALA R 194 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA R 202 " --> pdb=" O   GLY R 198 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 204 through 222
      removed outlier: 3.826A  pdb=" N   VAL R 213 " --> pdb=" O   VAL R 209 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 392 through 423
      removed outlier: 3.705A  pdb=" N   ALA R 404 " --> pdb=" O   ARG R 400 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ALA R 408 " --> pdb=" O   ALA R 404 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   PHE R 409 " --> pdb=" O   ILE R 405 " (cutoff:3.500A)
      Proline residue:  R 415  - end of helix
    Processing helix  chain 'R' and resid 432 through 439
      removed outlier: 4.029A  pdb=" N   SER R 436 " --> pdb=" O   ASP R 432 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 440 through 455
      Proline residue:  R 450  - end of helix
    Processing helix  chain 'R' and resid 457 through 471
    Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199
      removed outlier: 6.851A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.606A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.792A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.290A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.850A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.267A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.199A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.725A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.552A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B 328 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY B 319 " --> pdb=" O   ALA B 328 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 61
      removed outlier: 6.777A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105
      removed outlier: 3.607A  pdb=" N   ALA B 104 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 5.835A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150
      removed outlier: 6.836A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.676A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 5.883A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192
      removed outlier: 3.631A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   SER B 191 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   VAL B 200 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.018A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.370A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
    Processing sheet with id=AA9, first strand: chain 'S' and resid 4 through 7
      removed outlier: 4.089A  pdb=" N   VAL S   5 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12
      removed outlier: 6.859A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 135 through 136
      removed outlier: 6.626A  pdb=" N   VAL S 135 " --> pdb=" O   GLU S 234 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'S' and resid 144 through 148
      removed outlier: 3.534A  pdb=" N   PHE S 200 " --> pdb=" O   CYS S 147 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 177
      removed outlier: 6.782A  pdb=" N   TRP S 164 " --> pdb=" O   LEU S 176 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   MET S 218 " --> pdb=" O   TYR S 163 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR S 216 " --> pdb=" O   PHE S 165 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1017 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: 2.53

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2717
        1.34 -     1.46: 2006
        1.46 -     1.58: 3905
        1.58 -     1.70: 0
        1.70 -     1.81: 94
  Bond restraints: 8722
  Sorted by residual:
  bond pdb=" C   GLY B 116 "
       pdb=" O   GLY B 116 "
    ideal  model  delta    sigma   weight residual
    1.239  1.230  0.009 8.50e-03 1.38e+04 1.08e+00
  bond pdb=" C   SER R 191 "
       pdb=" N   ASN R 192 "
    ideal  model  delta    sigma   weight residual
    1.326  1.343 -0.017 1.66e-02 3.63e+03 1.01e+00
  bond pdb=" CA  THR B 263 "
       pdb=" CB  THR B 263 "
    ideal  model  delta    sigma   weight residual
    1.529  1.542 -0.013 1.38e-02 5.25e+03 9.53e-01
  bond pdb=" CA  ASP B 247 "
       pdb=" CB  ASP B 247 "
    ideal  model  delta    sigma   weight residual
    1.529  1.546 -0.017 1.78e-02 3.16e+03 8.77e-01
  bond pdb=" N   GLY B 185 "
       pdb=" CA  GLY B 185 "
    ideal  model  delta    sigma   weight residual
    1.446  1.456 -0.010 1.08e-02 8.57e+03 8.71e-01
  ... (remaining 8717 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.75: 11580
        1.75 -     3.50: 241
        3.50 -     5.25: 28
        5.25 -     7.01: 9
        7.01 -     8.76: 1
  Bond angle restraints: 11859
  Sorted by residual:
  angle pdb=" N   SER R 428 "
        pdb=" CA  SER R 428 "
        pdb=" C   SER R 428 "
      ideal   model   delta    sigma   weight residual
     114.64  109.07    5.57 1.52e+00 4.33e-01 1.34e+01
  angle pdb=" CB  MET B 262 "
        pdb=" CG  MET B 262 "
        pdb=" SD  MET B 262 "
      ideal   model   delta    sigma   weight residual
     112.70  103.94    8.76 3.00e+00 1.11e-01 8.52e+00
  angle pdb=" CA  SER R 428 "
        pdb=" C   SER R 428 "
        pdb=" N   CYS R 429 "
      ideal   model   delta    sigma   weight residual
     119.58  115.95    3.63 1.39e+00 5.18e-01 6.83e+00
  angle pdb=" N   GLY S 213 "
        pdb=" CA  GLY S 213 "
        pdb=" C   GLY S 213 "
      ideal   model   delta    sigma   weight residual
     110.58  114.06   -3.48 1.35e+00 5.49e-01 6.65e+00
  angle pdb=" C   GLY B 131 "
        pdb=" N   ASN B 132 "
        pdb=" CA  ASN B 132 "
      ideal   model   delta    sigma   weight residual
     121.54  126.35   -4.81 1.91e+00 2.74e-01 6.34e+00
  ... (remaining 11854 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 4692
       17.55 -    35.09: 362
       35.09 -    52.64: 51
       52.64 -    70.19: 6
       70.19 -    87.73: 7
  Dihedral angle restraints: 5118
    sinusoidal: 1859
      harmonic: 3259
  Sorted by residual:
  dihedral pdb=" CB  CYS R 426 "
           pdb=" SG  CYS R 426 "
           pdb=" SG  CYS R 429 "
           pdb=" CB  CYS R 429 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -15.41  -70.59     1      1.00e+01 1.00e-02 6.41e+01
  dihedral pdb=" CA  PHE B 234 "
           pdb=" C   PHE B 234 "
           pdb=" N   PHE B 235 "
           pdb=" CA  PHE B 235 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.77   20.23     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  PHE R  84 "
           pdb=" C   PHE R  84 "
           pdb=" N   SER R  85 "
           pdb=" CA  SER R  85 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.84  -18.16     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 5115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1055
       0.046 -    0.091: 265
       0.091 -    0.137: 56
       0.137 -    0.182: 7
       0.182 -    0.228: 2
  Chirality restraints: 1385
  Sorted by residual:
  chirality pdb=" CB  ILE R 201 "
            pdb=" CA  ILE R 201 "
            pdb=" CG1 ILE R 201 "
            pdb=" CG2 ILE R 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CB  THR B 181 "
            pdb=" CA  THR B 181 "
            pdb=" OG1 THR B 181 "
            pdb=" CG2 THR B 181 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.19e-01
  ... (remaining 1382 not shown)

  Planarity restraints: 1483
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 247 "   -0.008 2.00e-02 2.50e+03   1.54e-02 2.38e+00
        pdb=" C   ASP B 247 "    0.027 2.00e-02 2.50e+03
        pdb=" O   ASP B 247 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ALA B 248 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER S 172 "    0.024 5.00e-02 4.00e+02   3.68e-02 2.16e+00
        pdb=" N   PRO S 173 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO S 173 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO S 173 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE R 201 "   -0.007 2.00e-02 2.50e+03   1.39e-02 1.94e+00
        pdb=" C   ILE R 201 "    0.024 2.00e-02 2.50e+03
        pdb=" O   ILE R 201 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ALA R 202 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 1480 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 146
        2.66 -     3.22: 8107
        3.22 -     3.78: 13525
        3.78 -     4.34: 18262
        4.34 -     4.90: 29704
  Nonbonded interactions: 69744
  Sorted by model distance:
  nonbonded pdb=" O   ARG S  67 "
            pdb=" OG1 THR S  84 "
     model   vdw
     2.096 3.040
  nonbonded pdb=" OE2 GLU A   8 "
            pdb=" OH  TYR S 163 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" OG  SER R  85 "
            pdb=" OD1 ASP R 112 "
     model   vdw
     2.157 3.040
  nonbonded pdb=" NH1 ARG B  68 "
            pdb=" OD1 ASP B  83 "
     model   vdw
     2.177 3.120
  nonbonded pdb=" OE1 GLN A 304 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.213 3.040
  ... (remaining 69739 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.740
  Find NCS groups from input model:        0.090
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6252
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      :  0.003   0.029   8724  Z= 0.138
  Angle     :  0.654   8.757  11863  Z= 0.380
  Chirality :  0.042   0.228   1385
  Planarity :  0.004   0.046   1483
  Dihedral  : 12.638  87.731   3008
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.22 %
    Favored  : 99.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -2.02 (0.24), residues: 1104
  helix: -0.52 (0.27), residues: 386
  sheet: -2.17 (0.30), residues: 246
  loop : -1.40 (0.27), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 169 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.024   0.001   PHE B 234 
 TYR   0.018   0.001   TYR S 103 
 ARG   0.005   0.001   ARG B  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19353 (  363)
  hydrogen bonds       : angle       7.30817 ( 1017)
  SS BOND              : bond        0.00239 (    2)
  SS BOND              : angle       1.45880 (    4)
  covalent geometry    : bond        0.00252 ( 8722)
  covalent geometry    : angle       0.65331 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 MET cc_start: 0.6117 (tmm) cc_final: 0.5842 (tmm)
REVERT: B  100 VAL cc_start: 0.8258 (p) cc_final: 0.7987 (m)
REVERT: B  105 TYR cc_start: 0.7505 (t80) cc_final: 0.7206 (t80)
REVERT: B  129 ARG cc_start: 0.6082 (tmt-80) cc_final: 0.5026 (ttt-90)
REVERT: B  155 ASN cc_start: 0.7515 (t0) cc_final: 0.7239 (t0)
REVERT: B  188 MET cc_start: 0.6510 (mmm) cc_final: 0.5771 (mmm)
REVERT: B  308 LEU cc_start: 0.6990 (tt) cc_final: 0.6727 (tt)
REVERT: S   79 LEU cc_start: 0.7017 (tp) cc_final: 0.6810 (tp)
REVERT: S  162 LEU cc_start: 0.7824 (tt) cc_final: 0.7611 (tp)
REVERT: R   42 LEU cc_start: 0.6226 (mt) cc_final: 0.5975 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2334
  time to fit residues: 52.9933
Evaluate side-chains
  155 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 28 optimal weight:    0.9990
   chunk 55 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 98 optimal weight:    0.2980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  88 ASN
B 110 ASN
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN
S  39 GLN
** R 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.178494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.162363 restraints weight = 12777.555|
|-----------------------------------------------------------------------------|
r_work (start): 0.3989 rms_B_bonded: 1.85
r_work: 0.3909 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3781 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.1447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8724  Z= 0.172
  Angle     :  0.619   8.825  11863  Z= 0.322
  Chirality :  0.044   0.147   1385
  Planarity :  0.004   0.037   1483
  Dihedral  :  4.949  29.012   1205
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  :  9.72 %
    Favored  : 88.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.93 (0.24), residues: 1104
  helix: -0.28 (0.26), residues: 384
  sheet: -2.18 (0.28), residues: 265
  loop : -1.41 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.006   0.001   HIS C  44 
 PHE   0.021   0.002   PHE B 235 
 TYR   0.018   0.002   TYR B 264 
 ARG   0.004   0.001   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03812 (  363)
  hydrogen bonds       : angle       5.23856 ( 1017)
  SS BOND              : bond        0.00290 (    2)
  SS BOND              : angle       1.61758 (    4)
  covalent geometry    : bond        0.00374 ( 8722)
  covalent geometry    : angle       0.61810 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 175
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A   23 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8313 (mt)
REVERT: A   24 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7488 (mtm110)
REVERT: A  210 LYS cc_start: 0.8504 (mmmm) cc_final: 0.8276 (mmmm)
REVERT: A  253 ILE cc_start: 0.8101 (tt) cc_final: 0.7729 (pt)
REVERT: B   61 MET cc_start: 0.6922 (tmm) cc_final: 0.6446 (tmm)
REVERT: B  105 TYR cc_start: 0.7862 (t80) cc_final: 0.7483 (t80)
REVERT: B  188 MET cc_start: 0.7231 (mmm) cc_final: 0.7002 (mmm)
REVERT: B  233 CYS cc_start: 0.7764 (t) cc_final: 0.7427 (p)
REVERT: B  247 ASP cc_start: 0.6813 (t0) cc_final: 0.6511 (t0)
REVERT: B  255 LEU cc_start: 0.7759 (mt) cc_final: 0.7523 (mt)
REVERT: B  271 CYS cc_start: 0.7296 (p) cc_final: 0.7011 (p)
REVERT: B  300 LEU cc_start: 0.7707 (mt) cc_final: 0.7437 (mt)
REVERT: B  325 MET cc_start: 0.8035 (tpt) cc_final: 0.7834 (tpt)
REVERT: C   42 GLU cc_start: 0.6703 (pp20) cc_final: 0.6439 (pp20)
REVERT: S   67 ARG cc_start: 0.5031 (ptt180) cc_final: 0.4533 (ttp-170)
REVERT: S   79 LEU cc_start: 0.7285 (tp) cc_final: 0.7019 (tp)
REVERT: R   42 LEU cc_start: 0.6306 (mt) cc_final: 0.6071 (mt)
  outliers start: 14
  outliers final: 10
  residues processed: 177
  average time/residue: 0.2046
  time to fit residues: 49.6842
Evaluate side-chains
  172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 161
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  152 MET
Chi-restraints excluded: chain R residue  174 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 88 optimal weight:    0.4980
   chunk 47 optimal weight:    0.0970
   chunk 93 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   chunk 96 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
** B  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 225 HIS
B 293 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
R 423 ASN
R 449 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.179021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.162789 restraints weight = 12957.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 1.86
r_work: 0.3918 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3791 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6675
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8724  Z= 0.141
  Angle     :  0.568   8.093  11863  Z= 0.293
  Chirality :  0.042   0.146   1385
  Planarity :  0.004   0.036   1483
  Dihedral  :  4.768  30.077   1205
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 11.96 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.72 (0.25), residues: 1104
  helix: -0.04 (0.27), residues: 385
  sheet: -2.12 (0.28), residues: 265
  loop : -1.32 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.016   0.001   PHE B 235 
 TYR   0.014   0.002   TYR S  60 
 ARG   0.003   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03280 (  363)
  hydrogen bonds       : angle       4.89538 ( 1017)
  SS BOND              : bond        0.00291 (    2)
  SS BOND              : angle       1.28109 (    4)
  covalent geometry    : bond        0.00309 ( 8722)
  covalent geometry    : angle       0.56781 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 177
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7505 (mtm110)
REVERT: A  210 LYS cc_start: 0.8496 (mmmm) cc_final: 0.8231 (mmmm)
REVERT: B   61 MET cc_start: 0.6957 (tmm) cc_final: 0.6605 (tmm)
REVERT: B   79 LEU cc_start: 0.8298 (tt) cc_final: 0.8085 (tp)
REVERT: B  105 TYR cc_start: 0.7975 (t80) cc_final: 0.7742 (t80)
REVERT: B  151 PHE cc_start: 0.8108 (OUTLIER) cc_final: 0.7537 (m-80)
REVERT: B  155 ASN cc_start: 0.7947 (t0) cc_final: 0.7567 (t0)
REVERT: B  233 CYS cc_start: 0.7820 (t) cc_final: 0.7410 (p)
REVERT: B  247 ASP cc_start: 0.6855 (t0) cc_final: 0.6654 (t0)
REVERT: B  290 ASP cc_start: 0.7472 (m-30) cc_final: 0.7224 (m-30)
REVERT: B  300 LEU cc_start: 0.7621 (mt) cc_final: 0.7379 (mt)
REVERT: B  339 TRP cc_start: 0.8125 (m100) cc_final: 0.7920 (m100)
REVERT: C   42 GLU cc_start: 0.6765 (pp20) cc_final: 0.6552 (pp20)
REVERT: S   79 LEU cc_start: 0.7141 (tp) cc_final: 0.6901 (tp)
REVERT: S  128 MET cc_start: 0.7372 (mmm) cc_final: 0.6816 (mmm)
REVERT: R   42 LEU cc_start: 0.6344 (mt) cc_final: 0.6102 (mt)
  outliers start: 30
  outliers final: 17
  residues processed: 189
  average time/residue: 0.2000
  time to fit residues: 51.9798
Evaluate side-chains
  192 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 174
  time to evaluate  : 0.840 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  225 HIS
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  152 MET
Chi-restraints excluded: chain R residue  175 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0040
   chunk 91 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7392

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

Flipped N/Q/H residues before XYZ refinement:
B 237 ASN
** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.178846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.162664 restraints weight = 12753.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 1.85
r_work: 0.3905 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3777 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.2094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8724  Z= 0.170
  Angle     :  0.587   7.715  11863  Z= 0.303
  Chirality :  0.043   0.142   1385
  Planarity :  0.004   0.038   1483
  Dihedral  :  4.859  30.581   1205
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 14.64 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.25), residues: 1104
  helix:  0.06 (0.27), residues: 385
  sheet: -2.10 (0.27), residues: 279
  loop : -1.23 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.005   0.001   HIS S  35 
 PHE   0.020   0.001   PHE B 235 
 TYR   0.015   0.002   TYR S 163 
 ARG   0.004   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03279 (  363)
  hydrogen bonds       : angle       4.87987 ( 1017)
  SS BOND              : bond        0.00237 (    2)
  SS BOND              : angle       1.35013 (    4)
  covalent geometry    : bond        0.00368 ( 8722)
  covalent geometry    : angle       0.58692 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 172
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8511 (mmmm) cc_final: 0.8211 (mmmm)
REVERT: B   79 LEU cc_start: 0.8304 (tt) cc_final: 0.8099 (tp)
REVERT: B  118 ASP cc_start: 0.7394 (p0) cc_final: 0.7111 (p0)
REVERT: B  151 PHE cc_start: 0.8168 (OUTLIER) cc_final: 0.7533 (m-80)
REVERT: B  155 ASN cc_start: 0.7918 (t0) cc_final: 0.7595 (t0)
REVERT: B  161 SER cc_start: 0.7917 (m) cc_final: 0.7645 (p)
REVERT: B  233 CYS cc_start: 0.7821 (t) cc_final: 0.7362 (p)
REVERT: B  247 ASP cc_start: 0.6927 (t0) cc_final: 0.6713 (t0)
REVERT: B  255 LEU cc_start: 0.7848 (mt) cc_final: 0.7623 (mt)
REVERT: S   32 PHE cc_start: 0.8289 (m-80) cc_final: 0.7653 (m-80)
REVERT: S   79 LEU cc_start: 0.7206 (tp) cc_final: 0.7002 (tp)
REVERT: S  128 MET cc_start: 0.7417 (mmm) cc_final: 0.6907 (mmm)
REVERT: R   42 LEU cc_start: 0.6361 (mt) cc_final: 0.6124 (mt)
REVERT: R  163 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5371 (mm)
  outliers start: 27
  outliers final: 20
  residues processed: 185
  average time/residue: 0.1950
  time to fit residues: 50.0654
Evaluate side-chains
  197 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 175
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  152 MET
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 68 optimal weight:    2.9990
   chunk 71 optimal weight:    0.3980
   chunk 52 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 85 optimal weight:    0.3980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.178063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.161824 restraints weight = 12776.750|
|-----------------------------------------------------------------------------|
r_work (start): 0.3985 rms_B_bonded: 1.86
r_work: 0.3907 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6703
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8724  Z= 0.152
  Angle     :  0.573   7.651  11863  Z= 0.295
  Chirality :  0.042   0.143   1385
  Planarity :  0.004   0.037   1483
  Dihedral  :  4.765  30.151   1205
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 15.98 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.25), residues: 1104
  helix:  0.21 (0.27), residues: 386
  sheet: -2.12 (0.28), residues: 273
  loop : -1.19 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.016   0.001   PHE B 235 
 TYR   0.015   0.002   TYR S  60 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03138 (  363)
  hydrogen bonds       : angle       4.74483 ( 1017)
  SS BOND              : bond        0.00228 (    2)
  SS BOND              : angle       1.27611 (    4)
  covalent geometry    : bond        0.00332 ( 8722)
  covalent geometry    : angle       0.57277 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8447 (mmmm) cc_final: 0.8078 (mmmm)
REVERT: B  118 ASP cc_start: 0.7419 (p0) cc_final: 0.7144 (p0)
REVERT: B  151 PHE cc_start: 0.8198 (OUTLIER) cc_final: 0.7551 (m-80)
REVERT: B  161 SER cc_start: 0.7853 (m) cc_final: 0.7590 (p)
REVERT: B  233 CYS cc_start: 0.7718 (t) cc_final: 0.7275 (p)
REVERT: B  247 ASP cc_start: 0.6883 (t0) cc_final: 0.6635 (t0)
REVERT: B  255 LEU cc_start: 0.7857 (mt) cc_final: 0.7626 (mt)
REVERT: B  276 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7805 (t)
REVERT: C   42 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6795 (pp20)
REVERT: S   32 PHE cc_start: 0.8280 (m-80) cc_final: 0.7635 (m-80)
REVERT: S  128 MET cc_start: 0.7433 (mmm) cc_final: 0.6895 (mmm)
REVERT: R   42 LEU cc_start: 0.6428 (mt) cc_final: 0.6223 (mt)
  outliers start: 33
  outliers final: 21
  residues processed: 186
  average time/residue: 0.2061
  time to fit residues: 53.3719
Evaluate side-chains
  195 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 171
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 69 optimal weight:    0.0980
   chunk 92 optimal weight:    0.4980
   chunk 90 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 237 ASN
B 259 GLN
B 293 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.178408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.162178 restraints weight = 12682.332|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 1.84
r_work: 0.3914 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6689
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8724  Z= 0.140
  Angle     :  0.568   7.736  11863  Z= 0.291
  Chirality :  0.042   0.139   1385
  Planarity :  0.004   0.037   1483
  Dihedral  :  4.704  31.482   1205
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 16.09 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.25), residues: 1104
  helix:  0.37 (0.27), residues: 386
  sheet: -1.93 (0.29), residues: 271
  loop : -1.09 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  98 
 HIS   0.004   0.001   HIS B  54 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.014   0.001   TYR A 230 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03033 (  363)
  hydrogen bonds       : angle       4.64382 ( 1017)
  SS BOND              : bond        0.00223 (    2)
  SS BOND              : angle       1.28231 (    4)
  covalent geometry    : bond        0.00306 ( 8722)
  covalent geometry    : angle       0.56796 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 177
  time to evaluate  : 0.815 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7897 (mtm110) cc_final: 0.7651 (mtm110)
REVERT: A  210 LYS cc_start: 0.8476 (mmmm) cc_final: 0.8061 (mmmm)
REVERT: B  118 ASP cc_start: 0.7377 (p0) cc_final: 0.7090 (p0)
REVERT: B  151 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7532 (m-80)
REVERT: B  155 ASN cc_start: 0.7772 (t0) cc_final: 0.7449 (t0)
REVERT: B  233 CYS cc_start: 0.7772 (t) cc_final: 0.7334 (p)
REVERT: B  247 ASP cc_start: 0.6826 (t0) cc_final: 0.6559 (t0)
REVERT: B  255 LEU cc_start: 0.7861 (mt) cc_final: 0.7640 (mt)
REVERT: C   42 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6771 (pp20)
REVERT: S   32 PHE cc_start: 0.8302 (m-80) cc_final: 0.7627 (m-80)
REVERT: S   78 THR cc_start: 0.7683 (p) cc_final: 0.7400 (m)
REVERT: S   79 LEU cc_start: 0.7076 (tp) cc_final: 0.6836 (tp)
REVERT: S  212 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7891 (t)
REVERT: R   42 LEU cc_start: 0.6435 (mt) cc_final: 0.6190 (mt)
REVERT: R   71 LEU cc_start: 0.6434 (tt) cc_final: 0.6104 (tt)
REVERT: R  419 MET cc_start: 0.3420 (tpt) cc_final: 0.2529 (tpt)
  outliers start: 35
  outliers final: 22
  residues processed: 194
  average time/residue: 0.2229
  time to fit residues: 59.3090
Evaluate side-chains
  203 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 178
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 93 optimal weight:    0.6980
   chunk 49 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.5980
   chunk 32 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.178606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.162436 restraints weight = 12777.503|
|-----------------------------------------------------------------------------|
r_work (start): 0.3986 rms_B_bonded: 1.85
r_work: 0.3908 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.3779 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8724  Z= 0.147
  Angle     :  0.585   7.899  11863  Z= 0.299
  Chirality :  0.043   0.274   1385
  Planarity :  0.004   0.039   1483
  Dihedral  :  4.720  31.626   1205
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 17.21 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.25), residues: 1104
  helix:  0.33 (0.27), residues: 394
  sheet: -1.96 (0.29), residues: 277
  loop : -1.06 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  98 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.013   0.001   PHE B 235 
 TYR   0.016   0.001   TYR S  60 
 ARG   0.006   0.000   ARG B  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03070 (  363)
  hydrogen bonds       : angle       4.61198 ( 1017)
  SS BOND              : bond        0.00207 (    2)
  SS BOND              : angle       1.27004 (    4)
  covalent geometry    : bond        0.00323 ( 8722)
  covalent geometry    : angle       0.58451 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 177
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
REVERT: A   24 ARG cc_start: 0.7938 (mtm110) cc_final: 0.7722 (mtm110)
REVERT: A  210 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8069 (mmmm)
REVERT: B  151 PHE cc_start: 0.8140 (OUTLIER) cc_final: 0.7499 (m-80)
REVERT: B  155 ASN cc_start: 0.7798 (t0) cc_final: 0.7423 (t0)
REVERT: B  247 ASP cc_start: 0.6760 (t0) cc_final: 0.6495 (t0)
REVERT: B  276 VAL cc_start: 0.8068 (OUTLIER) cc_final: 0.7811 (t)
REVERT: S   32 PHE cc_start: 0.8349 (m-80) cc_final: 0.7747 (m-80)
REVERT: S   83 MET cc_start: 0.3045 (mtp) cc_final: 0.2807 (mtp)
REVERT: S  191 PHE cc_start: 0.7479 (m-80) cc_final: 0.7248 (m-80)
REVERT: R   42 LEU cc_start: 0.6462 (mt) cc_final: 0.6194 (mt)
REVERT: R   71 LEU cc_start: 0.6444 (tt) cc_final: 0.6108 (tt)
REVERT: R  419 MET cc_start: 0.3429 (tpt) cc_final: 0.2562 (tpt)
  outliers start: 33
  outliers final: 27
  residues processed: 192
  average time/residue: 0.2238
  time to fit residues: 59.4719
Evaluate side-chains
  199 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 170
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  276 VAL
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  163 LEU
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  190 LEU
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
B 293 ASN
** S  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.179239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.163045 restraints weight = 12932.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3978 rms_B_bonded: 1.86
r_work: 0.3897 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3768 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6719
moved from start:          0.2849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8724  Z= 0.166
  Angle     :  0.604   8.099  11863  Z= 0.308
  Chirality :  0.043   0.214   1385
  Planarity :  0.004   0.043   1483
  Dihedral  :  4.851  31.472   1205
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.66 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.26), residues: 1104
  helix:  0.30 (0.27), residues: 394
  sheet: -1.85 (0.29), residues: 271
  loop : -1.03 (0.31), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.014   0.002   TYR A 230 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03184 (  363)
  hydrogen bonds       : angle       4.73004 ( 1017)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       1.37960 (    4)
  covalent geometry    : bond        0.00360 ( 8722)
  covalent geometry    : angle       0.60364 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 176
  time to evaluate  : 0.832 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8487 (mmmm) cc_final: 0.8098 (mmmm)
REVERT: B  151 PHE cc_start: 0.8122 (OUTLIER) cc_final: 0.7521 (m-80)
REVERT: B  155 ASN cc_start: 0.7709 (t0) cc_final: 0.7384 (t0)
REVERT: B  247 ASP cc_start: 0.6744 (t0) cc_final: 0.6508 (t0)
REVERT: B  300 LEU cc_start: 0.7628 (mt) cc_final: 0.7363 (mt)
REVERT: S   32 PHE cc_start: 0.8369 (m-80) cc_final: 0.7663 (m-80)
REVERT: S  191 PHE cc_start: 0.7504 (m-80) cc_final: 0.7278 (m-80)
REVERT: R   42 LEU cc_start: 0.6465 (mt) cc_final: 0.6206 (mt)
REVERT: R  419 MET cc_start: 0.3475 (tpt) cc_final: 0.2610 (tpt)
  outliers start: 35
  outliers final: 27
  residues processed: 192
  average time/residue: 0.2000
  time to fit residues: 53.4766
Evaluate side-chains
  203 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain R residue   74 LEU
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   chunk 87 optimal weight:    4.9990
   chunk 103 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 108 optimal weight:    0.6980
   chunk 68 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 237 ASN
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** S  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.178494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.162397 restraints weight = 12925.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 1.87
r_work: 0.3902 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3773 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6709
moved from start:          0.2943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8724  Z= 0.157
  Angle     :  0.617   8.675  11863  Z= 0.311
  Chirality :  0.044   0.195   1385
  Planarity :  0.004   0.042   1483
  Dihedral  :  4.832  32.069   1205
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 20.34 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.21 (0.26), residues: 1104
  helix:  0.32 (0.27), residues: 394
  sheet: -1.81 (0.30), residues: 266
  loop : -1.00 (0.31), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.005   0.001   HIS B  54 
 PHE   0.014   0.001   PHE B 235 
 TYR   0.015   0.002   TYR S 103 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03162 (  363)
  hydrogen bonds       : angle       4.70902 ( 1017)
  SS BOND              : bond        0.00196 (    2)
  SS BOND              : angle       1.32129 (    4)
  covalent geometry    : bond        0.00343 ( 8722)
  covalent geometry    : angle       0.61674 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 174
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8474 (mmmm) cc_final: 0.8149 (mmmm)
REVERT: B   68 ARG cc_start: 0.8051 (tpt-90) cc_final: 0.7796 (tpt90)
REVERT: B   83 ASP cc_start: 0.8063 (t0) cc_final: 0.6842 (m-30)
REVERT: B  151 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7530 (m-80)
REVERT: B  219 ARG cc_start: 0.6386 (mtp85) cc_final: 0.6182 (mtp85)
REVERT: B  247 ASP cc_start: 0.6717 (t0) cc_final: 0.6458 (t0)
REVERT: B  300 LEU cc_start: 0.7640 (mt) cc_final: 0.7351 (mt)
REVERT: S   32 PHE cc_start: 0.8371 (m-80) cc_final: 0.7732 (m-80)
REVERT: R   42 LEU cc_start: 0.6466 (mt) cc_final: 0.6200 (mt)
REVERT: R  406 LEU cc_start: 0.7491 (tp) cc_final: 0.7250 (mp)
REVERT: R  419 MET cc_start: 0.3473 (tpt) cc_final: 0.2639 (tpt)
  outliers start: 33
  outliers final: 29
  residues processed: 189
  average time/residue: 0.2030
  time to fit residues: 53.3245
Evaluate side-chains
  205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 175
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 MET
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue   95 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain R residue   74 LEU
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 84 optimal weight:    0.7980
   chunk 76 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 82 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 155 ASN
** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** S  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.178563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.162488 restraints weight = 12812.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3983 rms_B_bonded: 1.86
r_work: 0.3905 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3775 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8724  Z= 0.170
  Angle     :  0.632   8.757  11863  Z= 0.320
  Chirality :  0.044   0.184   1385
  Planarity :  0.004   0.042   1483
  Dihedral  :  4.921  31.750   1205
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.56 %
    Favored  : 75.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.26), residues: 1104
  helix:  0.26 (0.27), residues: 395
  sheet: -1.74 (0.30), residues: 264
  loop : -1.01 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP R  98 
 HIS   0.006   0.001   HIS B  54 
 PHE   0.015   0.001   PHE B 235 
 TYR   0.016   0.002   TYR S  60 
 ARG   0.006   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (  363)
  hydrogen bonds       : angle       4.73242 ( 1017)
  SS BOND              : bond        0.00199 (    2)
  SS BOND              : angle       1.35291 (    4)
  covalent geometry    : bond        0.00372 ( 8722)
  covalent geometry    : angle       0.63211 (11859)

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

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

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2208 Ramachandran restraints generated.
    1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 178
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A  210 LYS cc_start: 0.8477 (mmmm) cc_final: 0.8147 (mmmm)
REVERT: B   68 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7806 (tpt90)
REVERT: B   83 ASP cc_start: 0.8096 (t0) cc_final: 0.6871 (m-30)
REVERT: B  120 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7343 (mt)
REVERT: B  151 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7617 (m-80)
REVERT: B  219 ARG cc_start: 0.6395 (mtp85) cc_final: 0.6189 (mtp85)
REVERT: B  247 ASP cc_start: 0.6724 (t0) cc_final: 0.6478 (t0)
REVERT: B  300 LEU cc_start: 0.7628 (mt) cc_final: 0.7344 (mt)
REVERT: S   32 PHE cc_start: 0.8335 (m-80) cc_final: 0.7547 (m-80)
REVERT: R   42 LEU cc_start: 0.6472 (mt) cc_final: 0.6204 (mt)
REVERT: R  406 LEU cc_start: 0.7498 (tp) cc_final: 0.7226 (mp)
REVERT: R  419 MET cc_start: 0.3634 (tpt) cc_final: 0.2774 (tpt)
  outliers start: 34
  outliers final: 29
  residues processed: 190
  average time/residue: 0.2144
  time to fit residues: 56.4202
Evaluate side-chains
  209 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 178
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  351 CYS
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  151 PHE
Chi-restraints excluded: chain B residue  165 THR
Chi-restraints excluded: chain B residue  213 VAL
Chi-restraints excluded: chain B residue  229 ILE
Chi-restraints excluded: chain B residue  232 ILE
Chi-restraints excluded: chain B residue  262 MET
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain C residue   42 GLU
Chi-restraints excluded: chain S residue   51 ILE
Chi-restraints excluded: chain S residue   81 LEU
Chi-restraints excluded: chain S residue  115 THR
Chi-restraints excluded: chain S residue  157 ASN
Chi-restraints excluded: chain S residue  160 THR
Chi-restraints excluded: chain S residue  162 LEU
Chi-restraints excluded: chain S residue  212 VAL
Chi-restraints excluded: chain S residue  214 VAL
Chi-restraints excluded: chain S residue  221 LEU
Chi-restraints excluded: chain R residue   74 LEU
Chi-restraints excluded: chain R residue  107 LEU
Chi-restraints excluded: chain R residue  112 ASP
Chi-restraints excluded: chain R residue  123 LEU
Chi-restraints excluded: chain R residue  126 ILE
Chi-restraints excluded: chain R residue  152 MET
Chi-restraints excluded: chain R residue  175 VAL
Chi-restraints excluded: chain R residue  442 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 52 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0170
   chunk 48 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   overall best weight:    0.4018

-------------------------------------------------------------------------------
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 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 259 GLN
** S  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.181132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.164835 restraints weight = 12983.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 1.92
r_work: 0.3926 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3794 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8724  Z= 0.121
  Angle     :  0.592   8.771  11863  Z= 0.297
  Chirality :  0.042   0.172   1385
  Planarity :  0.004   0.042   1483
  Dihedral  :  4.679  32.548   1205
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 21.12 %
    Favored  : 75.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.26), residues: 1104
  helix:  0.49 (0.27), residues: 390
  sheet: -1.69 (0.30), residues: 268
  loop : -0.97 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP R  98 
 HIS   0.004   0.001   HIS S  35 
 PHE   0.016   0.001   PHE S  27 
 TYR   0.015   0.001   TYR A 230 
 ARG   0.005   0.000   ARG B 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02991 (  363)
  hydrogen bonds       : angle       4.57367 ( 1017)
  SS BOND              : bond        0.00218 (    2)
  SS BOND              : angle       1.11665 (    4)
  covalent geometry    : bond        0.00267 ( 8722)
  covalent geometry    : angle       0.59157 (11859)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4951.25 seconds
wall clock time: 86 minutes 54.28 seconds (5214.28 seconds total)