Starting phenix.real_space_refine
on Thu Mar 13 03:11:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ihi_35445/03_2025/8ihi_35445.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ihi_35445/03_2025/8ihi_35445.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ihi_35445/03_2025/8ihi_35445.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ihi_35445/03_2025/8ihi_35445.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ihi_35445/03_2025/8ihi_35445.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ihi_35445/03_2025/8ihi_35445.cif"
  }
  resolution = 3.11
  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=  -0.000 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    5545      2.51       5
     N    1472      2.21       5
     O    1591      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8665
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1695
          Classifications: {'peptide': 218}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 1, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 30
    Chain: "S"
      Number of atoms: 1706
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 226, 1706
          Classifications: {'peptide': 226}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 10, 'TRANS': 215}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      Number of atoms: 2477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 339, 2477
          Classifications: {'peptide': 339}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 5, 'TRANS': 333}
          Unresolved non-hydrogen bonds: 129
          Unresolved non-hydrogen angles: 156
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 5, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 6}
          Unresolved non-hydrogen planarities: 91
    Chain: "C"
      Number of atoms: 376
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 376
          Classifications: {'peptide': 56}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "R"
      Number of atoms: 2381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 292, 2381
          Classifications: {'peptide': 292}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 10, 'TRANS': 281}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "R"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {'NAG': 1, 'P9X': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 6.07, per 1000 atoms: 0.70
  Number of scatterers: 8665
  At special positions: 0
  Unit cell: (89.1, 117.81, 135.63, 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      57     16.00
     O    1591      8.00
     N    1472      7.00
     C    5545      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS S 159 " - pdb=" SG  CYS S 229 " distance=2.86
    Simple disulfide: pdb=" SG  CYS R  18 " - pdb=" SG  CYS R 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  19 " - pdb=" SG  CYS R 266 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 100 " - pdb=" SG  CYS R 177 " 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
  Links applied
    NAG-ASN
      " NAG R 601 " - " ASN R  17 "
  Time building additional restraints: 3.74
  Conformation dependent library (CDL) restraints added in 2.2 seconds
  

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      26 helices and 15 sheets defined
      36.4% alpha, 20.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 32
      removed outlier: 3.517A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASN A  22 " --> pdb=" O   MET A  18 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ARG A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.718A  pdb=" N   ILE A 212 " --> pdb=" O   LYS A 209 " (cutoff:3.500A)
      removed outlier: 5.550A  pdb=" N   HIS A 213 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   CYS A 214 " --> pdb=" O   TRP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 241 through 255
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.293A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 310
      removed outlier: 3.726A  pdb=" N   LEU A 310 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 351
      removed outlier: 3.523A  pdb=" N   LYS A 349 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP A 350 " --> pdb=" O   ASN A 346 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 62 through 65
      removed outlier: 3.973A  pdb=" N   LYS S  65 " --> pdb=" O   ASP S  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 62 through 65'
    Processing helix  chain 'B' and resid 3 through 25
      removed outlier: 3.534A  pdb=" N   CYS B  25 " --> pdb=" O   ALA B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
    Processing helix  chain 'C' and resid 9 through 24
      removed outlier: 3.545A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.581A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 59
    Processing helix  chain 'R' and resid 24 through 55
      removed outlier: 3.842A  pdb=" N   LYS R  28 " --> pdb=" O   ASP R  24 " (cutoff:3.500A)
      Proline residue:  R  31  - end of helix
      removed outlier: 3.520A  pdb=" N   LEU R  36 " --> pdb=" O   PRO R  32 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   GLU R  37 " --> pdb=" O   VAL R  33 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE R  38 " --> pdb=" O   LEU R  34 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU R  43 " --> pdb=" O   ILE R  39 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 60 through 78
      removed outlier: 3.548A  pdb=" N   ILE R  78 " --> pdb=" O   PHE R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 89
      removed outlier: 3.529A  pdb=" N   ASN R  86 " --> pdb=" O   PHE R  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 97 through 128
      removed outlier: 3.863A  pdb=" N   LEU R 107 " --> pdb=" O   MET R 103 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   ARG R 111 " --> pdb=" O   LEU R 107 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   VAL R 121 " --> pdb=" O   PHE R 117 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 134 through 139
      removed outlier: 3.798A  pdb=" N   ILE R 139 " --> pdb=" O   LEU R 136 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 158
    Processing helix  chain 'R' and resid 159 through 163
    Processing helix  chain 'R' and resid 187 through 218
      removed outlier: 4.064A  pdb=" N   PHE R 197 " --> pdb=" O   PHE R 193 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU R 199 " --> pdb=" O   LEU R 195 " (cutoff:3.500A)
      Proline residue:  R 200  - end of helix
    Processing helix  chain 'R' and resid 223 through 261
      removed outlier: 3.536A  pdb=" N   PHE R 232 " --> pdb=" O   ARG R 228 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   MET R 234 " --> pdb=" O   ILE R 230 " (cutoff:3.500A)
      Proline residue:  R 246  - end of helix
    Processing helix  chain 'R' and resid 269 through 281
      removed outlier: 3.615A  pdb=" N   LEU R 274 " --> pdb=" O   ARG R 270 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 282 through 295
      removed outlier: 3.827A  pdb=" N   ASN R 286 " --> pdb=" O   PHE R 282 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   SER R 287 " --> pdb=" O   THR R 283 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 3.683A  pdb=" N   PHE A 189 " --> pdb=" O   PHE A 196 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.232A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'S' and resid 6 through 7
      removed outlier: 3.715A  pdb=" N   SER S   7 " --> pdb=" O   SER S  23 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 58 through 60
      removed outlier: 3.538A  pdb=" N   VAL S  97 " --> pdb=" O   HIS S  35 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'S' and resid 45 through 46
      removed outlier: 3.582A  pdb=" N   ALA S  92 " --> pdb=" O   LEU S 117 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'S' and resid 155 through 160
    Processing sheet with id=AA6, first strand: chain 'S' and resid 194 through 195
      removed outlier: 5.383A  pdb=" N   LEU S 187 " --> pdb=" O   LEU S 178 " (cutoff:3.500A)
      removed outlier: 6.305A  pdb=" N   LEU S 178 " --> pdb=" O   LEU S 187 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR S 227 " --> pdb=" O   THR S 243 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.720A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.738A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.070A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 100 through 105
      removed outlier: 3.616A  pdb=" N   GLY B 115 " --> pdb=" O   THR B 102 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.781A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.815A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.132A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.217A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.465A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.559A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'R' and resid 10 through 12
      removed outlier: 3.962A  pdb=" N   ILE R 182 " --> pdb=" O   CYS R  19 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'R' and resid 169 through 171
      removed outlier: 3.584A  pdb=" N   ILE R 169 " --> pdb=" O   LEU R 176 " (cutoff:3.500A)

    404 hydrogen bonds defined for protein.
    1131 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: 2.32

  Time building geometry restraints manager: 3.38 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: 2784
        1.34 -     1.46: 2206
        1.46 -     1.58: 3792
        1.58 -     1.70: 0
        1.70 -     1.82: 79
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" C5  P9X R 602 "
       pdb=" O2  P9X R 602 "
    ideal  model  delta    sigma   weight residual
    1.250  1.306 -0.056 2.00e-02 2.50e+03 7.81e+00
  bond pdb=" C4  P9X R 602 "
       pdb=" C5  P9X R 602 "
    ideal  model  delta    sigma   weight residual
    1.530  1.476  0.054 2.00e-02 2.50e+03 7.34e+00
  bond pdb=" CA  LYS R 165 "
       pdb=" C   LYS R 165 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.24e-02 6.50e+03 5.43e+00
  bond pdb=" N   LYS R 165 "
       pdb=" CA  LYS R 165 "
    ideal  model  delta    sigma   weight residual
    1.455  1.432  0.024 1.22e-02 6.72e+03 3.83e+00
  bond pdb=" CB  PRO S 151 "
       pdb=" CG  PRO S 151 "
    ideal  model  delta    sigma   weight residual
    1.492  1.569 -0.077 5.00e-02 4.00e+02 2.40e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 11912
        2.16 -     4.33: 106
        4.33 -     6.49: 15
        6.49 -     8.65: 3
        8.65 -    10.81: 2
  Bond angle restraints: 12038
  Sorted by residual:
  angle pdb=" CB  MET R 167 "
        pdb=" CG  MET R 167 "
        pdb=" SD  MET R 167 "
      ideal   model   delta    sigma   weight residual
     112.70  123.51  -10.81 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" CA  PRO S 151 "
        pdb=" N   PRO S 151 "
        pdb=" CD  PRO S 151 "
      ideal   model   delta    sigma   weight residual
     112.00  107.01    4.99 1.40e+00 5.10e-01 1.27e+01
  angle pdb=" C   ASP R  97 "
        pdb=" N   ILE R  98 "
        pdb=" CA  ILE R  98 "
      ideal   model   delta    sigma   weight residual
     120.33  122.69   -2.36 8.00e-01 1.56e+00 8.73e+00
  angle pdb=" CA  LEU A 283 "
        pdb=" CB  LEU A 283 "
        pdb=" CG  LEU A 283 "
      ideal   model   delta    sigma   weight residual
     116.30  125.82   -9.52 3.50e+00 8.16e-02 7.41e+00
  angle pdb=" CA  LEU R  47 "
        pdb=" CB  LEU R  47 "
        pdb=" CG  LEU R  47 "
      ideal   model   delta    sigma   weight residual
     116.30  124.60   -8.30 3.50e+00 8.16e-02 5.62e+00
  ... (remaining 12033 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 4497
       17.92 -    35.84: 543
       35.84 -    53.77: 138
       53.77 -    71.69: 29
       71.69 -    89.61: 5
  Dihedral angle restraints: 5212
    sinusoidal: 1936
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" CB  CYS R 100 "
           pdb=" SG  CYS R 100 "
           pdb=" SG  CYS R 177 "
           pdb=" CB  CYS R 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -138.25   52.25     1      1.00e+01 1.00e-02 3.72e+01
  dihedral pdb=" CA  PHE R 117 "
           pdb=" C   PHE R 117 "
           pdb=" N   LEU R 118 "
           pdb=" CA  LEU R 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.66   24.34     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CB  CYS R  19 "
           pdb=" SG  CYS R  19 "
           pdb=" SG  CYS R 266 "
           pdb=" CB  CYS R 266 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -55.41  -30.59     1      1.00e+01 1.00e-02 1.34e+01
  ... (remaining 5209 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 804
       0.027 -    0.054: 360
       0.054 -    0.080: 120
       0.080 -    0.107: 67
       0.107 -    0.134: 27
  Chirality restraints: 1378
  Sorted by residual:
  chirality pdb=" CA  VAL S 147 "
            pdb=" N   VAL S 147 "
            pdb=" C   VAL S 147 "
            pdb=" CB  VAL S 147 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.50e-01
  chirality pdb=" CA  ASP S  90 "
            pdb=" N   ASP S  90 "
            pdb=" C   ASP S  90 "
            pdb=" CB  ASP S  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  VAL B 327 "
            pdb=" N   VAL B 327 "
            pdb=" C   VAL B 327 "
            pdb=" CB  VAL B 327 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 1375 not shown)

  Planarity restraints: 1523
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR S 150 "   -0.082 5.00e-02 4.00e+02   1.22e-01 2.39e+01
        pdb=" N   PRO S 151 "    0.211 5.00e-02 4.00e+02
        pdb=" CA  PRO S 151 "   -0.065 5.00e-02 4.00e+02
        pdb=" CD  PRO S 151 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R  31 "    0.038 5.00e-02 4.00e+02   5.77e-02 5.32e+00
        pdb=" N   PRO R  32 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO R  32 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO R  32 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR C  52 "   -0.032 5.00e-02 4.00e+02   4.84e-02 3.75e+00
        pdb=" N   PRO C  53 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO C  53 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  53 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1520 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1386
        2.76 -     3.29: 7952
        3.29 -     3.83: 13782
        3.83 -     4.36: 16840
        4.36 -     4.90: 29890
  Nonbonded interactions: 69850
  Sorted by model distance:
  nonbonded pdb=" O   LEU R 280 "
            pdb=" OG1 THR R 283 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" OG1 THR B 274 "
            pdb=" O   VAL B 315 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   GLY R 262 "
            pdb=" OH  TYR R 269 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   LEU R 257 "
            pdb=" OG  SER R 261 "
     model   vdw
     2.264 3.040
  ... (remaining 69845 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:             8.320
  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:             0.000
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     28.890
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  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:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
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   0.077   8861  Z= 0.176
  Angle     :  0.532  10.813  12038  Z= 0.273
  Chirality :  0.040   0.134   1378
  Planarity :  0.005   0.122   1522
  Dihedral  : 16.775  89.608   3082
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 25.98 %
    Favored  : 73.80 %
  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: -0.60 (0.25), residues: 1115
  helix:  0.14 (0.28), residues: 352
  sheet: -0.02 (0.31), residues: 269
  loop : -0.92 (0.28), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP R 152 
 HIS   0.002   0.000   HIS R 189 
 PHE   0.026   0.001   PHE R  38 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.005   0.000   ARG S  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 144
  time to evaluate  : 1.012 
Fit side-chains
   revert: symmetry clash
REVERT: S   69 THR cc_start: 0.8404 (t) cc_final: 0.8071 (m)
REVERT: S   87 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7526 (mtm-85)
REVERT: C   42 GLU cc_start: 0.7684 (mp0) cc_final: 0.7262 (mp0)
  outliers start: 2
  outliers final: 2
  residues processed: 145
  average time/residue: 0.2139
  time to fit residues: 42.9375
Evaluate side-chains
  136 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 134
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain R residue  272 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 83 optimal weight:    6.9990
   chunk 46 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:    5.9990
   chunk 86 optimal weight:    3.9990
   chunk 33 optimal weight:    9.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:   10.0000
   chunk 99 optimal weight:    0.9980
   overall best weight:    3.1586

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.147457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.114016 restraints weight = 11209.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.40
r_work: 0.3308 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3169 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.1209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8861  Z= 0.330
  Angle     :  0.615   7.902  12038  Z= 0.324
  Chirality :  0.044   0.185   1378
  Planarity :  0.005   0.082   1522
  Dihedral  :  5.356  59.881   1259
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 24.30 %
    Favored  : 72.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -0.09 (0.25), residues: 1115
  helix:  1.07 (0.27), residues: 360
  sheet:  0.04 (0.32), residues: 262
  loop : -0.91 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S  47 
 HIS   0.004   0.001   HIS A 188 
 PHE   0.015   0.002   PHE R 232 
 TYR   0.024   0.002   TYR S 235 
 ARG   0.005   0.001   ARG S  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 135
  time to evaluate  : 0.914 
Fit side-chains
REVERT: A   24 ARG cc_start: 0.7425 (mtm110) cc_final: 0.7068 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8426 (mtmt)
REVERT: A  244 HIS cc_start: 0.7298 (m90) cc_final: 0.6963 (m90)
REVERT: S   67 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7562 (mtm180)
REVERT: S  202 ARG cc_start: 0.8379 (mtm110) cc_final: 0.8113 (mtm110)
REVERT: B  234 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.8676 (m-80)
  outliers start: 25
  outliers final: 15
  residues processed: 155
  average time/residue: 0.2309
  time to fit residues: 47.9847
Evaluate side-chains
  138 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   44 SER
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  186 GLN
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  154 ILE
Chi-restraints excluded: chain R residue  268 VAL
Chi-restraints excluded: chain R residue  284 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 8 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 53 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.152422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.118985 restraints weight = 11337.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 2.45
r_work: 0.3379 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.1480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8861  Z= 0.145
  Angle     :  0.516  10.128  12038  Z= 0.267
  Chirality :  0.041   0.163   1378
  Planarity :  0.004   0.064   1522
  Dihedral  :  4.573  45.289   1256
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 25.20 %
    Favored  : 71.68 %
  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:  0.31 (0.25), residues: 1115
  helix:  1.78 (0.27), residues: 360
  sheet:  0.10 (0.32), residues: 269
  loop : -0.92 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 339 
 HIS   0.003   0.001   HIS A 188 
 PHE   0.017   0.001   PHE R  38 
 TYR   0.021   0.001   TYR S 235 
 ARG   0.003   0.000   ARG S  18 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 139
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8163 (t0) cc_final: 0.7846 (m-30)
REVERT: A   24 ARG cc_start: 0.7320 (mtm110) cc_final: 0.7033 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8872 (mmtm) cc_final: 0.8456 (mtmt)
REVERT: S   13 GLN cc_start: 0.7869 (pm20) cc_final: 0.7628 (pm20)
REVERT: S   67 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7745 (mtm180)
REVERT: S  202 ARG cc_start: 0.8325 (mtm110) cc_final: 0.8050 (mtm110)
REVERT: B  234 PHE cc_start: 0.9026 (OUTLIER) cc_final: 0.8618 (m-80)
REVERT: R   14 ASP cc_start: 0.7327 (m-30) cc_final: 0.6560 (t0)
REVERT: R   47 LEU cc_start: 0.8299 (tt) cc_final: 0.8019 (mp)
REVERT: R   89 ARG cc_start: 0.7259 (mtt90) cc_final: 0.7056 (mtt90)
REVERT: R  165 LYS cc_start: 0.7304 (mmtt) cc_final: 0.6585 (mtmt)
REVERT: R  167 MET cc_start: 0.6042 (tpp) cc_final: 0.5709 (tpp)
REVERT: R  217 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7495 (tt0)
REVERT: R  285 MET cc_start: 0.7646 (tpt) cc_final: 0.7409 (tpt)
  outliers start: 28
  outliers final: 13
  residues processed: 161
  average time/residue: 0.2342
  time to fit residues: 50.8298
Evaluate side-chains
  144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 128
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  179 SER
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 18 optimal weight:    9.9990
   chunk 53 optimal weight:    8.9990
   chunk 92 optimal weight:    1.9990
   chunk 93 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 40 optimal weight:    8.9990
   chunk 70 optimal weight:    0.8980
   chunk 99 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.155132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.120938 restraints weight = 11296.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.52
r_work: 0.3377 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8861  Z= 0.145
  Angle     :  0.498   7.191  12038  Z= 0.258
  Chirality :  0.041   0.135   1378
  Planarity :  0.004   0.055   1522
  Dihedral  :  4.159  26.119   1256
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 26.53 %
    Favored  : 70.68 %
  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:  0.50 (0.26), residues: 1115
  helix:  2.06 (0.28), residues: 360
  sheet:  0.21 (0.32), residues: 271
  loop : -0.92 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.022   0.001   PHE R  38 
 TYR   0.020   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8214 (t0) cc_final: 0.7899 (m-30)
REVERT: A   24 ARG cc_start: 0.7249 (mtm110) cc_final: 0.6991 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8454 (mtmt)
REVERT: S  202 ARG cc_start: 0.8182 (mtm110) cc_final: 0.7922 (mtm110)
REVERT: B  234 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8633 (m-80)
REVERT: R   14 ASP cc_start: 0.7339 (m-30) cc_final: 0.6570 (t0)
REVERT: R   47 LEU cc_start: 0.8249 (tt) cc_final: 0.8009 (mp)
REVERT: R  150 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7909 (tt)
REVERT: R  165 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6626 (mtmt)
REVERT: R  190 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6709 (mm-30)
REVERT: R  217 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7463 (tt0)
  outliers start: 25
  outliers final: 11
  residues processed: 156
  average time/residue: 0.2281
  time to fit residues: 48.0098
Evaluate side-chains
  140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 34 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0570
   chunk 55 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    0.4980
   chunk 101 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 3 optimal weight:    0.6980
   chunk 78 optimal weight:    8.9990
   overall best weight:    0.8100

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.155834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.121764 restraints weight = 11228.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.50
r_work: 0.3392 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8861  Z= 0.140
  Angle     :  0.493   6.594  12038  Z= 0.255
  Chirality :  0.041   0.132   1378
  Planarity :  0.004   0.049   1522
  Dihedral  :  3.944  20.398   1256
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 26.53 %
    Favored  : 70.68 %
  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:  0.63 (0.26), residues: 1115
  helix:  2.23 (0.28), residues: 361
  sheet:  0.15 (0.31), residues: 281
  loop : -0.84 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  82 
 HIS   0.002   0.000   HIS A 188 
 PHE   0.023   0.001   PHE R  38 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 1.027 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8218 (t0) cc_final: 0.7947 (m-30)
REVERT: A   24 ARG cc_start: 0.7361 (mtm110) cc_final: 0.7104 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8465 (mtmt)
REVERT: S  202 ARG cc_start: 0.8249 (mtm110) cc_final: 0.8022 (mtm110)
REVERT: B  137 ARG cc_start: 0.8267 (tpt90) cc_final: 0.7672 (tpp-160)
REVERT: B  234 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8627 (m-80)
REVERT: R   14 ASP cc_start: 0.7369 (m-30) cc_final: 0.6484 (t0)
REVERT: R   47 LEU cc_start: 0.8184 (tt) cc_final: 0.7969 (mp)
REVERT: R  150 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7968 (tt)
REVERT: R  165 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6540 (mtmt)
REVERT: R  190 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.6751 (mm-30)
REVERT: R  217 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7613 (tt0)
  outliers start: 25
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2222
  time to fit residues: 46.5983
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   67 ARG
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  150 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 90 optimal weight:    9.9990
   chunk 20 optimal weight:    0.6980
   chunk 109 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   chunk 75 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 76 optimal weight:   30.0000
   chunk 24 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.153475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.119149 restraints weight = 11250.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.50
r_work: 0.3351 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8861  Z= 0.223
  Angle     :  0.528   7.001  12038  Z= 0.274
  Chirality :  0.042   0.162   1378
  Planarity :  0.004   0.053   1522
  Dihedral  :  4.122  19.247   1256
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.98 %
    Favored  : 70.35 %
  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:  0.55 (0.26), residues: 1115
  helix:  2.12 (0.28), residues: 361
  sheet:  0.27 (0.32), residues: 269
  loop : -0.94 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.003   0.001   HIS R 134 
 PHE   0.025   0.002   PHE R  38 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.004   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8302 (t0) cc_final: 0.7992 (m-30)
REVERT: A   24 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6998 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8474 (mtmt)
REVERT: B  137 ARG cc_start: 0.8236 (tpt90) cc_final: 0.7588 (tpp-160)
REVERT: B  234 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8660 (m-80)
REVERT: C   42 GLU cc_start: 0.7543 (mp0) cc_final: 0.6739 (mp0)
REVERT: R   14 ASP cc_start: 0.7375 (m-30) cc_final: 0.6460 (t0)
REVERT: R  165 LYS cc_start: 0.7389 (mmtt) cc_final: 0.6616 (mtmt)
REVERT: R  217 GLN cc_start: 0.8165 (OUTLIER) cc_final: 0.7622 (tt0)
  outliers start: 33
  outliers final: 19
  residues processed: 157
  average time/residue: 0.2213
  time to fit residues: 47.0890
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  247 MET
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  116 ILE
Chi-restraints excluded: chain R residue  179 SER
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 94 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 34 optimal weight:    0.2980
   chunk 73 optimal weight:    9.9990
   chunk 86 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
S 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.153384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.119180 restraints weight = 11341.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 2.50
r_work: 0.3356 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.3219 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8861  Z= 0.212
  Angle     :  0.526   7.038  12038  Z= 0.274
  Chirality :  0.042   0.155   1378
  Planarity :  0.004   0.046   1522
  Dihedral  :  4.148  19.578   1256
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.46 %
    Allowed  : 26.31 %
    Favored  : 70.23 %
  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: 1115
  helix:  2.09 (0.28), residues: 361
  sheet:  0.29 (0.32), residues: 267
  loop : -0.95 (0.28), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B  91 
 PHE   0.026   0.001   PHE R  38 
 TYR   0.024   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 130
  time to evaluate  : 1.039 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8331 (t0) cc_final: 0.8034 (m-30)
REVERT: A   24 ARG cc_start: 0.7375 (mtm110) cc_final: 0.7065 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8520 (mtmt)
REVERT: B  137 ARG cc_start: 0.8255 (tpt90) cc_final: 0.7632 (tpp-160)
REVERT: B  234 PHE cc_start: 0.9030 (OUTLIER) cc_final: 0.8684 (m-80)
REVERT: C   42 GLU cc_start: 0.7536 (mp0) cc_final: 0.6728 (mp0)
REVERT: R   14 ASP cc_start: 0.7312 (m-30) cc_final: 0.6431 (t0)
REVERT: R  165 LYS cc_start: 0.7452 (mmtt) cc_final: 0.6703 (mtmt)
REVERT: R  217 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7602 (tt0)
  outliers start: 31
  outliers final: 20
  residues processed: 151
  average time/residue: 0.2087
  time to fit residues: 43.8963
Evaluate side-chains
  151 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 128
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  189 ILE
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue   67 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   43 LEU
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 68 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 38 optimal weight:    6.9990
   chunk 54 optimal weight:    0.6980
   chunk 46 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 98 optimal weight:   10.0000
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
R 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.153895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.119640 restraints weight = 11393.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.52
r_work: 0.3359 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work: 0.3223 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8861  Z= 0.191
  Angle     :  0.530   7.552  12038  Z= 0.272
  Chirality :  0.042   0.171   1378
  Planarity :  0.004   0.050   1522
  Dihedral  :  4.109  19.123   1256
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.76 %
    Favored  : 70.01 %
  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:  0.57 (0.26), residues: 1115
  helix:  2.12 (0.28), residues: 360
  sheet:  0.32 (0.32), residues: 267
  loop : -0.94 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.002   0.001   HIS B  91 
 PHE   0.027   0.001   PHE R  38 
 TYR   0.023   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 132
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8319 (t0) cc_final: 0.8032 (m-30)
REVERT: A   24 ARG cc_start: 0.7440 (mtm110) cc_final: 0.7202 (ttp-110)
REVERT: A  197 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8489 (mtmt)
REVERT: B  137 ARG cc_start: 0.8253 (tpt90) cc_final: 0.7639 (tpp-160)
REVERT: B  234 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8679 (m-80)
REVERT: C   42 GLU cc_start: 0.7509 (mp0) cc_final: 0.6696 (mp0)
REVERT: R   14 ASP cc_start: 0.7336 (m-30) cc_final: 0.6392 (t0)
REVERT: R  165 LYS cc_start: 0.7446 (mmtt) cc_final: 0.6727 (mtmt)
REVERT: R  167 MET cc_start: 0.5663 (tpp) cc_final: 0.5408 (tpp)
REVERT: R  190 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6756 (mm-30)
REVERT: R  217 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7605 (tt0)
  outliers start: 29
  outliers final: 19
  residues processed: 151
  average time/residue: 0.2093
  time to fit residues: 43.3743
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 LYS
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue   71 SER
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  217 GLN
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Chi-restraints excluded: chain R residue  268 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 100 optimal weight:    0.7980
   chunk 94 optimal weight:    0.1980
   chunk 22 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0980
   chunk 58 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 18 optimal weight:    5.9990
   chunk 89 optimal weight:    5.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS
S 186 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.156275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.122157 restraints weight = 11268.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.51
r_work: 0.3386 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8861  Z= 0.142
  Angle     :  0.516   9.777  12038  Z= 0.262
  Chirality :  0.041   0.132   1378
  Planarity :  0.004   0.048   1522
  Dihedral  :  3.901  17.457   1256
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 28.21 %
    Favored  : 69.45 %
  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:  0.69 (0.26), residues: 1115
  helix:  2.27 (0.28), residues: 360
  sheet:  0.27 (0.31), residues: 278
  loop : -0.84 (0.29), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.002   0.000   HIS C  44 
 PHE   0.028   0.001   PHE R  38 
 TYR   0.019   0.001   TYR S 235 
 ARG   0.003   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 128
  time to evaluate  : 0.954 
Fit side-chains
REVERT: A    9 ASP cc_start: 0.8249 (t0) cc_final: 0.7985 (m-30)
REVERT: A  197 LYS cc_start: 0.8837 (mmtm) cc_final: 0.8379 (mtmt)
REVERT: S   82 GLN cc_start: 0.7830 (tp40) cc_final: 0.7614 (tp-100)
REVERT: B  137 ARG cc_start: 0.8226 (tpt90) cc_final: 0.7615 (tpp-160)
REVERT: B  234 PHE cc_start: 0.8999 (OUTLIER) cc_final: 0.8615 (m-80)
REVERT: C   42 GLU cc_start: 0.7450 (mp0) cc_final: 0.6613 (mp0)
REVERT: R   14 ASP cc_start: 0.7310 (m-30) cc_final: 0.6284 (t0)
REVERT: R  165 LYS cc_start: 0.7513 (mmtt) cc_final: 0.6788 (mtmt)
REVERT: R  167 MET cc_start: 0.5719 (tpp) cc_final: 0.5450 (tpp)
REVERT: R  190 GLU cc_start: 0.7056 (OUTLIER) cc_final: 0.6616 (mp0)
  outliers start: 21
  outliers final: 17
  residues processed: 143
  average time/residue: 0.2061
  time to fit residues: 41.1271
Evaluate side-chains
  143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 124
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  109 ASP
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain S residue  237 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  140 SER
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 100 optimal weight:    0.4980
   chunk 12 optimal weight:    6.9990
   chunk 72 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 97 optimal weight:    9.9990
   chunk 79 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 63 optimal weight:    0.3980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.156588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.122473 restraints weight = 11295.444|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 2.52
r_work: 0.3392 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8861  Z= 0.136
  Angle     :  0.517  13.164  12038  Z= 0.261
  Chirality :  0.041   0.149   1378
  Planarity :  0.004   0.051   1522
  Dihedral  :  3.837  16.331   1256
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 28.32 %
    Favored  : 69.45 %
  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:  0.75 (0.26), residues: 1115
  helix:  2.33 (0.28), residues: 361
  sheet:  0.29 (0.31), residues: 278
  loop : -0.82 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP S  47 
 HIS   0.001   0.000   HIS B 225 
 PHE   0.028   0.001   PHE R  38 
 TYR   0.019   0.001   TYR A 287 
 ARG   0.003   0.000   ARG R 270 

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

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

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2230 Ramachandran restraints generated.
    1115 Oldfield, 0 Emsley, 1115 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 ASP cc_start: 0.8052 (t0) cc_final: 0.7788 (m-30)
REVERT: B  137 ARG cc_start: 0.8061 (tpt90) cc_final: 0.7663 (tpp80)
REVERT: B  234 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8556 (m-80)
REVERT: C   42 GLU cc_start: 0.7312 (mp0) cc_final: 0.6502 (mp0)
REVERT: R   14 ASP cc_start: 0.7222 (m-30) cc_final: 0.6250 (t0)
REVERT: R  165 LYS cc_start: 0.7396 (mmtt) cc_final: 0.6714 (mtmt)
REVERT: R  190 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6556 (mp0)
  outliers start: 20
  outliers final: 16
  residues processed: 139
  average time/residue: 0.2009
  time to fit residues: 39.5139
Evaluate side-chains
  140 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.929 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue    6 GLU
Chi-restraints excluded: chain S residue   57 THR
Chi-restraints excluded: chain S residue   69 THR
Chi-restraints excluded: chain S residue  172 THR
Chi-restraints excluded: chain S residue  217 SER
Chi-restraints excluded: chain S residue  237 LEU
Chi-restraints excluded: chain B residue  146 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  277 SER
Chi-restraints excluded: chain C residue   37 LEU
Chi-restraints excluded: chain R residue   56 LEU
Chi-restraints excluded: chain R residue  190 GLU
Chi-restraints excluded: chain R residue  221 ASP
Chi-restraints excluded: chain R residue  263 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 64 optimal weight:    4.9990
   chunk 72 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 76 optimal weight:   40.0000
   chunk 52 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 109 optimal weight:    0.6980
   chunk 92 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.150594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.116471 restraints weight = 11430.115|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.50
r_work: 0.3309 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.89 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.2139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   8861  Z= 0.351
  Angle     :  0.625  12.887  12038  Z= 0.322
  Chirality :  0.045   0.142   1378
  Planarity :  0.004   0.045   1522
  Dihedral  :  4.645  23.635   1256
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.86 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 28.09 %
    Favored  : 69.23 %
  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:  0.41 (0.25), residues: 1115
  helix:  1.96 (0.28), residues: 362
  sheet:  0.24 (0.32), residues: 267
  loop : -1.02 (0.28), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP S  47 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.028   0.002   PHE R  38 
 TYR   0.041   0.002   TYR S 235 
 ARG   0.007   0.001   ARG S 180 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5225.52 seconds
wall clock time: 90 minutes 34.22 seconds (5434.22 seconds total)