Starting phenix.real_space_refine
on Thu Mar 13 23:50:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lml_0918/03_2025/6lml_0918.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lml_0918/03_2025/6lml_0918.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2025/6lml_0918.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2025/6lml_0918.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2025/6lml_0918.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lml_0918/03_2025/6lml_0918.cif"
  }
  resolution = 3.9
  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=   0.002
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      59      5.16       5
     C    6036      2.51       5
     N    1625      2.21       5
     O    1718      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 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: 9438
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1735
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1735
          Classifications: {'peptide': 224}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 2, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 72
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 59
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 38
    Chain: "B"
      Number of atoms: 2322
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 306, 2322
          Classifications: {'peptide': 306}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 5, 'TRANS': 300}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "C"
      Number of atoms: 241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 241
          Classifications: {'peptide': 33}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 28}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "D"
      Number of atoms: 1742
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1742
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "E"
      Number of atoms: 245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 245
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "R"
      Number of atoms: 3153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 395, 3153
          Classifications: {'peptide': 395}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 15, 'TRANS': 379}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 43
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N   LEU A 234 " occ=0.00
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 234 " occ=0.00
    residue:
      pdb=" N   ALA A 235 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA A 235 " occ=0.00
    residue:
      pdb=" N   GLU A 236 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 236 " occ=0.00
    residue:
      pdb=" N   ASP A 237 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ASP A 237 " occ=0.00
    residue:
      pdb=" N   GLU A 238 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 238 " occ=0.00
    residue:
      pdb=" N   GLU A 239 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  GLU A 239 " occ=0.00
    residue:
      pdb=" N   MET A 240 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  MET A 240 " occ=0.00
  Time building chain proxies: 5.30, per 1000 atoms: 0.56
  Number of scatterers: 9438
  At special positions: 0
  Unit cell: (153.34, 112.34, 109.06, 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      59     16.00
     O    1718      8.00
     N    1625      7.00
     C    6036      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  43 " - pdb=" SG  CYS R  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  58 " - pdb=" SG  CYS R 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  81 " - pdb=" SG  CYS R 121 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 224 " - pdb=" SG  CYS R 294 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.03
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 19 sheets defined
      32.3% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 30
      removed outlier: 4.255A  pdb=" N   ASP A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A  24 " --> pdb=" O   ASP A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 4.130A  pdb=" N   ILE A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A  50 " --> pdb=" O   LYS A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 216
      removed outlier: 3.517A  pdb=" N   PHE A 215 " --> pdb=" O   ILE A 212 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 216 " --> pdb=" O   HIS A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 255
      removed outlier: 3.572A  pdb=" N   MET A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ILE A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.699A  pdb=" N   PHE A 259 " --> pdb=" O   ASN A 256 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 256 through 260'
    Processing helix  chain 'A' and resid 270 through 278
    Processing helix  chain 'A' and resid 295 through 308
      removed outlier: 4.738A  pdb=" N   ALA A 301 " --> pdb=" O   GLU A 297 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   CYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 348
      removed outlier: 3.533A  pdb=" N   THR A 340 " --> pdb=" O   PHE A 336 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ASP A 341 " --> pdb=" O   ASP A 337 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LYS A 345 " --> pdb=" O   ASP A 341 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 44
      removed outlier: 3.726A  pdb=" N   ALA C  34 " --> pdb=" O   VAL C  30 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   ASP C  36 " --> pdb=" O   LYS C  32 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TYR C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLU C  42 " --> pdb=" O   MET C  38 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA C  43 " --> pdb=" O   ALA C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
      removed outlier: 3.630A  pdb=" N   ASP C  48 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 45 through 48'
    Processing helix  chain 'D' and resid 28 through 32
      removed outlier: 3.640A  pdb=" N   SER D  31 " --> pdb=" O   ALA D  28 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 62 through 65
      removed outlier: 3.596A  pdb=" N   LYS D  65 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 62 through 65'
    Processing helix  chain 'E' and resid 2 through 27
      removed outlier: 4.430A  pdb=" N   SER E   8 " --> pdb=" O   GLY E   4 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   LYS E  12 " --> pdb=" O   SER E   8 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   SER E  16 " --> pdb=" O   LYS E  12 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ARG E  18 " --> pdb=" O   LEU E  14 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   VAL E  23 " --> pdb=" O   ALA E  19 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 28 through 41
      removed outlier: 3.511A  pdb=" N   GLU R  34 " --> pdb=" O   ASP R  30 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 41 through 46
    Processing helix  chain 'R' and resid 118 through 122
      removed outlier: 3.632A  pdb=" N   GLN R 122 " --> pdb=" O   SER R 119 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 124 through 166
      removed outlier: 3.521A  pdb=" N   ILE R 128 " --> pdb=" O   ASP R 124 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   VAL R 134 " --> pdb=" O   VAL R 130 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   VAL R 143 " --> pdb=" O   SER R 139 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   THR R 146 " --> pdb=" O   GLN R 142 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL R 147 " --> pdb=" O   VAL R 143 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   LEU R 157 " --> pdb=" O   LEU R 153 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU R 158 " --> pdb=" O   GLY R 154 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ILE R 162 " --> pdb=" O   LEU R 158 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   LEU R 163 " --> pdb=" O   ALA R 159 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY R 164 " --> pdb=" O   LEU R 160 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU R 166 " --> pdb=" O   ILE R 162 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 171 through 182
    Processing helix  chain 'R' and resid 184 through 197
      removed outlier: 3.921A  pdb=" N   SER R 190 " --> pdb=" O   LEU R 186 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   ILE R 194 " --> pdb=" O   SER R 190 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 210 through 216
      removed outlier: 3.594A  pdb=" N   THR R 214 " --> pdb=" O   LEU R 210 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LEU R 216 " --> pdb=" O   VAL R 212 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 222 through 235
      removed outlier: 3.824A  pdb=" N   ALA R 228 " --> pdb=" O   CYS R 224 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL R 229 " --> pdb=" O   ARG R 225 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 240 through 253
      removed outlier: 3.523A  pdb=" N   VAL R 244 " --> pdb=" O   CYS R 240 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU R 249 " --> pdb=" O   GLU R 245 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ASN R 251 " --> pdb=" O   LEU R 247 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 263 through 272
      removed outlier: 3.641A  pdb=" N   TYR R 267 " --> pdb=" O   PHE R 263 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   GLY R 269 " --> pdb=" O   SER R 265 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 274 through 277
    Processing helix  chain 'R' and resid 278 through 288
      removed outlier: 3.595A  pdb=" N   LEU R 288 " --> pdb=" O   VAL R 284 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 300 through 305
    Processing helix  chain 'R' and resid 308 through 330
      removed outlier: 3.715A  pdb=" N   ILE R 315 " --> pdb=" O   VAL R 311 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU R 316 " --> pdb=" O   PHE R 312 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASN R 318 " --> pdb=" O   ALA R 314 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE R 320 " --> pdb=" O   LEU R 316 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ILE R 325 " --> pdb=" O   ILE R 321 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   GLN R 327 " --> pdb=" O   VAL R 323 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU R 329 " --> pdb=" O   ILE R 325 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 331 through 333
      No H-bonds generated for 'chain 'R' and resid 331 through 333'
    Processing helix  chain 'R' and resid 334 through 338
      removed outlier: 3.776A  pdb=" N   GLN R 337 " --> pdb=" O   ARG R 334 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   MET R 338 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 334 through 338'
    Processing helix  chain 'R' and resid 340 through 344
      removed outlier: 3.545A  pdb=" N   TYR R 343 " --> pdb=" O   HIS R 340 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LYS R 344 " --> pdb=" O   THR R 341 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 340 through 344'
    Processing helix  chain 'R' and resid 345 through 350
    Processing helix  chain 'R' and resid 375 through 403
      removed outlier: 3.874A  pdb=" N   SER R 379 " --> pdb=" O   GLY R 375 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU R 382 " --> pdb=" O   ARG R 378 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   PHE R 383 " --> pdb=" O   SER R 379 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   LEU R 386 " --> pdb=" O   LEU R 382 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   GLY R 393 " --> pdb=" O   SER R 389 " (cutoff:3.500A)
      removed outlier: 5.217A  pdb=" N   LEU R 394 " --> pdb=" O   SER R 390 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL R 396 " --> pdb=" O   GLN R 392 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   TYR R 400 " --> pdb=" O   VAL R 396 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   CYS R 401 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU R 403 " --> pdb=" O   LEU R 399 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 406 through 418
      removed outlier: 3.586A  pdb=" N   ARG R 413 " --> pdb=" O   SER R 409 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.207A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 197 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40
      removed outlier: 6.592A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   HIS A 322 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.905A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 5.894A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 7.195A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.770A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 111 through 113
      removed outlier: 6.023A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 5.508A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.837A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151
    Processing sheet with id=AA6, first strand: chain 'B' and resid 169 through 170
      removed outlier: 3.894A  pdb=" N   GLN B 175 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.453A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   LYS B 209 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B 203 " --> pdb=" O   SER B 207 " (cutoff:3.500A)
      removed outlier: 5.092A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.560A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.523A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN B 295 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 328 through 329
      removed outlier: 3.689A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 3 through 7
      removed outlier: 4.006A  pdb=" N   GLN D   3 " --> pdb=" O   SER D  25 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER D  25 " --> pdb=" O   GLN D   3 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.503A  pdb=" N   THR D 115 " --> pdb=" O   TYR D  94 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 59 through 60
      removed outlier: 4.165A  pdb=" N   TYR D  50 " --> pdb=" O   TYR D  59 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 38 through 39
    Processing sheet with id=AB6, first strand: chain 'D' and resid 146 through 148
      removed outlier: 6.510A  pdb=" N   VAL D 147 " --> pdb=" O   GLU D 246 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'D' and resid 155 through 159
      removed outlier: 3.666A  pdb=" N   SER D 206 " --> pdb=" O   THR D 213 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 177 through 179
    Processing sheet with id=AB9, first strand: chain 'D' and resid 189 through 190
    Processing sheet with id=AC1, first strand: chain 'R' and resid 79 through 80
      removed outlier: 4.097A  pdb=" N   ILE R  79 " --> pdb=" O   VAL R  96 " (cutoff:3.500A)

    269 hydrogen bonds defined for protein.
    762 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: 2.24

  Time building geometry restraints manager: 2.45 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: 3020
        1.34 -     1.46: 2422
        1.46 -     1.58: 4144
        1.58 -     1.70: 0
        1.70 -     1.82: 80
  Bond restraints: 9666
  Sorted by residual:
  bond pdb=" C   ILE R 355 "
       pdb=" N   PRO R 356 "
    ideal  model  delta    sigma   weight residual
    1.334  1.402 -0.068 2.34e-02 1.83e+03 8.47e+00
  bond pdb=" C   TRP B  99 "
       pdb=" N   VAL B 100 "
    ideal  model  delta    sigma   weight residual
    1.334  1.307  0.027 1.29e-02 6.01e+03 4.49e+00
  bond pdb=" N   THR R 257 "
       pdb=" CA  THR R 257 "
    ideal  model  delta    sigma   weight residual
    1.460  1.485 -0.025 1.54e-02 4.22e+03 2.74e+00
  bond pdb=" CB  ASN R 238 "
       pdb=" CG  ASN R 238 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.42e+00
  bond pdb=" CA  ASN R 238 "
       pdb=" CB  ASN R 238 "
    ideal  model  delta    sigma   weight residual
    1.534  1.512  0.022 1.45e-02 4.76e+03 2.23e+00
  ... (remaining 9661 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 12851
        2.73 -     5.46: 243
        5.46 -     8.18: 27
        8.18 -    10.91: 4
       10.91 -    13.64: 3
  Bond angle restraints: 13128
  Sorted by residual:
  angle pdb=" N   VAL R 191 "
        pdb=" CA  VAL R 191 "
        pdb=" C   VAL R 191 "
      ideal   model   delta    sigma   weight residual
     112.96  106.65    6.31 1.00e+00 1.00e+00 3.98e+01
  angle pdb=" C   THR B  86 "
        pdb=" N   THR B  87 "
        pdb=" CA  THR B  87 "
      ideal   model   delta    sigma   weight residual
     122.46  129.03   -6.57 1.41e+00 5.03e-01 2.17e+01
  angle pdb=" C   VAL R 368 "
        pdb=" N   THR R 369 "
        pdb=" CA  THR R 369 "
      ideal   model   delta    sigma   weight residual
     121.54  130.16   -8.62 1.91e+00 2.74e-01 2.04e+01
  angle pdb=" N   VAL R 236 "
        pdb=" CA  VAL R 236 "
        pdb=" C   VAL R 236 "
      ideal   model   delta    sigma   weight residual
     113.53  109.12    4.41 9.80e-01 1.04e+00 2.02e+01
  angle pdb=" C   ASP B 118 "
        pdb=" N   ASN B 119 "
        pdb=" CA  ASN B 119 "
      ideal   model   delta    sigma   weight residual
     121.54  129.65   -8.11 1.91e+00 2.74e-01 1.80e+01
  ... (remaining 13123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 4893
       17.10 -    34.21: 597
       34.21 -    51.31: 126
       51.31 -    68.41: 13
       68.41 -    85.52: 7
  Dihedral angle restraints: 5636
    sinusoidal: 2115
      harmonic: 3521
  Sorted by residual:
  dihedral pdb=" CA  PRO R 356 "
           pdb=" C   PRO R 356 "
           pdb=" N   LEU R 357 "
           pdb=" CA  LEU R 357 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.63   39.37     0      5.00e+00 4.00e-02 6.20e+01
  dihedral pdb=" CA  VAL R 292 "
           pdb=" C   VAL R 292 "
           pdb=" N   GLN R 293 "
           pdb=" CA  GLN R 293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -144.91  -35.09     0      5.00e+00 4.00e-02 4.93e+01
  dihedral pdb=" CA  GLY B  77 "
           pdb=" C   GLY B  77 "
           pdb=" N   LYS B  78 "
           pdb=" CA  LYS B  78 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.84  -28.16     0      5.00e+00 4.00e-02 3.17e+01
  ... (remaining 5633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1128
       0.062 -    0.123: 290
       0.123 -    0.185: 40
       0.185 -    0.246: 6
       0.246 -    0.307: 3
  Chirality restraints: 1467
  Sorted by residual:
  chirality pdb=" CB  VAL R  91 "
            pdb=" CA  VAL R  91 "
            pdb=" CG1 VAL R  91 "
            pdb=" CG2 VAL R  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.36e+00
  chirality pdb=" CB  ILE B 157 "
            pdb=" CA  ILE B 157 "
            pdb=" CG1 ILE B 157 "
            pdb=" CG2 ILE B 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  ILE D 100 "
            pdb=" CA  ILE D 100 "
            pdb=" CG1 ILE D 100 "
            pdb=" CG2 ILE D 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.25 2.00e-01 2.50e+01 1.56e+00
  ... (remaining 1464 not shown)

  Planarity restraints: 1661
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  59 "    0.031 2.00e-02 2.50e+03   2.23e-02 9.97e+00
        pdb=" CG  TYR B  59 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  59 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  59 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  59 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  59 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B  59 "    0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE R 355 "    0.042 5.00e-02 4.00e+02   6.45e-02 6.66e+00
        pdb=" N   PRO R 356 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO R 356 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO R 356 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D 184 "   -0.040 5.00e-02 4.00e+02   6.12e-02 5.99e+00
        pdb=" N   PRO D 185 "    0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO D 185 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 185 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1658 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2621
        2.79 -     3.32: 8200
        3.32 -     3.84: 15594
        3.84 -     4.37: 17849
        4.37 -     4.90: 30125
  Nonbonded interactions: 74389
  Sorted by model distance:
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OG  SER B 331 "
            pdb=" OD1 ASP B 333 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER B 245 "
            pdb=" OD1 ASP B 247 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" OG1 THR B 321 "
            pdb=" OD1 ASP B 323 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   SER R 183 "
            pdb=" OG  SER R 183 "
     model   vdw
     2.296 3.040
  ... (remaining 74384 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.890
  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:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     22.230
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070   9666  Z= 0.413
  Angle     :  0.959  13.638  13128  Z= 0.539
  Chirality :  0.055   0.307   1467
  Planarity :  0.006   0.065   1661
  Dihedral  : 15.401  85.516   3355
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.81 %
    Favored  : 91.19 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  : 14.69 %
    Favored  : 84.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

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: -5.53 (0.18), residues: 1203
  helix: -4.57 (0.11), residues: 373
  sheet: -3.27 (0.28), residues: 247
  loop : -3.13 (0.22), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 258 
 HIS   0.010   0.002   HIS R 250 
 PHE   0.026   0.002   PHE R 264 
 TYR   0.054   0.002   TYR B  59 
 ARG   0.006   0.001   ARG B  68 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 209
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 LYS cc_start: 0.7451 (ttmt) cc_final: 0.7246 (tmtt)
REVERT: A  287 TYR cc_start: 0.7042 (m-10) cc_final: 0.6792 (m-10)
REVERT: B  129 ARG cc_start: 0.7525 (ttt-90) cc_final: 0.7194 (mtp180)
REVERT: B  291 ASP cc_start: 0.7748 (t0) cc_final: 0.7494 (t0)
REVERT: D   13 GLN cc_start: 0.7547 (pp30) cc_final: 0.7347 (pp30)
REVERT: D   18 ARG cc_start: 0.7619 (tpp-160) cc_final: 0.7237 (tpp80)
REVERT: D   19 LYS cc_start: 0.8430 (tmmt) cc_final: 0.8044 (tttt)
REVERT: D  109 ASP cc_start: 0.7976 (t0) cc_final: 0.7754 (t0)
REVERT: D  139 VAL cc_start: 0.8383 (t) cc_final: 0.8066 (p)
REVERT: D  188 LEU cc_start: 0.8942 (mp) cc_final: 0.8739 (mp)
REVERT: E   21 ASP cc_start: 0.8373 (m-30) cc_final: 0.8151 (t0)
REVERT: E   24 GLN cc_start: 0.8334 (tp40) cc_final: 0.7791 (tm-30)
REVERT: R   39 TYR cc_start: 0.8538 (t80) cc_final: 0.8074 (t80)
REVERT: R  231 MET cc_start: 0.7937 (tmm) cc_final: 0.7691 (tmm)
  outliers start: 5
  outliers final: 2
  residues processed: 212
  average time/residue: 0.2610
  time to fit residues: 73.2192
Evaluate side-chains
  151 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain B residue  295 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:    5.9990
   chunk 69 optimal weight:    9.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 333 GLN
B  62 HIS
B 142 HIS
B 266 HIS
B 295 ASN
D  77 ASN
D  82 GLN
** D 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   1 HIS
** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 131 GLN
R 250 HIS
R 408 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.116127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.087446 restraints weight = 20046.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.089247 restraints weight = 13276.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.090050 restraints weight = 9945.756|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9666  Z= 0.190
  Angle     :  0.630   8.764  13128  Z= 0.332
  Chirality :  0.042   0.162   1467
  Planarity :  0.005   0.058   1661
  Dihedral  :  6.128  35.535   1321
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 17.53 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -4.40 (0.20), residues: 1203
  helix: -3.20 (0.19), residues: 368
  sheet: -2.76 (0.29), residues: 251
  loop : -2.72 (0.23), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B  82 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.015   0.001   PHE A 191 
 TYR   0.018   0.001   TYR R 145 
 ARG   0.006   0.000   ARG D  87 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 175
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8310 (ttm-80)
REVERT: A   54 LYS cc_start: 0.7456 (ttmt) cc_final: 0.7131 (tmtt)
REVERT: A  287 TYR cc_start: 0.7291 (m-10) cc_final: 0.7048 (m-10)
REVERT: A  333 GLN cc_start: 0.8628 (tp40) cc_final: 0.7950 (tm-30)
REVERT: B  129 ARG cc_start: 0.7906 (ttt-90) cc_final: 0.7531 (mtp180)
REVERT: B  278 PHE cc_start: 0.7619 (OUTLIER) cc_final: 0.7091 (m-10)
REVERT: B  294 CYS cc_start: 0.8827 (m) cc_final: 0.8378 (m)
REVERT: B  295 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7641 (p0)
REVERT: D   14 PRO cc_start: 0.7494 (Cg_endo) cc_final: 0.7231 (Cg_exo)
REVERT: D   83 MET cc_start: 0.6524 (ptp) cc_final: 0.6293 (ptp)
REVERT: D  188 LEU cc_start: 0.8983 (mp) cc_final: 0.8638 (mp)
REVERT: D  235 TYR cc_start: 0.7605 (m-80) cc_final: 0.7375 (m-80)
REVERT: E   21 ASP cc_start: 0.8542 (m-30) cc_final: 0.8224 (t0)
REVERT: E   24 GLN cc_start: 0.8272 (tp40) cc_final: 0.7601 (tm-30)
REVERT: R   39 TYR cc_start: 0.8365 (t80) cc_final: 0.7965 (t80)
REVERT: R  131 GLN cc_start: 0.8375 (tt0) cc_final: 0.7541 (tm-30)
REVERT: R  140 SER cc_start: 0.8955 (m) cc_final: 0.8704 (p)
REVERT: R  231 MET cc_start: 0.7737 (tmm) cc_final: 0.7411 (tmm)
  outliers start: 31
  outliers final: 17
  residues processed: 197
  average time/residue: 0.2429
  time to fit residues: 64.6616
Evaluate side-chains
  160 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  213 HIS
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 48 optimal weight:    6.9990
   chunk 109 optimal weight:    1.9990
   chunk 62 optimal weight:   20.0000
   chunk 63 optimal weight:   30.0000
   chunk 30 optimal weight:    7.9990
   chunk 60 optimal weight:    1.9990
   chunk 19 optimal weight:    6.9990
   chunk 39 optimal weight:   20.0000
   chunk 86 optimal weight:    0.6980
   chunk 52 optimal weight:    8.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 239 ASN
E   1 HIS
** R 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 361 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.112630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.084817 restraints weight = 20687.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.085607 restraints weight = 15601.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.086586 restraints weight = 11498.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9666  Z= 0.270
  Angle     :  0.634   7.633  13128  Z= 0.338
  Chirality :  0.043   0.151   1467
  Planarity :  0.004   0.057   1661
  Dihedral  :  5.994  35.390   1321
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 20.06 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -3.81 (0.22), residues: 1203
  helix: -2.41 (0.23), residues: 371
  sheet: -2.49 (0.30), residues: 250
  loop : -2.56 (0.24), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  82 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.019   0.002   PHE R 264 
 TYR   0.023   0.002   TYR R 145 
 ARG   0.007   0.000   ARG D  87 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 158
  time to evaluate  : 1.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   36 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8853 (pp)
REVERT: A   54 LYS cc_start: 0.7415 (ttmt) cc_final: 0.7183 (tmtt)
REVERT: A  287 TYR cc_start: 0.7167 (m-10) cc_final: 0.6951 (m-10)
REVERT: A  333 GLN cc_start: 0.8548 (tp40) cc_final: 0.7989 (tm-30)
REVERT: B   68 ARG cc_start: 0.8261 (tpt90) cc_final: 0.8034 (tpt90)
REVERT: B  188 MET cc_start: 0.7931 (mmm) cc_final: 0.7544 (tpt)
REVERT: B  278 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7108 (m-10)
REVERT: B  294 CYS cc_start: 0.8801 (m) cc_final: 0.8442 (m)
REVERT: B  295 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.7874 (p0)
REVERT: D  188 LEU cc_start: 0.8968 (mp) cc_final: 0.8638 (mp)
REVERT: D  235 TYR cc_start: 0.7736 (m-80) cc_final: 0.7486 (m-80)
REVERT: E   21 ASP cc_start: 0.8515 (m-30) cc_final: 0.8265 (t0)
REVERT: E   24 GLN cc_start: 0.8127 (tp40) cc_final: 0.7613 (tm-30)
REVERT: R  131 GLN cc_start: 0.8435 (tt0) cc_final: 0.7623 (tm-30)
REVERT: R  140 SER cc_start: 0.8912 (m) cc_final: 0.8675 (p)
REVERT: R  231 MET cc_start: 0.7691 (tmm) cc_final: 0.7441 (tmm)
  outliers start: 39
  outliers final: 26
  residues processed: 187
  average time/residue: 0.1998
  time to fit residues: 52.9961
Evaluate side-chains
  172 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  105 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  321 THR
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 94 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 5 optimal weight:    0.5980
   chunk 118 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
B 295 ASN
R 361 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.113644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.087220 restraints weight = 20440.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.087253 restraints weight = 12860.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.087822 restraints weight = 11411.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9666  Z= 0.220
  Angle     :  0.599   7.473  13128  Z= 0.315
  Chirality :  0.042   0.148   1467
  Planarity :  0.004   0.059   1661
  Dihedral  :  5.808  42.847   1321
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.58 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -3.45 (0.22), residues: 1203
  helix: -1.94 (0.24), residues: 367
  sheet: -2.37 (0.30), residues: 250
  loop : -2.43 (0.24), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  82 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.018   0.001   PHE B 292 
 TYR   0.019   0.001   TYR R 145 
 ARG   0.006   0.000   ARG R 308 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 156
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8587 (ttm-80) cc_final: 0.8318 (ttm110)
REVERT: A   36 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8850 (pp)
REVERT: A   54 LYS cc_start: 0.7411 (ttmt) cc_final: 0.7151 (tmtt)
REVERT: A  287 TYR cc_start: 0.7285 (m-10) cc_final: 0.7058 (m-10)
REVERT: A  333 GLN cc_start: 0.8548 (tp40) cc_final: 0.8039 (tm-30)
REVERT: B  188 MET cc_start: 0.7856 (mmm) cc_final: 0.7456 (tpt)
REVERT: B  198 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8371 (pt)
REVERT: B  278 PHE cc_start: 0.7865 (OUTLIER) cc_final: 0.7087 (m-10)
REVERT: B  292 PHE cc_start: 0.8170 (OUTLIER) cc_final: 0.7846 (m-80)
REVERT: B  294 CYS cc_start: 0.8780 (m) cc_final: 0.8349 (m)
REVERT: B  295 ASN cc_start: 0.8248 (OUTLIER) cc_final: 0.7796 (p0)
REVERT: D  113 GLN cc_start: 0.8431 (tp40) cc_final: 0.8226 (pp30)
REVERT: D  188 LEU cc_start: 0.8983 (mp) cc_final: 0.8640 (mp)
REVERT: D  235 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80)
REVERT: E   21 ASP cc_start: 0.8507 (m-30) cc_final: 0.8245 (t0)
REVERT: E   24 GLN cc_start: 0.8099 (tp40) cc_final: 0.7582 (tm-30)
REVERT: R   29 MET cc_start: 0.8429 (ppp) cc_final: 0.8089 (ppp)
REVERT: R  131 GLN cc_start: 0.8461 (tt0) cc_final: 0.7614 (tm-30)
REVERT: R  140 SER cc_start: 0.8875 (m) cc_final: 0.8624 (p)
REVERT: R  231 MET cc_start: 0.7694 (tmm) cc_final: 0.7466 (tmm)
REVERT: R  241 TRP cc_start: 0.8300 (t-100) cc_final: 0.8077 (t-100)
REVERT: R  371 GLU cc_start: 0.6632 (pm20) cc_final: 0.6191 (pm20)
  outliers start: 42
  outliers final: 28
  residues processed: 183
  average time/residue: 0.2326
  time to fit residues: 60.3617
Evaluate side-chains
  177 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  278 PHE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 85 optimal weight:    0.0870
   chunk 102 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:   10.0000
   chunk 93 optimal weight:    0.8980
   chunk 16 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   overall best weight:    0.9964

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
R 361 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.115530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.086917 restraints weight = 20116.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.088935 restraints weight = 12835.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.089689 restraints weight = 9801.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9666  Z= 0.172
  Angle     :  0.571   7.455  13128  Z= 0.299
  Chirality :  0.041   0.145   1467
  Planarity :  0.003   0.056   1661
  Dihedral  :  5.518  43.781   1321
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.30 %
    Favored  : 72.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -3.10 (0.23), residues: 1203
  helix: -1.48 (0.25), residues: 365
  sheet: -2.24 (0.30), residues: 267
  loop : -2.28 (0.25), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 111 
 HIS   0.013   0.001   HIS B 142 
 PHE   0.020   0.001   PHE R 365 
 TYR   0.017   0.001   TYR R 145 
 ARG   0.003   0.000   ARG R 308 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 150
  time to evaluate  : 1.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8572 (ttm-80) cc_final: 0.8304 (ttm110)
REVERT: A   36 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8700 (pp)
REVERT: A   54 LYS cc_start: 0.7478 (ttmt) cc_final: 0.7168 (tmtt)
REVERT: A  287 TYR cc_start: 0.7324 (m-10) cc_final: 0.7076 (m-10)
REVERT: A  333 GLN cc_start: 0.8481 (tp40) cc_final: 0.8021 (tm-30)
REVERT: B  198 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8360 (pt)
REVERT: B  294 CYS cc_start: 0.8775 (m) cc_final: 0.8245 (m)
REVERT: B  295 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7616 (p0)
REVERT: D  235 TYR cc_start: 0.7709 (m-80) cc_final: 0.7503 (m-80)
REVERT: E   21 ASP cc_start: 0.8550 (m-30) cc_final: 0.8227 (t0)
REVERT: E   24 GLN cc_start: 0.8102 (tp40) cc_final: 0.7547 (tm-30)
REVERT: R   29 MET cc_start: 0.8462 (ppp) cc_final: 0.8047 (ppp)
REVERT: R   34 GLU cc_start: 0.8134 (pp20) cc_final: 0.7663 (pp20)
REVERT: R  111 ARG cc_start: 0.8297 (tpt170) cc_final: 0.7509 (mpp80)
REVERT: R  140 SER cc_start: 0.8930 (m) cc_final: 0.8682 (p)
REVERT: R  231 MET cc_start: 0.7634 (tmm) cc_final: 0.7386 (tmm)
  outliers start: 39
  outliers final: 27
  residues processed: 182
  average time/residue: 0.3753
  time to fit residues: 97.8969
Evaluate side-chains
  171 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 2.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain E residue    3 GLN
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 117 optimal weight:    0.3980
   chunk 52 optimal weight:    5.9990
   chunk 113 optimal weight:    0.4980
   chunk 5 optimal weight:    3.9990
   chunk 96 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   chunk 43 optimal weight:   10.0000
   chunk 85 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 142 HIS
B 295 ASN
R 361 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.113052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.085579 restraints weight = 20599.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.087427 restraints weight = 14638.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.088395 restraints weight = 11022.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.3086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9666  Z= 0.249
  Angle     :  0.613   7.190  13128  Z= 0.320
  Chirality :  0.043   0.155   1467
  Planarity :  0.004   0.055   1661
  Dihedral  :  5.628  39.334   1321
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 23.40 %
    Favored  : 71.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.98 (0.23), residues: 1203
  helix: -1.40 (0.25), residues: 368
  sheet: -2.15 (0.31), residues: 247
  loop : -2.23 (0.25), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 111 
 HIS   0.004   0.001   HIS A 213 
 PHE   0.017   0.002   PHE D  68 
 TYR   0.019   0.001   TYR R 145 
 ARG   0.004   0.000   ARG B  68 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 142
  time to evaluate  : 0.979 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8305 (ttm110)
REVERT: A   36 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8868 (pp)
REVERT: A  333 GLN cc_start: 0.8603 (tp40) cc_final: 0.8108 (tm-30)
REVERT: B  198 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8424 (pt)
REVERT: B  294 CYS cc_start: 0.8693 (m) cc_final: 0.8272 (m)
REVERT: B  295 ASN cc_start: 0.8445 (OUTLIER) cc_final: 0.7890 (p0)
REVERT: E   21 ASP cc_start: 0.8465 (m-30) cc_final: 0.8217 (t0)
REVERT: E   24 GLN cc_start: 0.8038 (tp40) cc_final: 0.7615 (tm-30)
REVERT: R   29 MET cc_start: 0.8372 (ppp) cc_final: 0.8141 (ppp)
REVERT: R   34 GLU cc_start: 0.8010 (pp20) cc_final: 0.7528 (pp20)
REVERT: R  111 ARG cc_start: 0.8184 (tpt170) cc_final: 0.7497 (mpp80)
REVERT: R  131 GLN cc_start: 0.8386 (tt0) cc_final: 0.7505 (tm-30)
REVERT: R  140 SER cc_start: 0.8852 (m) cc_final: 0.8609 (p)
REVERT: R  231 MET cc_start: 0.7671 (tmm) cc_final: 0.7450 (tmm)
REVERT: R  401 CYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8572 (m)
  outliers start: 50
  outliers final: 37
  residues processed: 183
  average time/residue: 0.1973
  time to fit residues: 51.6748
Evaluate side-chains
  175 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 134
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 110 optimal weight:    9.9990
   chunk 83 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 39 optimal weight:   10.0000
   chunk 67 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 117 optimal weight:    5.9990
   chunk 118 optimal weight:   10.0000
   chunk 42 optimal weight:    0.9980
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 304 GLN
B  91 HIS
B 142 HIS
** R 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.111482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.084489 restraints weight = 20720.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.084840 restraints weight = 15043.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.085614 restraints weight = 14307.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.053   9666  Z= 0.369
  Angle     :  0.694   9.950  13128  Z= 0.362
  Chirality :  0.046   0.152   1467
  Planarity :  0.004   0.058   1661
  Dihedral  :  5.982  38.974   1321
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.14 %
    Favored  : 90.86 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 24.62 %
    Favored  : 69.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -3.03 (0.23), residues: 1203
  helix: -1.48 (0.25), residues: 372
  sheet: -2.18 (0.31), residues: 249
  loop : -2.22 (0.25), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP D 111 
 HIS   0.007   0.001   HIS B 142 
 PHE   0.024   0.002   PHE R 365 
 TYR   0.023   0.002   TYR R 145 
 ARG   0.004   0.000   ARG A  32 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 134
  time to evaluate  : 1.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8579 (ttm-80) cc_final: 0.8328 (ttm110)
REVERT: A   23 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8323 (mp)
REVERT: A   36 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8995 (pp)
REVERT: A  333 GLN cc_start: 0.8638 (tp40) cc_final: 0.8237 (tm-30)
REVERT: B  198 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8452 (pt)
REVERT: D  235 TYR cc_start: 0.7798 (m-80) cc_final: 0.7543 (m-80)
REVERT: E   21 ASP cc_start: 0.8362 (m-30) cc_final: 0.8158 (t0)
REVERT: E   24 GLN cc_start: 0.7972 (tp40) cc_final: 0.7604 (tm-30)
REVERT: R   34 GLU cc_start: 0.8092 (pp20) cc_final: 0.7539 (pp20)
REVERT: R  131 GLN cc_start: 0.8399 (tt0) cc_final: 0.7632 (tm-30)
REVERT: R  231 MET cc_start: 0.7751 (tmm) cc_final: 0.7532 (tmm)
REVERT: R  401 CYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8611 (m)
  outliers start: 54
  outliers final: 40
  residues processed: 181
  average time/residue: 0.2021
  time to fit residues: 53.0760
Evaluate side-chains
  171 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 127
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  184 ILE
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  143 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue   99 SER
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  288 LEU
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  351 THR
Chi-restraints excluded: chain R residue  352 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 41 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 110 optimal weight:    9.9990
   chunk 22 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 69 optimal weight:    8.9990
   chunk 90 optimal weight:    0.0980
   chunk 51 optimal weight:    1.9990
   chunk 73 optimal weight:    4.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 142 HIS
B 295 ASN
R 361 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.113194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.085594 restraints weight = 20723.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.086738 restraints weight = 14211.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.088151 restraints weight = 10437.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9666  Z= 0.209
  Angle     :  0.614   8.174  13128  Z= 0.317
  Chirality :  0.042   0.145   1467
  Planarity :  0.004   0.059   1661
  Dihedral  :  5.560  41.659   1321
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 25.63 %
    Favored  : 69.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.74 (0.23), residues: 1203
  helix: -1.19 (0.26), residues: 370
  sheet: -2.05 (0.32), residues: 249
  loop : -2.06 (0.25), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D 111 
 HIS   0.003   0.001   HIS B  54 
 PHE   0.024   0.001   PHE E  22 
 TYR   0.017   0.001   TYR A 287 
 ARG   0.004   0.000   ARG A  32 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 135
  time to evaluate  : 0.995 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8570 (ttm-80) cc_final: 0.8318 (ttm110)
REVERT: A   32 ARG cc_start: 0.8203 (mtm-85) cc_final: 0.7975 (ptp90)
REVERT: A   36 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8836 (pp)
REVERT: A  333 GLN cc_start: 0.8554 (tp40) cc_final: 0.8289 (tm-30)
REVERT: B  198 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8415 (pt)
REVERT: B  294 CYS cc_start: 0.8687 (m) cc_final: 0.8128 (m)
REVERT: B  295 ASN cc_start: 0.8297 (OUTLIER) cc_final: 0.7875 (p0)
REVERT: E   21 ASP cc_start: 0.8518 (m-30) cc_final: 0.8211 (t0)
REVERT: E   24 GLN cc_start: 0.8017 (tp40) cc_final: 0.7591 (tm-30)
REVERT: R   34 GLU cc_start: 0.8016 (pp20) cc_final: 0.7516 (pp20)
REVERT: R  231 MET cc_start: 0.7729 (tmm) cc_final: 0.7511 (tmm)
REVERT: R  312 PHE cc_start: 0.7885 (t80) cc_final: 0.7589 (t80)
  outliers start: 48
  outliers final: 37
  residues processed: 171
  average time/residue: 0.1924
  time to fit residues: 47.4029
Evaluate side-chains
  170 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 130
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  233 CYS
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  352 LEU
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 97 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 50 optimal weight:    0.0980
   chunk 111 optimal weight:    9.9990
   chunk 94 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0170
   chunk 14 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 80 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.9620

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

Flipped N/Q/H residues before XYZ refinement:
A 304 GLN
B 142 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.115568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.088875 restraints weight = 20346.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088985 restraints weight = 13443.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.089582 restraints weight = 12325.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9666  Z= 0.174
  Angle     :  0.608   9.673  13128  Z= 0.310
  Chirality :  0.042   0.143   1467
  Planarity :  0.003   0.058   1661
  Dihedral  :  5.297  41.173   1321
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 27.05 %
    Favored  : 68.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.24), residues: 1203
  helix: -0.92 (0.26), residues: 369
  sheet: -1.92 (0.32), residues: 259
  loop : -1.92 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 111 
 HIS   0.004   0.001   HIS B 142 
 PHE   0.019   0.001   PHE R 365 
 TYR   0.014   0.001   TYR R 145 
 ARG   0.002   0.000   ARG A  32 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 139
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8289 (ttm110)
REVERT: A   36 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8785 (pp)
REVERT: A  333 GLN cc_start: 0.8505 (tp40) cc_final: 0.8302 (tm-30)
REVERT: B  198 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8372 (pt)
REVERT: B  294 CYS cc_start: 0.8599 (m) cc_final: 0.8227 (m)
REVERT: B  295 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.7771 (p0)
REVERT: D   19 LYS cc_start: 0.8226 (tttt) cc_final: 0.7878 (mmtm)
REVERT: E   21 ASP cc_start: 0.8472 (m-30) cc_final: 0.8206 (t0)
REVERT: E   24 GLN cc_start: 0.7974 (tp40) cc_final: 0.7566 (tm-30)
REVERT: R   29 MET cc_start: 0.8359 (ppp) cc_final: 0.7842 (ppp)
REVERT: R   34 GLU cc_start: 0.8004 (pp20) cc_final: 0.7524 (pp20)
  outliers start: 40
  outliers final: 35
  residues processed: 170
  average time/residue: 0.2017
  time to fit residues: 50.2880
Evaluate side-chains
  167 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 129
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 10 optimal weight:    9.9990
   chunk 118 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 108 optimal weight:    0.2980
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 57 optimal weight:    8.9990
   overall best weight:    2.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.113189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.086010 restraints weight = 20738.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.087807 restraints weight = 14706.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.088292 restraints weight = 11507.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9666  Z= 0.243
  Angle     :  0.632   9.142  13128  Z= 0.326
  Chirality :  0.043   0.144   1467
  Planarity :  0.004   0.058   1661
  Dihedral  :  5.397  38.647   1321
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.66 %
    Allowed  : 26.55 %
    Favored  : 68.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.45 (0.24), residues: 1203
  helix: -0.95 (0.26), residues: 376
  sheet: -1.83 (0.33), residues: 248
  loop : -1.93 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 111 
 HIS   0.007   0.001   HIS B 266 
 PHE   0.026   0.001   PHE E  22 
 TYR   0.017   0.001   TYR R 145 
 ARG   0.005   0.000   ARG A  32 

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 131
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8313 (ttm110)
REVERT: A   23 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8219 (mp)
REVERT: A   36 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8828 (pp)
REVERT: A  333 GLN cc_start: 0.8499 (tp40) cc_final: 0.8297 (tm-30)
REVERT: B  198 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8404 (pt)
REVERT: B  294 CYS cc_start: 0.8680 (m) cc_final: 0.8101 (m)
REVERT: B  295 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.7911 (p0)
REVERT: D   19 LYS cc_start: 0.8155 (tttt) cc_final: 0.7892 (mmtm)
REVERT: E   21 ASP cc_start: 0.8448 (m-30) cc_final: 0.8187 (t0)
REVERT: E   24 GLN cc_start: 0.7948 (tp40) cc_final: 0.7575 (tm-30)
REVERT: R   29 MET cc_start: 0.8366 (ppp) cc_final: 0.7847 (ppp)
REVERT: R   34 GLU cc_start: 0.7959 (pp20) cc_final: 0.7496 (pp20)
  outliers start: 46
  outliers final: 39
  residues processed: 166
  average time/residue: 0.1925
  time to fit residues: 45.9210
Evaluate side-chains
  171 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 128
  time to evaluate  : 1.060 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  200 ASP
Chi-restraints excluded: chain A residue  221 ILE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue   59 TYR
Chi-restraints excluded: chain B residue   69 LEU
Chi-restraints excluded: chain B residue  120 ILE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  135 VAL
Chi-restraints excluded: chain B residue  142 HIS
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  204 CYS
Chi-restraints excluded: chain B residue  210 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  295 ASN
Chi-restraints excluded: chain B residue  336 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  144 THR
Chi-restraints excluded: chain D residue  186 GLN
Chi-restraints excluded: chain D residue  195 LEU
Chi-restraints excluded: chain D residue  226 VAL
Chi-restraints excluded: chain R residue   32 LEU
Chi-restraints excluded: chain R residue   45 HIS
Chi-restraints excluded: chain R residue   49 LEU
Chi-restraints excluded: chain R residue  137 MET
Chi-restraints excluded: chain R residue  162 ILE
Chi-restraints excluded: chain R residue  285 VAL
Chi-restraints excluded: chain R residue  313 LEU
Chi-restraints excluded: chain R residue  315 ILE
Chi-restraints excluded: chain R residue  329 LEU
Chi-restraints excluded: chain R residue  339 HIS
Chi-restraints excluded: chain R residue  355 ILE
Chi-restraints excluded: chain R residue  358 LEU
Chi-restraints excluded: chain R residue  401 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 73 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 89 optimal weight:    9.9990
   chunk 107 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 83 optimal weight:    9.9990
   chunk 60 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
B 142 HIS
** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.114634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.087247 restraints weight = 20368.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.089202 restraints weight = 14468.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.089873 restraints weight = 10669.935|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.3688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9666  Z= 0.199
  Angle     :  0.635  11.289  13128  Z= 0.323
  Chirality :  0.042   0.145   1467
  Planarity :  0.003   0.059   1661
  Dihedral  :  5.313  38.101   1321
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  4.15 %
    Allowed  : 27.15 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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: -2.32 (0.24), residues: 1203
  helix: -0.79 (0.27), residues: 376
  sheet: -1.77 (0.33), residues: 248
  loop : -1.88 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 111 
 HIS   0.005   0.001   HIS B 266 
 PHE   0.020   0.001   PHE B 253 
 TYR   0.018   0.001   TYR R  39 
 ARG   0.004   0.000   ARG A  32 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3530.69 seconds
wall clock time: 63 minutes 33.50 seconds (3813.50 seconds total)