Starting phenix.real_space_refine
on Sat Dec 28 02:28:28 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hti_35010/12_2024/8hti_35010_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hti_35010/12_2024/8hti_35010.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.97
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hti_35010/12_2024/8hti_35010.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hti_35010/12_2024/8hti_35010.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hti_35010/12_2024/8hti_35010_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hti_35010/12_2024/8hti_35010_neut.cif"
  }
  resolution = 2.97
  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=   0.024 sd=   0.080
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      51      5.16       5
     C    4757      2.51       5
     N    1274      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 7390
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 1311
          Classifications: {'peptide': 157}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 1, 'TRANS': 155}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 33
    Chain: "B"
      Number of atoms: 2454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 328, 2454
          Classifications: {'peptide': 328}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 18}
          Link IDs: {'PTRANS': 5, 'TRANS': 322}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'ASP:plan': 7}
          Unresolved non-hydrogen planarities: 49
    Chain: "G"
      Number of atoms: 364
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 52, 364
          Classifications: {'peptide': 52}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "N"
      Number of atoms: 848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 848
          Classifications: {'peptide': 122}
          Incomplete info: {'truncation_to_alanine': 23}
          Link IDs: {'PTRANS': 5, 'TRANS': 116}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 106
          Unresolved non-hydrogen dihedrals: 68
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 3, 'PHE:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "R"
      Number of atoms: 2403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 303, 2403
          Classifications: {'peptide': 303}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 17, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "R"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'OCA': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C1  OCA R 401 " occ=0.00
      ... (8 atoms not shown)
      pdb=" O2  OCA R 401 " occ=0.00
  Time building chain proxies: 6.11, per 1000 atoms: 0.83
  Number of scatterers: 7390
  At special positions: 0
  Unit cell: (82.547, 95.312, 133.607, 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      51     16.00
     O    1308      8.00
     N    1274      7.00
     C    4757      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  99 " - pdb=" SG  CYS R 181 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 171 " - pdb=" SG  CYS R 191 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.78
  Conformation dependent library (CDL) restraints added in 874.1 milliseconds
  

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1810

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 11 sheets defined
      39.5% alpha, 22.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 39
      removed outlier: 3.539A  pdb=" N   LYS A  25 " --> pdb=" O   GLU A  21 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASP A  33 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LYS A  34 " --> pdb=" O   LEU A  30 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 225
      removed outlier: 3.739A  pdb=" N   CYS A 223 " --> pdb=" O   TRP A 220 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ASN A 225 " --> pdb=" O   GLN A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
    Processing helix  chain 'A' and resid 325 through 336
      removed outlier: 3.590A  pdb=" N   ILE A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 377
    Processing helix  chain 'B' and resid 10 through 26
      removed outlier: 3.612A  pdb=" N   ALA B  26 " --> pdb=" O   ARG B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.587A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 11 through 23
    Processing helix  chain 'G' and resid 30 through 44
      removed outlier: 3.558A  pdb=" N   ALA G  35 " --> pdb=" O   SER G  31 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.744A  pdb=" N   THR N  91 " --> pdb=" O   PRO N  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 22 through 26
      removed outlier: 3.882A  pdb=" N   HIS R  26 " --> pdb=" O   GLU R  23 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 29 through 54
      removed outlier: 4.285A  pdb=" N   PHE R  33 " --> pdb=" O   ILE R  29 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA R  35 " --> pdb=" O   ILE R  31 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ASN R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   SER R  45 " --> pdb=" O   LEU R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 59 through 78
      removed outlier: 3.530A  pdb=" N   THR R  77 " --> pdb=" O   LEU R  73 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   SER R  78 " --> pdb=" O   VAL R  74 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 90
    Processing helix  chain 'R' and resid 96 through 130
    Processing helix  chain 'R' and resid 133 through 138
    Processing helix  chain 'R' and resid 139 through 159
    Processing helix  chain 'R' and resid 159 through 166
      removed outlier: 4.567A  pdb=" N   PHE R 163 " --> pdb=" O   ILE R 159 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 182 through 188
      removed outlier: 3.771A  pdb=" N   VAL R 186 " --> pdb=" O   GLU R 182 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 194 through 228
      removed outlier: 3.607A  pdb=" N   GLY R 210 " --> pdb=" O   LEU R 206 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LEU R 211 " --> pdb=" O   LEU R 207 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 234 through 267
      removed outlier: 4.233A  pdb=" N   LYS R 238 " --> pdb=" O   ASP R 234 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   LEU R 240 " --> pdb=" O   ARG R 236 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   SER R 245 " --> pdb=" O   SER R 241 " (cutoff:3.500A)
      Proline residue:  R 256  - end of helix
      removed outlier: 4.397A  pdb=" N   ARG R 265 " --> pdb=" O   PHE R 261 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLY R 267 " --> pdb=" O   THR R 263 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 271 through 280
      removed outlier: 3.670A  pdb=" N   HIS R 275 " --> pdb=" O   PRO R 271 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 284 through 295
      removed outlier: 3.596A  pdb=" N   MET R 288 " --> pdb=" O   LEU R 284 " (cutoff:3.500A)
      Proline residue:  R 291  - end of helix
    Processing helix  chain 'R' and resid 298 through 310
      removed outlier: 3.739A  pdb=" N   ARG R 302 " --> pdb=" O   THR R 298 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLU R 303 " --> pdb=" O   LYS R 299 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ARG R 304 " --> pdb=" O   GLN R 300 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE R 308 " --> pdb=" O   ARG R 304 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   PHE R 309 " --> pdb=" O   VAL R 305 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199
      removed outlier: 3.588A  pdb=" N   PHE A 208 " --> pdb=" O   LEU A  43 " (cutoff:3.500A)
      removed outlier: 9.884A  pdb=" N   ALA A 229 " --> pdb=" O   THR A  40 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 8.108A  pdb=" N   ILE A 231 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 231 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   VAL A 233 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 233 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE A 230 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
      removed outlier: 7.520A  pdb=" N   PHE A 276 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   PHE A 232 " --> pdb=" O   PHE A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.858A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.866A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62
      removed outlier: 7.080A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.877A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.151A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.742A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.980A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.208A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.297A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153
      removed outlier: 6.783A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.833A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 7.205A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.475A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.786A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.942A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.543A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60
      removed outlier: 3.573A  pdb=" N   SER N  59 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
      removed outlier: 4.892A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 7.033A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'R' and resid 93 through 95
      removed outlier: 8.244A  pdb=" N   ILE R 176 " --> pdb=" O   SER R  13 " (cutoff:3.500A)
      removed outlier: 6.210A  pdb=" N   LEU R  15 " --> pdb=" O   ILE R 176 " (cutoff:3.500A)

    348 hydrogen bonds defined for protein.
    1008 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: 1.99

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2367
        1.34 -     1.46: 1821
        1.46 -     1.58: 3291
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 7551
  Sorted by residual:
  bond pdb=" N   ASP B 312 "
       pdb=" CA  ASP B 312 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.35e-02 5.49e+03 6.24e+00
  bond pdb=" N   HIS R 183 "
       pdb=" CA  HIS R 183 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.029 1.24e-02 6.50e+03 5.42e+00
  bond pdb=" CE1 HIS R 183 "
       pdb=" NE2 HIS R 183 "
    ideal  model  delta    sigma   weight residual
    1.321  1.338 -0.017 1.00e-02 1.00e+04 2.86e+00
  bond pdb=" C   HIS R 183 "
       pdb=" O   HIS R 183 "
    ideal  model  delta    sigma   weight residual
    1.236  1.247 -0.012 1.19e-02 7.06e+03 9.35e-01
  bond pdb=" CA  ILE R 159 "
       pdb=" C   ILE R 159 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.05e-02 9.07e+03 8.68e-01
  ... (remaining 7546 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 9911
        1.45 -     2.90: 294
        2.90 -     4.35: 32
        4.35 -     5.81: 10
        5.81 -     7.26: 5
  Bond angle restraints: 10252
  Sorted by residual:
  angle pdb=" N   ILE R 159 "
        pdb=" CA  ILE R 159 "
        pdb=" C   ILE R 159 "
      ideal   model   delta    sigma   weight residual
     108.88  114.86   -5.98 2.16e+00 2.14e-01 7.66e+00
  angle pdb=" C   HIS R  10 "
        pdb=" N   PRO R  11 "
        pdb=" CA  PRO R  11 "
      ideal   model   delta    sigma   weight residual
     120.03  122.72   -2.69 9.90e-01 1.02e+00 7.38e+00
  angle pdb=" N   ASP B 312 "
        pdb=" CA  ASP B 312 "
        pdb=" C   ASP B 312 "
      ideal   model   delta    sigma   weight residual
     113.38  110.28    3.10 1.23e+00 6.61e-01 6.34e+00
  angle pdb=" N   GLY B 306 "
        pdb=" CA  GLY B 306 "
        pdb=" C   GLY B 306 "
      ideal   model   delta    sigma   weight residual
     110.38  114.03   -3.65 1.48e+00 4.57e-01 6.09e+00
  angle pdb=" CA  HIS R 183 "
        pdb=" C   HIS R 183 "
        pdb=" O   HIS R 183 "
      ideal   model   delta    sigma   weight residual
     120.55  117.99    2.56 1.07e+00 8.73e-01 5.73e+00
  ... (remaining 10247 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 3913
       17.74 -    35.49: 418
       35.49 -    53.23: 96
       53.23 -    70.98: 18
       70.98 -    88.72: 7
  Dihedral angle restraints: 4452
    sinusoidal: 1657
      harmonic: 2795
  Sorted by residual:
  dihedral pdb=" CB  CYS R 171 "
           pdb=" SG  CYS R 171 "
           pdb=" SG  CYS R 191 "
           pdb=" CB  CYS R 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -134.25   48.25     1      1.00e+01 1.00e-02 3.21e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.96  -22.04     0      5.00e+00 4.00e-02 1.94e+01
  dihedral pdb=" CA  ASP R 123 "
           pdb=" CB  ASP R 123 "
           pdb=" CG  ASP R 123 "
           pdb=" OD1 ASP R 123 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.16   59.16     1      2.00e+01 2.50e-03 1.17e+01
  ... (remaining 4449 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 774
       0.036 -    0.073: 309
       0.073 -    0.109: 76
       0.109 -    0.146: 28
       0.146 -    0.182: 1
  Chirality restraints: 1188
  Sorted by residual:
  chirality pdb=" CB  ILE R 159 "
            pdb=" CA  ILE R 159 "
            pdb=" CG1 ILE R 159 "
            pdb=" CG2 ILE R 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CA  PHE R 109 "
            pdb=" N   PHE R 109 "
            pdb=" C   PHE R 109 "
            pdb=" CB  PHE R 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.84e-01
  chirality pdb=" CA  PRO B 236 "
            pdb=" N   PRO B 236 "
            pdb=" C   PRO B 236 "
            pdb=" CB  PRO B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.68e-01
  ... (remaining 1185 not shown)

  Planarity restraints: 1288
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 159 "    0.042 5.00e-02 4.00e+02   6.39e-02 6.53e+00
        pdb=" N   PRO R 160 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO R 160 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 160 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO R 286 "    0.042 5.00e-02 4.00e+02   6.26e-02 6.27e+00
        pdb=" N   PRO R 287 "   -0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO R 287 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO R 287 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.12e+00
        pdb=" N   PRO B 236 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1285 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1874
        2.80 -     3.33: 6272
        3.33 -     3.85: 11515
        3.85 -     4.38: 13093
        4.38 -     4.90: 24242
  Nonbonded interactions: 56996
  Sorted by model distance:
  nonbonded pdb=" O   ASN N  77 "
            pdb=" OD1 ASN N  77 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG  SER R 114 "
            pdb=" OD2 ASP R 212 "
     model   vdw
     2.305 3.040
  nonbonded pdb=" NE2 GLN G  18 "
            pdb=" OE2 GLU G  22 "
     model   vdw
     2.306 3.120
  nonbonded pdb=" O   ILE R 276 "
            pdb=" ND2 ASN R 280 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O   SER R   8 "
            pdb=" OG  SER R   8 "
     model   vdw
     2.342 3.040
  ... (remaining 56991 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=0.00 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:             4.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.850
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
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      :  0.004   0.045   7551  Z= 0.234
  Angle     :  0.603   7.257  10252  Z= 0.341
  Chirality :  0.043   0.182   1188
  Planarity :  0.005   0.064   1288
  Dihedral  : 15.486  88.721   2633
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.04 %
    Favored  : 82.96 %
  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:  0.28 (0.28), residues: 940
  helix:  1.81 (0.30), residues: 345
  sheet:  0.26 (0.37), residues: 201
  loop : -1.35 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B 339 
 HIS   0.006   0.001   HIS R 178 
 PHE   0.021   0.001   PHE A 259 
 TYR   0.016   0.002   TYR N 117 
 ARG   0.003   0.000   ARG B 150 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.949 
Fit side-chains
REVERT: B  294 CYS cc_start: 0.8392 (p) cc_final: 0.8171 (m)
REVERT: G   19 LEU cc_start: 0.8130 (mt) cc_final: 0.7906 (mm)
REVERT: R    9 PHE cc_start: 0.8071 (t80) cc_final: 0.7786 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 1.3386
  time to fit residues: 150.8090
Evaluate side-chains
  91 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 73 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 343 HIS
A 376 GLN
R 107 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.0886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   7551  Z= 0.202
  Angle     :  0.545   7.071  10252  Z= 0.286
  Chirality :  0.043   0.142   1188
  Planarity :  0.005   0.061   1288
  Dihedral  :  4.149  28.939   1042
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 18.87 %
    Favored  : 78.11 %
  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:  0.59 (0.28), residues: 940
  helix:  2.14 (0.30), residues: 342
  sheet:  0.33 (0.38), residues: 200
  loop : -1.18 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 220 
 HIS   0.005   0.001   HIS R 178 
 PHE   0.016   0.001   PHE R 109 
 TYR   0.011   0.001   TYR N 117 
 ARG   0.008   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 99
  time to evaluate  : 0.843 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8791 (tp-100) cc_final: 0.8434 (tp-100)
REVERT: B   96 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6789 (ttt-90)
REVERT: B  101 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8454 (ptm)
REVERT: B  294 CYS cc_start: 0.8459 (p) cc_final: 0.8079 (p)
REVERT: G   19 LEU cc_start: 0.8072 (mt) cc_final: 0.7866 (mm)
REVERT: R   93 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7107 (tm-30)
REVERT: R  304 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.5818 (mpp80)
  outliers start: 23
  outliers final: 7
  residues processed: 111
  average time/residue: 1.2058
  time to fit residues: 141.5791
Evaluate side-chains
  104 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.888 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue   20 LEU
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   93 GLU
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 92 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0170
   chunk 84 optimal weight:    0.5980
   chunk 29 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
B 176 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   7551  Z= 0.151
  Angle     :  0.497   6.955  10252  Z= 0.260
  Chirality :  0.041   0.134   1188
  Planarity :  0.004   0.058   1288
  Dihedral  :  3.967  28.667   1042
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 19.53 %
    Favored  : 76.93 %
  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 (0.28), residues: 940
  helix:  2.43 (0.30), residues: 341
  sheet:  0.31 (0.37), residues: 211
  loop : -1.21 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.003   0.001   HIS R 178 
 PHE   0.015   0.001   PHE R 109 
 TYR   0.010   0.001   TYR R 134 
 ARG   0.003   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.834 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8779 (tp-100) cc_final: 0.8356 (tp-100)
REVERT: B   52 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7308 (ptp90)
REVERT: B   96 ARG cc_start: 0.7204 (OUTLIER) cc_final: 0.6781 (ttt-90)
REVERT: B  101 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8480 (ptm)
REVERT: B  294 CYS cc_start: 0.8419 (p) cc_final: 0.8026 (p)
REVERT: G   19 LEU cc_start: 0.8072 (mt) cc_final: 0.7855 (mm)
REVERT: R  304 ARG cc_start: 0.7011 (OUTLIER) cc_final: 0.5762 (mpp80)
REVERT: R  307 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7373 (ttmm)
  outliers start: 27
  outliers final: 7
  residues processed: 115
  average time/residue: 1.1572
  time to fit residues: 141.3392
Evaluate side-chains
  108 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  206 LEU
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 57 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 75 optimal weight:    0.5980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
G  59 ASN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7551  Z= 0.176
  Angle     :  0.518   7.138  10252  Z= 0.268
  Chirality :  0.042   0.135   1188
  Planarity :  0.004   0.058   1288
  Dihedral  :  4.005  28.479   1042
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.18 %
    Favored  : 76.28 %
  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:  0.79 (0.28), residues: 940
  helix:  2.43 (0.30), residues: 342
  sheet:  0.43 (0.37), residues: 210
  loop : -1.22 (0.29), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS R 178 
 PHE   0.015   0.001   PHE R 109 
 TYR   0.011   0.001   TYR R 134 
 ARG   0.004   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8788 (tp-100) cc_final: 0.8458 (tp-100)
REVERT: B   52 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7296 (ptp90)
REVERT: B   96 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6726 (ttt-90)
REVERT: B  101 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8443 (ptm)
REVERT: B  294 CYS cc_start: 0.8411 (p) cc_final: 0.8011 (p)
REVERT: R   26 HIS cc_start: 0.8149 (OUTLIER) cc_final: 0.7766 (m170)
REVERT: R  304 ARG cc_start: 0.7042 (OUTLIER) cc_final: 0.5603 (mpp80)
REVERT: R  307 LYS cc_start: 0.7765 (ttmt) cc_final: 0.7434 (ttmm)
  outliers start: 27
  outliers final: 8
  residues processed: 117
  average time/residue: 1.2125
  time to fit residues: 149.9315
Evaluate side-chains
  109 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 51 optimal weight:    0.0770
   chunk 1 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0370
   chunk 77 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0970
   chunk 0 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.3814

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7551  Z= 0.141
  Angle     :  0.488   6.670  10252  Z= 0.254
  Chirality :  0.041   0.131   1188
  Planarity :  0.004   0.054   1288
  Dihedral  :  3.898  27.706   1042
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 21.23 %
    Favored  : 76.02 %
  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:  0.91 (0.28), residues: 940
  helix:  2.58 (0.29), residues: 345
  sheet:  0.41 (0.36), residues: 212
  loop : -1.19 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS A 343 
 PHE   0.014   0.001   PHE R 109 
 TYR   0.010   0.001   TYR N  80 
 ARG   0.004   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8346 (tp-100)
REVERT: B   52 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7286 (ptp90)
REVERT: B   96 ARG cc_start: 0.7198 (OUTLIER) cc_final: 0.6774 (ttt-90)
REVERT: B  101 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8485 (ptm)
REVERT: B  128 THR cc_start: 0.7659 (OUTLIER) cc_final: 0.7242 (m)
REVERT: B  294 CYS cc_start: 0.8397 (p) cc_final: 0.8017 (p)
REVERT: R   26 HIS cc_start: 0.8111 (OUTLIER) cc_final: 0.7706 (m170)
REVERT: R  304 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5658 (mpp80)
REVERT: R  307 LYS cc_start: 0.7686 (ttmt) cc_final: 0.7367 (ttmm)
  outliers start: 21
  outliers final: 10
  residues processed: 109
  average time/residue: 1.2415
  time to fit residues: 143.1030
Evaluate side-chains
  110 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  212 ASP
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 81 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 42 optimal weight:    0.6980
   chunk 7 optimal weight:    0.0170
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.7020

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
moved from start:          0.1457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7551  Z= 0.187
  Angle     :  0.505   7.166  10252  Z= 0.264
  Chirality :  0.042   0.134   1188
  Planarity :  0.004   0.055   1288
  Dihedral  :  4.002  27.909   1042
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 20.84 %
    Favored  : 75.88 %
  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:  0.92 (0.28), residues: 940
  helix:  2.50 (0.29), residues: 347
  sheet:  0.60 (0.36), residues: 209
  loop : -1.24 (0.29), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS R 275 
 PHE   0.021   0.001   PHE R  89 
 TYR   0.010   0.001   TYR R 134 
 ARG   0.004   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8796 (tp-100) cc_final: 0.8467 (tp-100)
REVERT: A   34 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8429 (ttpp)
REVERT: B   52 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7275 (ptp90)
REVERT: B   96 ARG cc_start: 0.7211 (OUTLIER) cc_final: 0.6726 (ttt-90)
REVERT: B  101 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8487 (ptm)
REVERT: B  128 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7232 (m)
REVERT: B  251 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.7956 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8420 (p) cc_final: 0.8020 (p)
REVERT: R   26 HIS cc_start: 0.8148 (OUTLIER) cc_final: 0.7748 (m170)
REVERT: R  304 ARG cc_start: 0.7094 (OUTLIER) cc_final: 0.5630 (mpp80)
REVERT: R  307 LYS cc_start: 0.7680 (ttmt) cc_final: 0.7366 (ttmm)
  outliers start: 25
  outliers final: 11
  residues processed: 109
  average time/residue: 1.1816
  time to fit residues: 136.6854
Evaluate side-chains
  114 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 76 optimal weight:    0.5980
   chunk 50 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   chunk 55 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  44 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
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      :  0.003   0.034   7551  Z= 0.181
  Angle     :  0.506   7.063  10252  Z= 0.265
  Chirality :  0.042   0.134   1188
  Planarity :  0.004   0.055   1288
  Dihedral  :  4.013  28.499   1042
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 21.10 %
    Favored  : 75.49 %
  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:  0.91 (0.28), residues: 940
  helix:  2.57 (0.29), residues: 346
  sheet:  0.42 (0.36), residues: 212
  loop : -1.20 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 220 
 HIS   0.004   0.001   HIS R 275 
 PHE   0.015   0.001   PHE R 109 
 TYR   0.012   0.001   TYR N  80 
 ARG   0.005   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 0.829 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8794 (tp-100) cc_final: 0.8474 (tp-100)
REVERT: A   34 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8414 (ttpp)
REVERT: B   52 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7272 (ptp90)
REVERT: B   96 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6723 (ttt-90)
REVERT: B  101 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8487 (ptm)
REVERT: B  251 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7954 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8400 (p) cc_final: 0.8180 (m)
REVERT: R   26 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7808 (m170)
REVERT: R  304 ARG cc_start: 0.7091 (OUTLIER) cc_final: 0.5620 (mpp80)
REVERT: R  307 LYS cc_start: 0.7663 (ttmt) cc_final: 0.7356 (ttmm)
  outliers start: 26
  outliers final: 14
  residues processed: 112
  average time/residue: 1.1573
  time to fit residues: 137.5055
Evaluate side-chains
  118 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue   34 LYS
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  136 SER
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 71 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0170
   chunk 86 optimal weight:    0.7980
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
B 259 GLN
N  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7551  Z= 0.134
  Angle     :  0.471   6.728  10252  Z= 0.246
  Chirality :  0.041   0.132   1188
  Planarity :  0.004   0.054   1288
  Dihedral  :  3.838  26.838   1042
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.23 %
    Favored  : 75.75 %
  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:  1.06 (0.28), residues: 940
  helix:  2.76 (0.30), residues: 344
  sheet:  0.47 (0.36), residues: 211
  loop : -1.15 (0.29), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 343 
 PHE   0.021   0.001   PHE R  89 
 TYR   0.008   0.001   TYR R 134 
 ARG   0.006   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.765 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8349 (tp-100)
REVERT: B   52 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7269 (ptp90)
REVERT: B   96 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6759 (ttt-90)
REVERT: B  101 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8519 (ptm)
REVERT: B  251 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8119 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8397 (p) cc_final: 0.8173 (m)
REVERT: R   26 HIS cc_start: 0.8098 (OUTLIER) cc_final: 0.7759 (m170)
REVERT: R  304 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.5631 (mpp80)
REVERT: R  307 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7384 (ttmm)
  outliers start: 23
  outliers final: 12
  residues processed: 117
  average time/residue: 1.1861
  time to fit residues: 147.2385
Evaluate side-chains
  118 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain A residue  367 ASP
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   26 HIS
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 66 optimal weight:    0.6980
   chunk 25 optimal weight:    3.9990
   chunk 76 optimal weight:    0.5980
   chunk 79 optimal weight:    0.6980
   chunk 84 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7551  Z= 0.192
  Angle     :  0.523   7.871  10252  Z= 0.271
  Chirality :  0.042   0.135   1188
  Planarity :  0.004   0.055   1288
  Dihedral  :  3.992  27.177   1042
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.89 %
    Favored  : 75.23 %
  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:  0.95 (0.28), residues: 940
  helix:  2.51 (0.29), residues: 351
  sheet:  0.46 (0.36), residues: 212
  loop : -1.15 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 220 
 HIS   0.004   0.001   HIS R 275 
 PHE   0.015   0.001   PHE R 109 
 TYR   0.015   0.001   TYR N  80 
 ARG   0.005   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.898 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8797 (tp-100) cc_final: 0.8478 (tp-100)
REVERT: B   52 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7238 (ptp90)
REVERT: B   96 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6729 (ttt-90)
REVERT: B  101 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8497 (ptm)
REVERT: B  251 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7963 (mtt-85)
REVERT: B  294 CYS cc_start: 0.8398 (p) cc_final: 0.8187 (m)
REVERT: R  304 ARG cc_start: 0.7051 (OUTLIER) cc_final: 0.5574 (mpp80)
REVERT: R  307 LYS cc_start: 0.7679 (ttmt) cc_final: 0.7373 (ttmm)
  outliers start: 22
  outliers final: 12
  residues processed: 114
  average time/residue: 1.1489
  time to fit residues: 139.1390
Evaluate side-chains
  118 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   93 GLU
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 93 optimal weight:    0.3980
   chunk 86 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0870
   chunk 57 optimal weight:    0.0370
   chunk 45 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 79 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.3836

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7551  Z= 0.139
  Angle     :  0.487   7.093  10252  Z= 0.252
  Chirality :  0.041   0.132   1188
  Planarity :  0.004   0.055   1288
  Dihedral  :  3.850  26.123   1042
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 22.15 %
    Favored  : 75.23 %
  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:  1.06 (0.28), residues: 940
  helix:  2.70 (0.29), residues: 348
  sheet:  0.46 (0.37), residues: 210
  loop : -1.10 (0.29), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 343 
 PHE   0.022   0.001   PHE R  89 
 TYR   0.009   0.001   TYR R 134 
 ARG   0.006   0.000   ARG A 342 

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

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

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1880 Ramachandran restraints generated.
    940 Oldfield, 0 Emsley, 940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.753 
Fit side-chains
REVERT: A   29 GLN cc_start: 0.8765 (tp-100) cc_final: 0.8459 (tp-100)
REVERT: B   52 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7271 (ptp90)
REVERT: B   96 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6747 (ttt-90)
REVERT: B  101 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8485 (ptm)
REVERT: B  251 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7971 (mtt-85)
REVERT: R  304 ARG cc_start: 0.7059 (OUTLIER) cc_final: 0.5619 (mpp80)
REVERT: R  307 LYS cc_start: 0.7745 (ttmt) cc_final: 0.7425 (ttmm)
  outliers start: 20
  outliers final: 12
  residues processed: 115
  average time/residue: 1.1424
  time to fit residues: 139.4394
Evaluate side-chains
  117 residues out of total 827 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  343 HIS
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   96 ARG
Chi-restraints excluded: chain B residue   97 SER
Chi-restraints excluded: chain B residue  101 MET
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  275 SER
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   35 ASN
Chi-restraints excluded: chain N residue   83 MET
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  176 ILE
Chi-restraints excluded: chain R residue  304 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 68 optimal weight:    0.0980
   chunk 11 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0970
   chunk 74 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
N  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.113416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.096724 restraints weight = 12194.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.93
r_work: 0.3239 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   7551  Z= 0.152
  Angle     :  0.491   6.949  10252  Z= 0.256
  Chirality :  0.041   0.131   1188
  Planarity :  0.004   0.055   1288
  Dihedral  :  3.839  25.281   1042
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 22.67 %
    Favored  : 75.10 %
  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:  1.07 (0.28), residues: 940
  helix:  2.80 (0.29), residues: 342
  sheet:  0.46 (0.36), residues: 212
  loop : -1.13 (0.29), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 343 
 PHE   0.014   0.001   PHE R 109 
 TYR   0.015   0.001   TYR N  80 
 ARG   0.006   0.000   ARG A 342 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3155.92 seconds
wall clock time: 57 minutes 19.12 seconds (3439.12 seconds total)