Starting phenix.real_space_refine
on Wed Mar 12 20:41:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wc4_37430/03_2025/8wc4_37430_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wc4_37430/03_2025/8wc4_37430.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wc4_37430/03_2025/8wc4_37430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wc4_37430/03_2025/8wc4_37430.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wc4_37430/03_2025/8wc4_37430_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wc4_37430/03_2025/8wc4_37430_neut.cif"
  }
  resolution = 3.1
  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=   0.079
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Br      1      7.06       5
     S      56      5.16       5
     C    5369      2.51       5
     N    1426      2.21       5
     O    1542      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8394
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1844
          Classifications: {'peptide': 233}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 5, 'TRANS': 227}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 67
    Chain: "B"
      Number of atoms: 2484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2484
          Classifications: {'peptide': 334}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 87
          Unresolved non-hydrogen angles: 104
          Unresolved non-hydrogen dihedrals: 70
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "R"
      Number of atoms: 2054
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 273, 2054
          Classifications: {'peptide': 273}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 12, 'TRANS': 260}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 130
          Unresolved non-hydrogen angles: 158
          Unresolved non-hydrogen dihedrals: 108
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 55
    Chain: "S"
      Number of atoms: 1622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1622
          Classifications: {'peptide': 214}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 9, 'TRANS': 204}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 38
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "Y"
      Number of atoms: 380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 380
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 53
          Unresolved non-hydrogen angles: 62
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'VMT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.50, per 1000 atoms: 0.66
  Number of scatterers: 8394
  At special positions: 0
  Unit cell: (89.25, 118.15, 124.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Br      1     34.99
     S      56     16.00
     O    1542      8.00
     N    1426      7.00
     C    5369      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.04

  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: 2.22
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      38.3% alpha, 19.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.680A  pdb=" N   LYS A  10 " --> pdb=" O   SER A   6 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 55
      removed outlier: 3.539A  pdb=" N   ARG A  54 " --> pdb=" O   VAL A  50 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A  55 " --> pdb=" O   LYS A  51 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 216
      removed outlier: 3.844A  pdb=" N   GLN A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASN A 216 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 245
      removed outlier: 3.676A  pdb=" N   ALA A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 3.729A  pdb=" N   LEU A 264 " --> pdb=" O   LYS A 260 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLY A 271 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 278
    Processing helix  chain 'A' and resid 279 through 285
      removed outlier: 3.596A  pdb=" N   TYR A 285 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 317
    Processing helix  chain 'A' and resid 337 through 358
    Processing helix  chain 'B' and resid 7 through 24
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.639A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 25 through 49
      removed outlier: 3.721A  pdb=" N   ILE R  42 " --> pdb=" O   VAL R  38 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL R  43 " --> pdb=" O   GLY R  39 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ILE R  44 " --> pdb=" O   ASN R  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 57 through 85
      removed outlier: 4.223A  pdb=" N   LEU R  61 " --> pdb=" O   THR R  57 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   MET R  76 " --> pdb=" O   GLY R  72 " (cutoff:3.500A)
      Proline residue:  R  77  - end of helix
    Processing helix  chain 'R' and resid 94 through 126
      removed outlier: 3.731A  pdb=" N   ALA R 123 " --> pdb=" O   ASP R 119 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   VAL R 124 " --> pdb=" O   ARG R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 129 through 134
    Processing helix  chain 'R' and resid 135 through 160
      removed outlier: 3.573A  pdb=" N   ILE R 139 " --> pdb=" O   ASN R 135 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LEU R 140 " --> pdb=" O   ILE R 136 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   VAL R 141 " --> pdb=" O   SER R 137 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   MET R 142 " --> pdb=" O   THR R 138 " (cutoff:3.500A)
      Proline residue:  R 150  - end of helix
    Processing helix  chain 'R' and resid 167 through 175
    Processing helix  chain 'R' and resid 188 through 198
    Processing helix  chain 'R' and resid 198 through 226
      removed outlier: 3.538A  pdb=" N   ILE R 223 " --> pdb=" O   GLN R 219 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASN R 224 " --> pdb=" O   ALA R 220 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 245 through 275
      removed outlier: 3.587A  pdb=" N   THR R 249 " --> pdb=" O   LYS R 245 " (cutoff:3.500A)
      Proline residue:  R 263  - end of helix
      Proline residue:  R 272  - end of helix
    Processing helix  chain 'R' and resid 279 through 302
      removed outlier: 4.043A  pdb=" N   ASN R 283 " --> pdb=" O   PRO R 279 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ASP R 284 " --> pdb=" O   PRO R 280 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ALA R 285 " --> pdb=" O   SER R 281 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLY R 290 " --> pdb=" O   LEU R 286 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   TYR R 291 " --> pdb=" O   TYR R 287 " (cutoff:3.500A)
      Proline residue:  R 298  - end of helix
    Processing helix  chain 'R' and resid 305 through 313
    Processing helix  chain 'S' and resid 28 through 32
      removed outlier: 3.666A  pdb=" N   PHE S  32 " --> pdb=" O   PHE S  29 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 220 through 224
      removed outlier: 3.903A  pdb=" N   VAL S 224 " --> pdb=" O   ALA S 221 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 9 through 24
      removed outlier: 3.654A  pdb=" N   ASN Y  24 " --> pdb=" O   LYS Y  20 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 29 through 45
      removed outlier: 3.604A  pdb=" N   ASP Y  36 " --> pdb=" O   LYS Y  32 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU Y  37 " --> pdb=" O   ALA Y  33 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 46 through 48
      No H-bonds generated for 'chain 'Y' and resid 46 through 48'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 190
      removed outlier: 3.541A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   VAL A 201 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 9.846A  pdb=" N   ALA A 220 " --> pdb=" O   THR A  33 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   ARG A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   ILE A 222 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 7.189A  pdb=" N   LEU A  39 " --> pdb=" O   VAL A 224 " (cutoff:3.500A)
      removed outlier: 8.941A  pdb=" N   ASP A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 7.513A  pdb=" N   PHE A 257 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ASN A 259 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 259 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.728A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.042A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.902A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.995A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.242A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.738A  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 153
      removed outlier: 6.574A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.996A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.439A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.564A  pdb=" N   SER B 189 " --> pdb=" O   GLY B 202 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.539A  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: 6.571A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG B 251 " --> pdb=" O   THR B 243 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 278
      removed outlier: 3.608A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 4
      removed outlier: 3.693A  pdb=" N   GLN S   3 " --> pdb=" O   SER S  25 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER S  25 " --> pdb=" O   GLN S   3 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ARG S  18 " --> pdb=" O   MET S  83 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'S' and resid 58 through 60
      removed outlier: 6.658A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 142
      removed outlier: 3.566A  pdb=" N   ARG S 160 " --> pdb=" O   THR S 141 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.445A  pdb=" N   VAL S 147 " --> pdb=" O   GLU S 246 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   TYR S 227 " --> pdb=" O   THR S 243 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLY S 225 " --> pdb=" O   LEU S 245 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195
      removed outlier: 3.577A  pdb=" N   ILE S 189 " --> pdb=" O   TRP S 176 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1077 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: 2.34

  Time building geometry restraints manager: 2.60 seconds

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

  Histogram of bond lengths:
        1.16 -     1.31: 1357
        1.31 -     1.47: 3583
        1.47 -     1.63: 3558
        1.63 -     1.78: 7
        1.78 -     1.94: 75
  Bond restraints: 8580
  Sorted by residual:
  bond pdb=" C   PRO R  56 "
       pdb=" O   PRO R  56 "
    ideal  model  delta    sigma   weight residual
    1.238  1.158  0.080 1.24e-02 6.50e+03 4.16e+01
  bond pdb=" C   MET R 195 "
       pdb=" O   MET R 195 "
    ideal  model  delta    sigma   weight residual
    1.236  1.177  0.059 1.16e-02 7.43e+03 2.59e+01
  bond pdb=" CA  ASN A 231 "
       pdb=" C   ASN A 231 "
    ideal  model  delta    sigma   weight residual
    1.525  1.474  0.051 1.02e-02 9.61e+03 2.49e+01
  bond pdb=" C   ASP B 312 "
       pdb=" O   ASP B 312 "
    ideal  model  delta    sigma   weight residual
    1.236  1.167  0.069 1.38e-02 5.25e+03 2.46e+01
  bond pdb=" CA  PHE R  50 "
       pdb=" C   PHE R  50 "
    ideal  model  delta    sigma   weight residual
    1.524  1.490  0.034 7.00e-03 2.04e+04 2.41e+01
  ... (remaining 8575 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 11535
        3.09 -     6.18: 112
        6.18 -     9.27: 16
        9.27 -    12.36: 2
       12.36 -    15.44: 1
  Bond angle restraints: 11666
  Sorted by residual:
  angle pdb=" N   GLN R  52 "
        pdb=" CA  GLN R  52 "
        pdb=" C   GLN R  52 "
      ideal   model   delta    sigma   weight residual
     112.45   97.01   15.44 1.39e+00 5.18e-01 1.23e+02
  angle pdb=" C   ILE R 223 "
        pdb=" CA  ILE R 223 "
        pdb=" CB  ILE R 223 "
      ideal   model   delta    sigma   weight residual
     111.70  102.14    9.56 1.28e+00 6.10e-01 5.58e+01
  angle pdb=" N   ALA R 311 "
        pdb=" CA  ALA R 311 "
        pdb=" C   ALA R 311 "
      ideal   model   delta    sigma   weight residual
     112.90  103.86    9.04 1.31e+00 5.83e-01 4.76e+01
  angle pdb=" C   THR R  55 "
        pdb=" N   PRO R  56 "
        pdb=" CA  PRO R  56 "
      ideal   model   delta    sigma   weight residual
     119.28  126.65   -7.37 1.10e+00 8.26e-01 4.49e+01
  angle pdb=" N   TYR R 305 "
        pdb=" CA  TYR R 305 "
        pdb=" C   TYR R 305 "
      ideal   model   delta    sigma   weight residual
     109.72  117.84   -8.12 1.25e+00 6.40e-01 4.22e+01
  ... (remaining 11661 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.03: 4569
       16.03 -    32.05: 349
       32.05 -    48.08: 75
       48.08 -    64.11: 12
       64.11 -    80.13: 14
  Dihedral angle restraints: 5019
    sinusoidal: 1794
      harmonic: 3225
  Sorted by residual:
  dihedral pdb=" N   LYS R  51 "
           pdb=" C   LYS R  51 "
           pdb=" CA  LYS R  51 "
           pdb=" CB  LYS R  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  139.77  -16.97     0      2.50e+00 1.60e-01 4.61e+01
  dihedral pdb=" C   LYS R  51 "
           pdb=" N   LYS R  51 "
           pdb=" CA  LYS R  51 "
           pdb=" CB  LYS R  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.57   13.97     0      2.50e+00 1.60e-01 3.12e+01
  dihedral pdb=" C   ILE R  45 "
           pdb=" N   ILE R  45 "
           pdb=" CA  ILE R  45 "
           pdb=" CB  ILE R  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.17   12.17     0      2.50e+00 1.60e-01 2.37e+01
  ... (remaining 5016 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.120: 1293
       0.120 -    0.239: 39
       0.239 -    0.359: 5
       0.359 -    0.478: 3
       0.478 -    0.598: 1
  Chirality restraints: 1341
  Sorted by residual:
  chirality pdb=" CA  LYS R  51 "
            pdb=" N   LYS R  51 "
            pdb=" C   LYS R  51 "
            pdb=" CB  LYS R  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.91    0.60 2.00e-01 2.50e+01 8.94e+00
  chirality pdb=" CA  PHE R  50 "
            pdb=" N   PHE R  50 "
            pdb=" C   PHE R  50 "
            pdb=" CB  PHE R  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CB  ILE R  45 "
            pdb=" CA  ILE R  45 "
            pdb=" CG1 ILE R  45 "
            pdb=" CG2 ILE R  45 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.61e+00
  ... (remaining 1338 not shown)

  Planarity restraints: 1474
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP R  88 "    0.022 2.00e-02 2.50e+03   4.57e-02 2.09e+01
        pdb=" C   TRP R  88 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   TRP R  88 "    0.030 2.00e-02 2.50e+03
        pdb=" N   TYR R  89 "    0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE R 194 "   -0.020 2.00e-02 2.50e+03   4.11e-02 1.69e+01
        pdb=" C   PHE R 194 "    0.071 2.00e-02 2.50e+03
        pdb=" O   PHE R 194 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   MET R 195 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR R  55 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   THR R  55 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   THR R  55 "    0.021 2.00e-02 2.50e+03
        pdb=" N   PRO R  56 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1471 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1141
        2.75 -     3.29: 7801
        3.29 -     3.83: 12896
        3.83 -     4.36: 14793
        4.36 -     4.90: 27137
  Nonbonded interactions: 63768
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN R  40 "
            pdb=" OD1 ASP R  68 "
     model   vdw
     2.216 3.120
  nonbonded pdb=" O   GLN S  39 "
            pdb=" OG1 THR S 116 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OD1 ASP B 205 "
            pdb=" OG  SER B 207 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" NH1 ARG B  49 "
            pdb=" O   TYR B  85 "
     model   vdw
     2.333 3.120
  nonbonded pdb=" ND1 HIS B 311 "
            pdb=" OG  SER B 331 "
     model   vdw
     2.334 3.120
  ... (remaining 63763 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:             1.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.620
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.010
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
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      :  0.006   0.080   8580  Z= 0.387
  Angle     :  0.808  15.445  11666  Z= 0.487
  Chirality :  0.059   0.598   1341
  Planarity :  0.005   0.047   1474
  Dihedral  : 13.024  80.132   2927
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  1.28 %
    Favored  : 97.79 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.26), residues: 1084
  helix:  1.22 (0.27), residues: 377
  sheet:  0.20 (0.33), residues: 256
  loop : -1.62 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 339 
 HIS   0.012   0.002   HIS R  49 
 PHE   0.018   0.002   PHE R 214 
 TYR   0.030   0.002   TYR A 230 
 ARG   0.006   0.000   ARG B  19 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 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: 8
    poor density    : 161
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A  234 GLN cc_start: 0.8086 (tp-100) cc_final: 0.7431 (tp-100)
REVERT: A  238 ASN cc_start: 0.8730 (m110) cc_final: 0.8403 (m110)
REVERT: A  323 ARG cc_start: 0.8034 (mtp85) cc_final: 0.7818 (ttm110)
REVERT: B  247 ASP cc_start: 0.7774 (t0) cc_final: 0.7573 (t0)
REVERT: R  157 MET cc_start: 0.7804 (ttm) cc_final: 0.7443 (ttm)
REVERT: R  224 ASN cc_start: 0.7546 (m-40) cc_final: 0.7288 (m110)
REVERT: S   18 ARG cc_start: 0.8407 (tpp80) cc_final: 0.7818 (ttm170)
  outliers start: 8
  outliers final: 5
  residues processed: 167
  average time/residue: 0.2294
  time to fit residues: 50.6968
Evaluate side-chains
  135 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 HIS
Chi-restraints excluded: chain R residue   54 HIS
Chi-restraints excluded: chain R residue  270 LEU
Chi-restraints excluded: chain R residue  310 ARG
Chi-restraints excluded: chain Y residue   28 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 85 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    7.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 204 GLN
B  32 GLN
R  52 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.148842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.113819 restraints weight = 10906.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3371 rms_B_bonded: 2.51
r_work: 0.3151 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8610
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8580  Z= 0.195
  Angle     :  0.589  10.165  11666  Z= 0.310
  Chirality :  0.044   0.145   1341
  Planarity :  0.004   0.042   1474
  Dihedral  :  5.874  59.781   1203
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  6.99 %
    Favored  : 91.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.25), residues: 1084
  helix:  1.85 (0.27), residues: 374
  sheet:  0.31 (0.34), residues: 249
  loop : -1.51 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 339 
 HIS   0.007   0.001   HIS R  62 
 PHE   0.019   0.001   PHE A 189 
 TYR   0.039   0.002   TYR R 287 
 ARG   0.004   0.000   ARG B  49 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.990 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8117 (tt0) cc_final: 0.7820 (mt0)
REVERT: A  204 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8233 (mm110)
REVERT: A  238 ASN cc_start: 0.8907 (m110) cc_final: 0.8654 (m110)
REVERT: B  247 ASP cc_start: 0.8063 (t0) cc_final: 0.7811 (t0)
REVERT: R  157 MET cc_start: 0.7908 (ttm) cc_final: 0.7451 (ttm)
REVERT: R  270 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7763 (mm)
REVERT: S   18 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8322 (tpp-160)
REVERT: Y   48 ASP cc_start: 0.8692 (t0) cc_final: 0.8448 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 147
  average time/residue: 0.2324
  time to fit residues: 45.6918
Evaluate side-chains
  132 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   49 HIS
Chi-restraints excluded: chain R residue   54 HIS
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  270 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 60 optimal weight:    6.9990
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    0.2980
   chunk 42 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 88 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 70 optimal weight:   20.0000
   chunk 105 optimal weight:    9.9990
   chunk 68 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    2.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  32 GLN
B 268 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.142902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.109615 restraints weight = 10880.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.33
r_work: 0.3102 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2971 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2971
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8580  Z= 0.352
  Angle     :  0.657  12.898  11666  Z= 0.343
  Chirality :  0.047   0.151   1341
  Planarity :  0.005   0.043   1474
  Dihedral  :  5.631  55.653   1197
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.31 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.25), residues: 1084
  helix:  1.96 (0.27), residues: 375
  sheet:  0.27 (0.34), residues: 248
  loop : -1.50 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 339 
 HIS   0.011   0.002   HIS R  62 
 PHE   0.018   0.002   PHE A 189 
 TYR   0.031   0.002   TYR R 287 
 ARG   0.006   0.001   ARG A  15 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8262 (tt0) cc_final: 0.8003 (mt0)
REVERT: A  204 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8154 (mm110)
REVERT: A  234 GLN cc_start: 0.8112 (tp-100) cc_final: 0.7856 (tp-100)
REVERT: A  238 ASN cc_start: 0.8965 (m110) cc_final: 0.8708 (m110)
REVERT: B   75 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8289 (tt0)
REVERT: R   54 HIS cc_start: 0.6971 (m170) cc_final: 0.6733 (m170)
REVERT: R  157 MET cc_start: 0.8002 (ttm) cc_final: 0.7554 (ttm)
  outliers start: 16
  outliers final: 12
  residues processed: 142
  average time/residue: 0.2263
  time to fit residues: 43.2496
Evaluate side-chains
  134 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   49 HIS
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  268 THR
Chi-restraints excluded: chain S residue   62 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 55 optimal weight:    1.9990
   chunk 106 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 44 optimal weight:    7.9990
   chunk 19 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 108 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    2.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  32 GLN
R  40 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.144094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.110228 restraints weight = 10783.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.36
r_work: 0.3091 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2960 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   8580  Z= 0.327
  Angle     :  0.637  13.937  11666  Z= 0.331
  Chirality :  0.046   0.147   1341
  Planarity :  0.004   0.042   1474
  Dihedral  :  5.170  52.149   1193
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 12.47 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1084
  helix:  2.01 (0.27), residues: 375
  sheet:  0.22 (0.33), residues: 255
  loop : -1.52 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 339 
 HIS   0.010   0.001   HIS R  62 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.021   0.002   TYR A 230 
 ARG   0.009   0.001   ARG A 323 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8271 (tt0) cc_final: 0.7982 (mt0)
REVERT: A  234 GLN cc_start: 0.8088 (tp-100) cc_final: 0.7774 (tp-100)
REVERT: A  238 ASN cc_start: 0.8987 (m110) cc_final: 0.8697 (m110)
REVERT: A  323 ARG cc_start: 0.8500 (mtp85) cc_final: 0.8226 (mtp180)
REVERT: B   75 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8263 (tt0)
REVERT: R   54 HIS cc_start: 0.6997 (m170) cc_final: 0.6744 (m170)
REVERT: R  157 MET cc_start: 0.7985 (ttm) cc_final: 0.7550 (ttm)
REVERT: R  170 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8125 (tt)
REVERT: S   18 ARG cc_start: 0.8482 (tpp80) cc_final: 0.8011 (tpt90)
REVERT: S   83 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.6543 (mmt)
  outliers start: 27
  outliers final: 16
  residues processed: 162
  average time/residue: 0.2179
  time to fit residues: 47.5442
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  181 THR
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   57 THR
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  100 SER
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   96 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0980
   chunk 78 optimal weight:    0.4980
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 60 optimal weight:    0.7980
   chunk 99 optimal weight:    0.7980
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    0.0040
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 261 GLN
B  32 GLN
** R  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.151093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.117451 restraints weight = 10950.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.60
r_work: 0.3170 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   8580  Z= 0.135
  Angle     :  0.525  10.906  11666  Z= 0.271
  Chirality :  0.042   0.135   1341
  Planarity :  0.004   0.039   1474
  Dihedral  :  4.226  24.114   1191
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 14.57 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1084
  helix:  2.38 (0.27), residues: 369
  sheet:  0.61 (0.33), residues: 254
  loop : -1.60 (0.26), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.016   0.001   PHE A 189 
 TYR   0.018   0.001   TYR A 230 
 ARG   0.005   0.000   ARG A 323 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 139
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8096 (tt0) cc_final: 0.7785 (mt0)
REVERT: A  238 ASN cc_start: 0.8886 (m110) cc_final: 0.8595 (m110)
REVERT: B   75 GLN cc_start: 0.8428 (mm-40) cc_final: 0.8142 (tt0)
REVERT: B  247 ASP cc_start: 0.7870 (t0) cc_final: 0.7638 (t0)
REVERT: R   54 HIS cc_start: 0.6952 (m170) cc_final: 0.6699 (m170)
REVERT: R  157 MET cc_start: 0.7935 (ttm) cc_final: 0.7519 (ttm)
REVERT: R  170 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7965 (tt)
REVERT: S   18 ARG cc_start: 0.8458 (tpp80) cc_final: 0.7905 (tpt90)
REVERT: Y   48 ASP cc_start: 0.8692 (t0) cc_final: 0.8421 (t0)
  outliers start: 15
  outliers final: 7
  residues processed: 145
  average time/residue: 0.2182
  time to fit residues: 43.0628
Evaluate side-chains
  142 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain S residue   62 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 64 optimal weight:    5.9990
   chunk 104 optimal weight:   20.0000
   chunk 91 optimal weight:    0.2980
   chunk 23 optimal weight:   30.0000
   chunk 25 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.148114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.114012 restraints weight = 10931.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.64
r_work: 0.3132 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8580  Z= 0.203
  Angle     :  0.562  11.490  11666  Z= 0.289
  Chirality :  0.043   0.138   1341
  Planarity :  0.004   0.041   1474
  Dihedral  :  4.282  23.533   1191
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.57 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.26), residues: 1084
  helix:  2.47 (0.27), residues: 369
  sheet:  0.57 (0.33), residues: 259
  loop : -1.53 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 339 
 HIS   0.009   0.001   HIS R  62 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.029   0.001   TYR R 287 
 ARG   0.004   0.000   ARG B  42 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.982 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8209 (tt0) cc_final: 0.7911 (mt0)
REVERT: A  238 ASN cc_start: 0.8947 (m110) cc_final: 0.8655 (m110)
REVERT: B   75 GLN cc_start: 0.8502 (mm-40) cc_final: 0.8203 (tt0)
REVERT: B  247 ASP cc_start: 0.8088 (t0) cc_final: 0.7882 (t0)
REVERT: R   54 HIS cc_start: 0.7013 (m170) cc_final: 0.6779 (m170)
REVERT: R  157 MET cc_start: 0.7953 (ttm) cc_final: 0.7528 (ttm)
REVERT: R  170 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8037 (tt)
REVERT: S   18 ARG cc_start: 0.8434 (tpp80) cc_final: 0.7989 (tpt170)
REVERT: S   83 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6229 (mmt)
  outliers start: 17
  outliers final: 12
  residues processed: 151
  average time/residue: 0.2157
  time to fit residues: 44.3610
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  125 CYS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 103 optimal weight:    6.9990
   chunk 97 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 204 GLN
A 261 GLN
B  32 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.145899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.110852 restraints weight = 10981.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.60
r_work: 0.3092 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8698
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8580  Z= 0.282
  Angle     :  0.607  11.782  11666  Z= 0.313
  Chirality :  0.044   0.142   1341
  Planarity :  0.004   0.046   1474
  Dihedral  :  4.548  27.237   1191
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 15.03 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1084
  helix:  2.37 (0.27), residues: 371
  sheet:  0.50 (0.32), residues: 259
  loop : -1.52 (0.26), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R  59 
 HIS   0.009   0.001   HIS R  62 
 PHE   0.017   0.002   PHE A 189 
 TYR   0.024   0.002   TYR R 287 
 ARG   0.011   0.000   ARG A 323 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 140
  time to evaluate  : 0.976 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8295 (tt0) cc_final: 0.7985 (mt0)
REVERT: A  234 GLN cc_start: 0.8145 (tp-100) cc_final: 0.7782 (tp40)
REVERT: A  238 ASN cc_start: 0.8966 (m110) cc_final: 0.8678 (m110)
REVERT: A  323 ARG cc_start: 0.8527 (mtp85) cc_final: 0.8241 (mtp180)
REVERT: B   75 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8264 (tt0)
REVERT: R   54 HIS cc_start: 0.7106 (m170) cc_final: 0.6866 (m170)
REVERT: R  157 MET cc_start: 0.7986 (ttm) cc_final: 0.7566 (ttm)
REVERT: R  170 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.8046 (tt)
REVERT: S   83 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.6374 (mmt)
  outliers start: 22
  outliers final: 17
  residues processed: 156
  average time/residue: 0.2206
  time to fit residues: 46.5706
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain R residue  296 LEU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0670
   chunk 59 optimal weight:    0.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    1.2124

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 204 GLN
A 261 GLN
B  32 GLN
** R  62 HIS ** 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 = 0.3807 r_free = 0.3807 target = 0.148248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112754 restraints weight = 10982.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 2.56
r_work: 0.3143 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8580  Z= 0.185
  Angle     :  0.559  10.242  11666  Z= 0.288
  Chirality :  0.042   0.134   1341
  Planarity :  0.004   0.044   1474
  Dihedral  :  4.290  24.739   1191
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 14.92 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.26), residues: 1084
  helix:  2.47 (0.27), residues: 369
  sheet:  0.59 (0.32), residues: 259
  loop : -1.49 (0.26), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.015   0.001   PHE A 189 
 TYR   0.020   0.001   TYR A 230 
 ARG   0.007   0.000   ARG A 323 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 142
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8223 (tt0) cc_final: 0.7903 (mt0)
REVERT: A  238 ASN cc_start: 0.8947 (m110) cc_final: 0.8677 (m110)
REVERT: A  323 ARG cc_start: 0.8431 (mtp85) cc_final: 0.8149 (mtp180)
REVERT: B   75 GLN cc_start: 0.8478 (mm-40) cc_final: 0.8226 (tt0)
REVERT: B  258 ASP cc_start: 0.7711 (t0) cc_final: 0.7429 (t0)
REVERT: R  157 MET cc_start: 0.8001 (ttm) cc_final: 0.7591 (ttm)
REVERT: R  170 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7999 (tt)
REVERT: S   83 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6402 (mmt)
  outliers start: 22
  outliers final: 15
  residues processed: 157
  average time/residue: 0.2210
  time to fit residues: 47.0217
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain R residue  294 SER
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 91 optimal weight:    0.0470
   chunk 23 optimal weight:   30.0000
   chunk 8 optimal weight:    0.0980
   chunk 0 optimal weight:    0.7980
   chunk 98 optimal weight:    0.4980
   chunk 108 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 70 optimal weight:    8.9990
   chunk 95 optimal weight:    8.9990
   overall best weight:    0.4478

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 190 GLN
A 204 GLN
** R  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.151688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.118386 restraints weight = 11013.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 2.61
r_work: 0.3192 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8580  Z= 0.138
  Angle     :  0.525   8.743  11666  Z= 0.272
  Chirality :  0.041   0.129   1341
  Planarity :  0.004   0.045   1474
  Dihedral  :  3.965  17.946   1191
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.08 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1084
  helix:  2.55 (0.27), residues: 369
  sheet:  0.80 (0.33), residues: 252
  loop : -1.44 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP S  47 
 HIS   0.007   0.001   HIS R  62 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.027   0.001   TYR R 287 
 ARG   0.006   0.000   ARG A 323 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  238 ASN cc_start: 0.8896 (m110) cc_final: 0.8613 (m110)
REVERT: A  323 ARG cc_start: 0.8406 (mtp85) cc_final: 0.8114 (mtp180)
REVERT: B   75 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8258 (tt0)
REVERT: B  258 ASP cc_start: 0.7676 (t0) cc_final: 0.7347 (t0)
REVERT: R  157 MET cc_start: 0.8016 (ttm) cc_final: 0.7194 (ttp)
REVERT: R  170 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7969 (tt)
REVERT: S   18 ARG cc_start: 0.8573 (tpp80) cc_final: 0.7856 (tpt170)
REVERT: S   83 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6227 (mmt)
  outliers start: 13
  outliers final: 9
  residues processed: 154
  average time/residue: 0.2838
  time to fit residues: 58.4437
Evaluate side-chains
  151 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  170 LEU
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 94 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
A 204 GLN
B  32 GLN
** R  62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.146029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.112161 restraints weight = 10939.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 2.70
r_work: 0.3089 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2956 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8580  Z= 0.301
  Angle     :  0.617  10.222  11666  Z= 0.321
  Chirality :  0.045   0.141   1341
  Planarity :  0.004   0.048   1474
  Dihedral  :  4.434  23.322   1191
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 16.08 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.26), residues: 1084
  helix:  2.42 (0.27), residues: 371
  sheet:  0.63 (0.33), residues: 259
  loop : -1.41 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP R  59 
 HIS   0.011   0.002   HIS R  54 
 PHE   0.016   0.002   PHE A 189 
 TYR   0.036   0.002   TYR R 287 
 ARG   0.008   0.000   ARG A 323 

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

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

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2168 Ramachandran restraints generated.
    1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.017 
Fit side-chains
REVERT: A   24 GLN cc_start: 0.8278 (tt0) cc_final: 0.7979 (mt0)
REVERT: A  234 GLN cc_start: 0.8132 (tp-100) cc_final: 0.7772 (tp-100)
REVERT: A  238 ASN cc_start: 0.8958 (m110) cc_final: 0.8664 (m110)
REVERT: A  323 ARG cc_start: 0.8485 (mtp85) cc_final: 0.8185 (mtp180)
REVERT: B   75 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8197 (tt0)
REVERT: B  258 ASP cc_start: 0.7822 (t0) cc_final: 0.7577 (t0)
REVERT: R  157 MET cc_start: 0.7951 (ttm) cc_final: 0.7533 (ttm)
REVERT: S   83 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6374 (mmt)
  outliers start: 16
  outliers final: 14
  residues processed: 151
  average time/residue: 0.2572
  time to fit residues: 51.7119
Evaluate side-chains
  153 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  301 VAL
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  187 VAL
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain R residue   53 LEU
Chi-restraints excluded: chain R residue   62 HIS
Chi-restraints excluded: chain R residue  124 VAL
Chi-restraints excluded: chain R residue  149 LEU
Chi-restraints excluded: chain R residue  164 LEU
Chi-restraints excluded: chain S residue   62 ASP
Chi-restraints excluded: chain S residue   83 MET
Chi-restraints excluded: chain S residue   84 THR
Chi-restraints excluded: chain S residue   96 CYS
Chi-restraints excluded: chain S residue  215 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 93 optimal weight:   10.0000
   chunk 8 optimal weight:    0.8980
   chunk 34 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
A  22 GLN
B  32 GLN
** R  62 HIS ** 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 = 0.3820 r_free = 0.3820 target = 0.149196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.114234 restraints weight = 11034.909|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 2.49
r_work: 0.3134 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8580  Z= 0.161
  Angle     :  0.557   8.946  11666  Z= 0.288
  Chirality :  0.042   0.135   1341
  Planarity :  0.004   0.046   1474
  Dihedral  :  4.189  19.929   1191
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 16.43 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1084
  helix:  2.45 (0.27), residues: 371
  sheet:  0.67 (0.33), residues: 259
  loop : -1.36 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 339 
 HIS   0.008   0.001   HIS R  62 
 PHE   0.014   0.001   PHE A 189 
 TYR   0.037   0.001   TYR R 287 
 ARG   0.006   0.000   ARG A 323 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5785.36 seconds
wall clock time: 100 minutes 50.75 seconds (6050.75 seconds total)