Starting phenix.real_space_refine
on Wed Jul 30 17:40:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6j0m_9764/07_2025/6j0m_9764.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6j0m_9764/07_2025/6j0m_9764.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/6j0m_9764/07_2025/6j0m_9764.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6j0m_9764/07_2025/6j0m_9764.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6j0m_9764/07_2025/6j0m_9764.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6j0m_9764/07_2025/6j0m_9764.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=   0.001 sd=   0.013
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      42      5.16       5
     C    7974      2.51       5
     N    2208      2.21       5
     O    2361      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 129 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12585
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4195
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 535, 4195
          Classifications: {'peptide': 535}
          Link IDs: {'PTRANS': 21, 'TRANS': 513}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 8.58, per 1000 atoms: 0.68
  Number of scatterers: 12585
  At special positions: 0
  Unit cell: (95.285, 96.406, 143.488, 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      42     16.00
     O    2361      8.00
     N    2208      7.00
     C    7974      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.02
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2994

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 30 sheets defined
      12.7% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.89
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 60
      removed outlier: 3.680A  pdb=" N   GLU A  56 " --> pdb=" O   ASP A  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 109
    Processing helix  chain 'A' and resid 122 through 132
      removed outlier: 3.581A  pdb=" N   THR A 129 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 172
      removed outlier: 3.741A  pdb=" N   LEU A 165 " --> pdb=" O   TRP A 161 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   CYS A 166 " --> pdb=" O   HIS A 162 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 170 " --> pdb=" O   CYS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 191
      removed outlier: 3.544A  pdb=" N   LYS A 191 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 294
      removed outlier: 3.594A  pdb=" N   GLN A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASN A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER A 294 " --> pdb=" O   ASN A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 429
      No H-bonds generated for 'chain 'A' and resid 427 through 429'
    Processing helix  chain 'B' and resid 50 through 60
      removed outlier: 3.681A  pdb=" N   GLU B  56 " --> pdb=" O   ASP B  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS B  59 " --> pdb=" O   THR B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 105 through 109
    Processing helix  chain 'B' and resid 122 through 132
      removed outlier: 3.582A  pdb=" N   THR B 129 " --> pdb=" O   ALA B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 172
      removed outlier: 3.742A  pdb=" N   LEU B 165 " --> pdb=" O   TRP B 161 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   CYS B 166 " --> pdb=" O   HIS B 162 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ALA B 170 " --> pdb=" O   CYS B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 191
      removed outlier: 3.543A  pdb=" N   LYS B 191 " --> pdb=" O   ASP B 188 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 294
      removed outlier: 3.594A  pdb=" N   GLN B 285 " --> pdb=" O   GLY B 281 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   SER B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 429
      No H-bonds generated for 'chain 'B' and resid 427 through 429'
    Processing helix  chain 'C' and resid 50 through 60
      removed outlier: 3.680A  pdb=" N   GLU C  56 " --> pdb=" O   ASP C  52 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   HIS C  59 " --> pdb=" O   THR C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 109
    Processing helix  chain 'C' and resid 122 through 132
      removed outlier: 3.582A  pdb=" N   THR C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 172
      removed outlier: 3.741A  pdb=" N   LEU C 165 " --> pdb=" O   TRP C 161 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   CYS C 166 " --> pdb=" O   HIS C 162 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA C 170 " --> pdb=" O   CYS C 166 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 191
      removed outlier: 3.544A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 188 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 276 through 294
      removed outlier: 3.594A  pdb=" N   GLN C 285 " --> pdb=" O   GLY C 281 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN C 290 " --> pdb=" O   GLY C 286 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   SER C 294 " --> pdb=" O   ASN C 290 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 427 through 429
      No H-bonds generated for 'chain 'C' and resid 427 through 429'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 14
      removed outlier: 4.747A  pdb=" N   ILE A   7 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE A  80 " --> pdb=" O   LEU A  68 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU A  70 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   VAL A  78 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ILE A  84 " --> pdb=" O   LYS A 103 " (cutoff:3.500A)
      removed outlier: 6.034A  pdb=" N   LYS A 103 " --> pdb=" O   ILE A  84 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   SER A  39 " --> pdb=" O   ALA A  19 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   ALA A  19 " --> pdb=" O   SER A  39 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 95 through 96
      removed outlier: 4.751A  pdb=" N   ASP C 212 " --> pdb=" O   LEU C 301 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   LEU C 301 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY C 325 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   TYR C 196 " --> pdb=" O   GLN C 315 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR C 317 " --> pdb=" O   TYR C 196 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   LEU C 198 " --> pdb=" O   THR C 317 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 116 through 118
    Processing sheet with id=AA4, first strand: chain 'A' and resid 138 through 139
      removed outlier: 3.608A  pdb=" N   VAL A 185 " --> pdb=" O   TRP A 174 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 195 through 199
      removed outlier: 6.476A  pdb=" N   TYR A 196 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR A 317 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
      removed outlier: 6.051A  pdb=" N   LEU A 198 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY A 325 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU A 301 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   ASP A 212 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 14
      removed outlier: 4.747A  pdb=" N   ILE B   7 " --> pdb=" O   LEU B  14 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   PHE B  80 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU B  70 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   VAL B  78 " --> pdb=" O   LEU B  70 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ILE B  84 " --> pdb=" O   LYS B 103 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LYS B 103 " --> pdb=" O   ILE B  84 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   SER B  39 " --> pdb=" O   ALA B  19 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ALA B  19 " --> pdb=" O   SER B  39 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 237 through 243
      removed outlier: 3.819A  pdb=" N   GLN A 237 " --> pdb=" O   ASP A 232 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLY A 230 " --> pdb=" O   GLN A 239 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 241 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL A 228 " --> pdb=" O   GLY A 241 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ARG A 243 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 5.184A  pdb=" N   LEU A 226 " --> pdb=" O   ARG A 243 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLU A 227 " --> pdb=" O   TRP A 267 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 365 through 369
      removed outlier: 7.587A  pdb=" N   TRP A 397 " --> pdb=" O   PRO A 433 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE A 435 " --> pdb=" O   TRP A 397 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ARG A 399 " --> pdb=" O   ILE A 435 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   GLY A 437 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE A 422 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA A 438 " --> pdb=" O   GLU A 420 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   GLU A 420 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 367 " --> pdb=" O   VAL A 421 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 411 through 412
    Processing sheet with id=AB1, first strand: chain 'A' and resid 488 through 491
    Processing sheet with id=AB2, first strand: chain 'A' and resid 461 through 462
    Processing sheet with id=AB3, first strand: chain 'A' and resid 503 through 508
      removed outlier: 6.174A  pdb=" N   LEU A 504 " --> pdb=" O   ASN C 512 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   THR C 514 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   LEU A 506 " --> pdb=" O   THR C 514 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 510 through 515
    Processing sheet with id=AB5, first strand: chain 'A' and resid 519 through 522
      removed outlier: 3.510A  pdb=" N   ILE C 529 " --> pdb=" O   ASN B 535 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 519 through 522
      removed outlier: 5.632A  pdb=" N   GLU A 528 " --> pdb=" O   MET B 521 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   VAL A 527 " --> pdb=" O   ASN C 535 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   THR C 537 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   ILE A 529 " --> pdb=" O   THR C 537 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 534 through 537
      removed outlier: 3.516A  pdb=" N   ASN A 535 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE B 529 " --> pdb=" O   ASN A 535 " (cutoff:3.500A)
      removed outlier: 5.616A  pdb=" N   GLU B 528 " --> pdb=" O   MET C 521 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 116 through 118
    Processing sheet with id=AB9, first strand: chain 'B' and resid 138 through 139
      removed outlier: 3.608A  pdb=" N   VAL B 185 " --> pdb=" O   TRP B 174 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 195 through 199
      removed outlier: 6.476A  pdb=" N   TYR B 196 " --> pdb=" O   GLN B 315 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   THR B 317 " --> pdb=" O   TYR B 196 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   LEU B 198 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLY B 325 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   LEU B 301 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   ASP B 212 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 12 through 14
      removed outlier: 4.746A  pdb=" N   ILE C   7 " --> pdb=" O   LEU C  14 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   PHE C  80 " --> pdb=" O   LEU C  68 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LEU C  70 " --> pdb=" O   VAL C  78 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   VAL C  78 " --> pdb=" O   LEU C  70 " (cutoff:3.500A)
      removed outlier: 5.380A  pdb=" N   ILE C  84 " --> pdb=" O   LYS C 103 " (cutoff:3.500A)
      removed outlier: 6.035A  pdb=" N   LYS C 103 " --> pdb=" O   ILE C  84 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   SER C  39 " --> pdb=" O   ALA C  19 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ALA C  19 " --> pdb=" O   SER C  39 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 237 through 243
      removed outlier: 3.819A  pdb=" N   GLN B 237 " --> pdb=" O   ASP B 232 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY B 230 " --> pdb=" O   GLN B 239 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY B 241 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.450A  pdb=" N   VAL B 228 " --> pdb=" O   GLY B 241 " (cutoff:3.500A)
      removed outlier: 4.498A  pdb=" N   ARG B 243 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LEU B 226 " --> pdb=" O   ARG B 243 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU B 227 " --> pdb=" O   TRP B 267 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 365 through 369
      removed outlier: 7.587A  pdb=" N   TRP B 397 " --> pdb=" O   PRO B 433 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   ILE B 435 " --> pdb=" O   TRP B 397 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   ARG B 399 " --> pdb=" O   ILE B 435 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   GLY B 437 " --> pdb=" O   ARG B 399 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE B 422 " --> pdb=" O   LEU B 436 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   ALA B 438 " --> pdb=" O   GLU B 420 " (cutoff:3.500A)
      removed outlier: 7.349A  pdb=" N   GLU B 420 " --> pdb=" O   ALA B 438 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA B 367 " --> pdb=" O   VAL B 421 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 411 through 412
    Processing sheet with id=AC6, first strand: chain 'B' and resid 461 through 462
    Processing sheet with id=AC7, first strand: chain 'B' and resid 510 through 515
    Processing sheet with id=AC8, first strand: chain 'C' and resid 116 through 118
    Processing sheet with id=AC9, first strand: chain 'C' and resid 138 through 139
      removed outlier: 3.607A  pdb=" N   VAL C 185 " --> pdb=" O   TRP C 174 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 237 through 243
      removed outlier: 3.818A  pdb=" N   GLN C 237 " --> pdb=" O   ASP C 232 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLY C 230 " --> pdb=" O   GLN C 239 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY C 241 " --> pdb=" O   VAL C 228 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   VAL C 228 " --> pdb=" O   GLY C 241 " (cutoff:3.500A)
      removed outlier: 4.499A  pdb=" N   ARG C 243 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 5.183A  pdb=" N   LEU C 226 " --> pdb=" O   ARG C 243 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   GLU C 227 " --> pdb=" O   TRP C 267 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 365 through 369
      removed outlier: 7.587A  pdb=" N   TRP C 397 " --> pdb=" O   PRO C 433 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   ILE C 435 " --> pdb=" O   TRP C 397 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   ARG C 399 " --> pdb=" O   ILE C 435 " (cutoff:3.500A)
      removed outlier: 7.793A  pdb=" N   GLY C 437 " --> pdb=" O   ARG C 399 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   ILE C 422 " --> pdb=" O   LEU C 436 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ALA C 438 " --> pdb=" O   GLU C 420 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   GLU C 420 " --> pdb=" O   ALA C 438 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA C 367 " --> pdb=" O   VAL C 421 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 461 through 462

    391 hydrogen bonds defined for protein.
    1020 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: 4.48

  Time building geometry restraints manager: 3.64 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: 4146
        1.34 -     1.46: 2122
        1.46 -     1.57: 6473
        1.57 -     1.69: 0
        1.69 -     1.81: 66
  Bond restraints: 12807
  Sorted by residual:
  bond pdb=" CA  TRP A 267 "
       pdb=" CB  TRP A 267 "
    ideal  model  delta    sigma   weight residual
    1.534  1.504  0.030 1.78e-02 3.16e+03 2.82e+00
  bond pdb=" CA  TRP B 267 "
       pdb=" CB  TRP B 267 "
    ideal  model  delta    sigma   weight residual
    1.534  1.504  0.029 1.78e-02 3.16e+03 2.72e+00
  bond pdb=" C   ASN A 222 "
       pdb=" N   PRO A 223 "
    ideal  model  delta    sigma   weight residual
    1.333  1.313  0.019 1.17e-02 7.31e+03 2.70e+00
  bond pdb=" C   ASN C 222 "
       pdb=" N   PRO C 223 "
    ideal  model  delta    sigma   weight residual
    1.333  1.314  0.019 1.17e-02 7.31e+03 2.68e+00
  bond pdb=" CA  TRP C 267 "
       pdb=" CB  TRP C 267 "
    ideal  model  delta    sigma   weight residual
    1.534  1.505  0.029 1.78e-02 3.16e+03 2.66e+00
  ... (remaining 12802 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 16400
        1.98 -     3.96: 798
        3.96 -     5.94: 85
        5.94 -     7.92: 28
        7.92 -     9.90: 5
  Bond angle restraints: 17316
  Sorted by residual:
  angle pdb=" N   GLY B 484 "
        pdb=" CA  GLY B 484 "
        pdb=" C   GLY B 484 "
      ideal   model   delta    sigma   weight residual
     112.68  107.56    5.12 1.26e+00 6.30e-01 1.65e+01
  angle pdb=" N   GLY A 484 "
        pdb=" CA  GLY A 484 "
        pdb=" C   GLY A 484 "
      ideal   model   delta    sigma   weight residual
     112.68  107.57    5.11 1.26e+00 6.30e-01 1.64e+01
  angle pdb=" N   GLY C 484 "
        pdb=" CA  GLY C 484 "
        pdb=" C   GLY C 484 "
      ideal   model   delta    sigma   weight residual
     112.68  107.61    5.07 1.26e+00 6.30e-01 1.62e+01
  angle pdb=" CA  LYS A 235 "
        pdb=" CB  LYS A 235 "
        pdb=" CG  LYS A 235 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  angle pdb=" CA  LYS C 235 "
        pdb=" CB  LYS C 235 "
        pdb=" CG  LYS C 235 "
      ideal   model   delta    sigma   weight residual
     114.10  121.64   -7.54 2.00e+00 2.50e-01 1.42e+01
  ... (remaining 17311 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 6825
       17.97 -    35.94: 806
       35.94 -    53.91: 151
       53.91 -    71.89: 21
       71.89 -    89.86: 15
  Dihedral angle restraints: 7818
    sinusoidal: 3189
      harmonic: 4629
  Sorted by residual:
  dihedral pdb=" CA  GLY B 304 "
           pdb=" C   GLY B 304 "
           pdb=" N   ASP B 305 "
           pdb=" CA  ASP B 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.82  -35.18     0      5.00e+00 4.00e-02 4.95e+01
  dihedral pdb=" CA  GLY A 304 "
           pdb=" C   GLY A 304 "
           pdb=" N   ASP A 305 "
           pdb=" CA  ASP A 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.82  -35.18     0      5.00e+00 4.00e-02 4.95e+01
  dihedral pdb=" CA  GLY C 304 "
           pdb=" C   GLY C 304 "
           pdb=" N   ASP C 305 "
           pdb=" CA  ASP C 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.88  -35.12     0      5.00e+00 4.00e-02 4.93e+01
  ... (remaining 7815 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1485
       0.059 -    0.117: 410
       0.117 -    0.176: 70
       0.176 -    0.235: 7
       0.235 -    0.293: 5
  Chirality restraints: 1977
  Sorted by residual:
  chirality pdb=" CB  ILE A  91 "
            pdb=" CA  ILE A  91 "
            pdb=" CG1 ILE A  91 "
            pdb=" CG2 ILE A  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CB  ILE C  91 "
            pdb=" CA  ILE C  91 "
            pdb=" CG1 ILE C  91 "
            pdb=" CG2 ILE C  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" CB  ILE B  91 "
            pdb=" CA  ILE B  91 "
            pdb=" CG1 ILE B  91 "
            pdb=" CG2 ILE B  91 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.29 2.00e-01 2.50e+01 2.09e+00
  ... (remaining 1974 not shown)

  Planarity restraints: 2226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 355 "   -0.045 5.00e-02 4.00e+02   6.57e-02 6.90e+00
        pdb=" N   PRO B 356 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO B 356 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 356 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 355 "    0.044 5.00e-02 4.00e+02   6.55e-02 6.86e+00
        pdb=" N   PRO C 356 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 356 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO C 356 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 355 "   -0.044 5.00e-02 4.00e+02   6.54e-02 6.85e+00
        pdb=" N   PRO A 356 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2223 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.81: 3407
        2.81 -     3.33: 10628
        3.33 -     3.85: 20037
        3.85 -     4.38: 23042
        4.38 -     4.90: 41234
  Nonbonded interactions: 98348
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 124 "
            pdb=" OG  SER A 128 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   LYS B 124 "
            pdb=" OG  SER B 128 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   LYS C 124 "
            pdb=" OG  SER C 128 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OG  SER B 255 "
            pdb=" O   ASP B 257 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" OG  SER C 255 "
            pdb=" O   ASP C 257 "
     model   vdw
     2.342 3.040
  ... (remaining 98343 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.740
  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:          0.460
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     33.530
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
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      :  0.007   0.047  12807  Z= 0.336
  Angle     :  0.980   9.902  17316  Z= 0.561
  Chirality :  0.056   0.293   1977
  Planarity :  0.007   0.066   2226
  Dihedral  : 15.907  89.858   4824
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 12.44 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.20 %

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: -4.05 (0.17), residues: 1593
  helix: -4.47 (0.15), residues: 159
  sheet: -2.50 (0.19), residues: 525
  loop : -2.47 (0.16), residues: 909

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP B 267 
 HIS   0.005   0.001   HIS A 407 
 PHE   0.023   0.002   PHE C 411 
 TYR   0.017   0.002   TYR B 354 
 ARG   0.004   0.001   ARG B 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27938 (  391)
  hydrogen bonds       : angle      11.42940 ( 1020)
  covalent geometry    : bond        0.00733 (12807)
  covalent geometry    : angle       0.98049 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 281
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 ASP cc_start: 0.5730 (p0) cc_final: 0.5490 (p0)
REVERT: A  257 ASP cc_start: 0.8331 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  312 ASP cc_start: 0.8275 (p0) cc_final: 0.7893 (p0)
REVERT: A  374 GLN cc_start: 0.7371 (tm-30) cc_final: 0.7102 (tm-30)
REVERT: A  494 LYS cc_start: 0.7602 (pttp) cc_final: 0.7291 (ptmt)
REVERT: B  218 ASP cc_start: 0.7240 (m-30) cc_final: 0.7021 (m-30)
REVERT: B  257 ASP cc_start: 0.8486 (m-30) cc_final: 0.8270 (m-30)
REVERT: B  269 ILE cc_start: 0.9036 (pt) cc_final: 0.8803 (mp)
REVERT: B  494 LYS cc_start: 0.7472 (pttp) cc_final: 0.7200 (ptmt)
REVERT: C   26 TYR cc_start: 0.8949 (m-80) cc_final: 0.8612 (m-80)
REVERT: C  120 ASP cc_start: 0.6305 (p0) cc_final: 0.6087 (p0)
REVERT: C  257 ASP cc_start: 0.8297 (m-30) cc_final: 0.8048 (m-30)
REVERT: C  494 LYS cc_start: 0.7258 (pttp) cc_final: 0.6950 (ptmt)
REVERT: C  521 MET cc_start: 0.6498 (ttm) cc_final: 0.6076 (tpp)
  outliers start: 12
  outliers final: 3
  residues processed: 287
  average time/residue: 0.2718
  time to fit residues: 107.8738
Evaluate side-chains
  175 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 172
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain C residue  461 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 120 optimal weight:    8.9990
   chunk 66 optimal weight:    7.9990
   chunk 41 optimal weight:    8.9990
   chunk 81 optimal weight:    6.9990
   chunk 64 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 48 optimal weight:    5.9990
   chunk 75 optimal weight:    4.9990
   chunk 92 optimal weight:    3.9990
   chunk 144 optimal weight:    1.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
A 152 GLN
A 222 ASN
A 322 GLN
A 373 GLN
A 428 ASN
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 482 ASN
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 GLN
B 152 GLN
B 220 GLN
B 222 ASN
B 322 GLN
B 428 ASN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 482 ASN
** B 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 509 GLN
C 152 GLN
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 222 ASN
C 428 ASN
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 482 ASN
** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 509 GLN

Total number of N/Q/H flips: 20

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.111820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.102693 restraints weight = 20368.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.103586 restraints weight = 15606.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.104391 restraints weight = 13709.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  12807  Z= 0.193
  Angle     :  0.669   8.976  17316  Z= 0.349
  Chirality :  0.047   0.155   1977
  Planarity :  0.005   0.043   2226
  Dihedral  :  6.374  30.378   1707
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.35 %
    Favored  : 79.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.19), residues: 1593
  helix: -2.19 (0.35), residues: 168
  sheet: -2.02 (0.20), residues: 561
  loop : -1.94 (0.19), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 267 
 HIS   0.004   0.001   HIS A 334 
 PHE   0.011   0.002   PHE C 163 
 TYR   0.016   0.002   TYR A 354 
 ARG   0.006   0.000   ARG C  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  391)
  hydrogen bonds       : angle       7.50006 ( 1020)
  covalent geometry    : bond        0.00442 (12807)
  covalent geometry    : angle       0.66904 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 209
  time to evaluate  : 1.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 ASP cc_start: 0.8117 (m-30) cc_final: 0.7892 (m-30)
REVERT: A  494 LYS cc_start: 0.7532 (pttp) cc_final: 0.7237 (ptmt)
REVERT: A  534 ILE cc_start: 0.5998 (OUTLIER) cc_final: 0.5552 (tp)
REVERT: B  358 LEU cc_start: 0.6391 (tt) cc_final: 0.5982 (tp)
REVERT: B  494 LYS cc_start: 0.7591 (pttp) cc_final: 0.7378 (ptmt)
REVERT: B  534 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6447 (tp)
REVERT: C   26 TYR cc_start: 0.8933 (m-80) cc_final: 0.8568 (m-80)
REVERT: C  120 ASP cc_start: 0.5798 (p0) cc_final: 0.5593 (p0)
REVERT: C  358 LEU cc_start: 0.6192 (tt) cc_final: 0.5739 (tp)
REVERT: C  534 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5226 (tp)
  outliers start: 44
  outliers final: 27
  residues processed: 236
  average time/residue: 0.2478
  time to fit residues: 85.2195
Evaluate side-chains
  191 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 161
  time to evaluate  : 1.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 7 optimal weight:    7.9990
   chunk 144 optimal weight:    7.9990
   chunk 93 optimal weight:    0.9990
   chunk 5 optimal weight:   10.0000
   chunk 10 optimal weight:    6.9990
   chunk 140 optimal weight:   10.0000
   chunk 31 optimal weight:   10.0000
   chunk 125 optimal weight:   20.0000
   chunk 20 optimal weight:    0.0050
   chunk 12 optimal weight:    9.9990
   overall best weight:    4.8002

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 322 GLN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 491 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.097099 restraints weight = 21498.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.098818 restraints weight = 15077.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.100070 restraints weight = 11516.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.2538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12807  Z= 0.225
  Angle     :  0.667   7.369  17316  Z= 0.346
  Chirality :  0.047   0.156   1977
  Planarity :  0.004   0.043   2226
  Dihedral  :  6.190  33.334   1707
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 18.44 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.83 (0.19), residues: 1593
  helix: -1.77 (0.38), residues: 183
  sheet: -1.72 (0.21), residues: 549
  loop : -1.98 (0.18), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 267 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.012   0.002   PHE A 411 
 TYR   0.013   0.002   TYR A 354 
 ARG   0.005   0.001   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03730 (  391)
  hydrogen bonds       : angle       7.14606 ( 1020)
  covalent geometry    : bond        0.00517 (12807)
  covalent geometry    : angle       0.66681 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 177
  time to evaluate  : 1.392 
Fit side-chains
REVERT: A  257 ASP cc_start: 0.8327 (m-30) cc_final: 0.8105 (m-30)
REVERT: A  315 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8133 (pt0)
REVERT: A  358 LEU cc_start: 0.6716 (tt) cc_final: 0.6380 (tp)
REVERT: A  494 LYS cc_start: 0.7579 (pttp) cc_final: 0.7080 (ptmt)
REVERT: A  534 ILE cc_start: 0.6241 (OUTLIER) cc_final: 0.5767 (tp)
REVERT: B  315 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8247 (pt0)
REVERT: B  358 LEU cc_start: 0.6652 (tt) cc_final: 0.6276 (tp)
REVERT: B  494 LYS cc_start: 0.7696 (pttp) cc_final: 0.7244 (ptmt)
REVERT: B  534 ILE cc_start: 0.6784 (OUTLIER) cc_final: 0.6312 (tp)
REVERT: C   26 TYR cc_start: 0.8937 (m-80) cc_final: 0.8555 (m-80)
REVERT: C  315 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8477 (pt0)
REVERT: C  358 LEU cc_start: 0.6160 (tt) cc_final: 0.5751 (tp)
REVERT: C  534 ILE cc_start: 0.6011 (OUTLIER) cc_final: 0.5589 (tp)
  outliers start: 67
  outliers final: 45
  residues processed: 230
  average time/residue: 0.2261
  time to fit residues: 77.9069
Evaluate side-chains
  208 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 157
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  490 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  315 GLN
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 33 optimal weight:    7.9990
   chunk 92 optimal weight:    8.9990
   chunk 77 optimal weight:   10.0000
   chunk 143 optimal weight:    9.9990
   chunk 56 optimal weight:    5.9990
   chunk 27 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 142 optimal weight:    1.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 322 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 ASN
C 337 ASN
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.108305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.096805 restraints weight = 21225.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.098449 restraints weight = 14932.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.099746 restraints weight = 11495.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  12807  Z= 0.214
  Angle     :  0.660  10.004  17316  Z= 0.337
  Chirality :  0.047   0.158   1977
  Planarity :  0.004   0.038   2226
  Dihedral  :  6.068  33.823   1707
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 21.26 %
    Favored  : 73.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.66 (0.20), residues: 1593
  helix: -1.45 (0.39), residues: 183
  sheet: -1.63 (0.22), residues: 549
  loop : -1.90 (0.19), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 267 
 HIS   0.004   0.001   HIS B 162 
 PHE   0.012   0.002   PHE A 411 
 TYR   0.011   0.002   TYR A 354 
 ARG   0.004   0.000   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  391)
  hydrogen bonds       : angle       6.91603 ( 1020)
  covalent geometry    : bond        0.00492 (12807)
  covalent geometry    : angle       0.65965 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 170
  time to evaluate  : 1.387 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.8675 (mp0) cc_final: 0.8464 (mp0)
REVERT: A  315 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8121 (pt0)
REVERT: A  534 ILE cc_start: 0.6211 (OUTLIER) cc_final: 0.5749 (tp)
REVERT: B  315 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8241 (pt0)
REVERT: B  358 LEU cc_start: 0.6552 (tt) cc_final: 0.6213 (tp)
REVERT: B  494 LYS cc_start: 0.7543 (pttp) cc_final: 0.7131 (ptmt)
REVERT: B  534 ILE cc_start: 0.7084 (OUTLIER) cc_final: 0.6643 (tp)
REVERT: C   26 TYR cc_start: 0.8924 (m-80) cc_final: 0.8577 (m-80)
REVERT: C   94 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.8380 (mtmt)
REVERT: C  315 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8509 (pt0)
REVERT: C  534 ILE cc_start: 0.6281 (OUTLIER) cc_final: 0.5854 (tp)
  outliers start: 77
  outliers final: 52
  residues processed: 225
  average time/residue: 0.2126
  time to fit residues: 72.4777
Evaluate side-chains
  207 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 148
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  315 GLN
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 76 optimal weight:    2.9990
   chunk 143 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   chunk 126 optimal weight:    0.0170
   chunk 8 optimal weight:   10.0000
   chunk 129 optimal weight:    1.9990
   chunk 111 optimal weight:   10.0000
   chunk 157 optimal weight:   20.0000
   chunk 69 optimal weight:    1.9990
   chunk 152 optimal weight:    5.9990
   overall best weight:    2.6026

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 337 ASN
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 492 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.110641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.099218 restraints weight = 21185.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.100945 restraints weight = 14860.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.102098 restraints weight = 11398.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12807  Z= 0.141
  Angle     :  0.596   8.406  17316  Z= 0.304
  Chirality :  0.045   0.151   1977
  Planarity :  0.003   0.035   2226
  Dihedral  :  5.721  33.586   1707
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 22.27 %
    Favored  : 72.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.20), residues: 1593
  helix: -1.19 (0.39), residues: 183
  sheet: -1.29 (0.23), residues: 531
  loop : -1.85 (0.19), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 215 
 HIS   0.003   0.001   HIS B 440 
 PHE   0.014   0.001   PHE C 411 
 TYR   0.011   0.001   TYR B 404 
 ARG   0.004   0.000   ARG C 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02928 (  391)
  hydrogen bonds       : angle       6.44453 ( 1020)
  covalent geometry    : bond        0.00323 (12807)
  covalent geometry    : angle       0.59554 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 183
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
REVERT: A  315 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8092 (pt0)
REVERT: A  321 SER cc_start: 0.8641 (p) cc_final: 0.8410 (t)
REVERT: A  494 LYS cc_start: 0.7587 (pttp) cc_final: 0.7001 (ptmt)
REVERT: B  272 SER cc_start: 0.9080 (t) cc_final: 0.8583 (p)
REVERT: B  315 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8198 (pt0)
REVERT: B  358 LEU cc_start: 0.6367 (tt) cc_final: 0.5923 (tp)
REVERT: B  494 LYS cc_start: 0.7480 (pttp) cc_final: 0.7030 (ptmt)
REVERT: B  534 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6174 (tp)
REVERT: C   26 TYR cc_start: 0.8859 (m-80) cc_final: 0.8594 (m-80)
REVERT: C   94 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8359 (mtmt)
  outliers start: 71
  outliers final: 53
  residues processed: 231
  average time/residue: 0.2180
  time to fit residues: 76.0381
Evaluate side-chains
  225 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 168
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    9.9990
   chunk 49 optimal weight:    6.9990
   chunk 142 optimal weight:   10.0000
   chunk 36 optimal weight:   10.0000
   chunk 30 optimal weight:    0.1980
   chunk 137 optimal weight:    9.9990
   chunk 112 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9980
   chunk 131 optimal weight:    9.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    5.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 HIS
B 150 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.107069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.095218 restraints weight = 21659.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.097010 restraints weight = 15077.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.098309 restraints weight = 11494.176|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049  12807  Z= 0.245
  Angle     :  0.684   8.559  17316  Z= 0.349
  Chirality :  0.047   0.157   1977
  Planarity :  0.004   0.037   2226
  Dihedral  :  5.990  34.730   1707
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  6.15 %
    Allowed  : 22.92 %
    Favored  : 70.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (0.20), residues: 1593
  helix: -1.10 (0.40), residues: 183
  sheet: -1.55 (0.22), residues: 555
  loop : -1.85 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 267 
 HIS   0.004   0.001   HIS C 334 
 PHE   0.012   0.002   PHE B 163 
 TYR   0.011   0.002   TYR A 354 
 ARG   0.005   0.001   ARG C 167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03407 (  391)
  hydrogen bonds       : angle       6.74529 ( 1020)
  covalent geometry    : bond        0.00566 (12807)
  covalent geometry    : angle       0.68427 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 161
  time to evaluate  : 1.623 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8254 (tpt) cc_final: 0.7216 (tpp)
REVERT: A  315 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8166 (pt0)
REVERT: A  534 ILE cc_start: 0.6302 (OUTLIER) cc_final: 0.5848 (tp)
REVERT: B  315 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8254 (pt0)
REVERT: B  358 LEU cc_start: 0.6621 (tt) cc_final: 0.6215 (tp)
REVERT: B  534 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6573 (tp)
REVERT: C   26 TYR cc_start: 0.8881 (m-80) cc_final: 0.8607 (m-80)
REVERT: C  308 TYR cc_start: 0.8311 (OUTLIER) cc_final: 0.7964 (m-80)
REVERT: C  534 ILE cc_start: 0.6487 (OUTLIER) cc_final: 0.6071 (tp)
  outliers start: 85
  outliers final: 69
  residues processed: 221
  average time/residue: 0.2154
  time to fit residues: 72.6162
Evaluate side-chains
  228 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 153
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue   70 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  308 TYR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  460 ILE
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 108 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 135 optimal weight:    8.9990
   chunk 139 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 36 optimal weight:   10.0000
   chunk 103 optimal weight:   10.0000
   chunk 150 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 67 optimal weight:    7.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.109437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.098056 restraints weight = 21205.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.099779 restraints weight = 14820.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.100918 restraints weight = 11345.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.3279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12807  Z= 0.161
  Angle     :  0.621   8.068  17316  Z= 0.314
  Chirality :  0.045   0.153   1977
  Planarity :  0.003   0.035   2226
  Dihedral  :  5.753  33.897   1707
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  6.22 %
    Allowed  : 23.07 %
    Favored  : 70.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.38 (0.20), residues: 1593
  helix: -1.00 (0.39), residues: 183
  sheet: -1.29 (0.23), residues: 537
  loop : -1.89 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 215 
 HIS   0.004   0.001   HIS B 162 
 PHE   0.014   0.001   PHE C 411 
 TYR   0.010   0.001   TYR B 404 
 ARG   0.003   0.000   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03012 (  391)
  hydrogen bonds       : angle       6.41759 ( 1020)
  covalent geometry    : bond        0.00370 (12807)
  covalent geometry    : angle       0.62069 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 167
  time to evaluate  : 1.503 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8167 (tpt) cc_final: 0.7490 (tpp)
REVERT: A  315 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8107 (pt0)
REVERT: A  534 ILE cc_start: 0.6132 (OUTLIER) cc_final: 0.5658 (tp)
REVERT: B  214 TYR cc_start: 0.8722 (t80) cc_final: 0.8018 (t80)
REVERT: B  272 SER cc_start: 0.9055 (t) cc_final: 0.8532 (p)
REVERT: B  315 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8218 (pt0)
REVERT: B  358 LEU cc_start: 0.6275 (tt) cc_final: 0.5995 (tp)
REVERT: B  534 ILE cc_start: 0.6957 (OUTLIER) cc_final: 0.6517 (tp)
REVERT: C   26 TYR cc_start: 0.8866 (m-80) cc_final: 0.8600 (m-80)
REVERT: C  308 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.8016 (m-80)
REVERT: C  534 ILE cc_start: 0.6340 (OUTLIER) cc_final: 0.5874 (tp)
  outliers start: 86
  outliers final: 69
  residues processed: 228
  average time/residue: 0.2196
  time to fit residues: 75.7626
Evaluate side-chains
  234 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 159
  time to evaluate  : 1.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue   68 LEU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  337 ASN
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  490 LEU
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  297 THR
Chi-restraints excluded: chain B residue  308 TYR
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  308 TYR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  337 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   chunk 45 optimal weight:    9.9990
   chunk 60 optimal weight:    8.9990
   chunk 77 optimal weight:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 88 optimal weight:    7.9990
   chunk 107 optimal weight:   10.0000
   chunk 158 optimal weight:    9.9990
   chunk 114 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 337 ASN
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 290 ASN
C 334 HIS
** C 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.103885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.092430 restraints weight = 21857.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.094070 restraints weight = 15576.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.095217 restraints weight = 12049.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8214
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.076  12807  Z= 0.373
  Angle     :  0.813   9.518  17316  Z= 0.413
  Chirality :  0.051   0.178   1977
  Planarity :  0.005   0.039   2226
  Dihedral  :  6.472  39.831   1707
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.04 %
    Favored  : 91.96 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 23.79 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.20), residues: 1593
  helix: -1.22 (0.38), residues: 183
  sheet: -1.65 (0.22), residues: 537
  loop : -2.03 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B 267 
 HIS   0.006   0.001   HIS C 334 
 PHE   0.016   0.002   PHE B 163 
 TYR   0.012   0.002   TYR A 354 
 ARG   0.005   0.001   ARG C 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04005 (  391)
  hydrogen bonds       : angle       7.10647 ( 1020)
  covalent geometry    : bond        0.00866 (12807)
  covalent geometry    : angle       0.81281 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 158
  time to evaluate  : 1.558 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.8752 (mp0) cc_final: 0.8528 (mp0)
REVERT: A  315 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8264 (pt0)
REVERT: A  482 ASN cc_start: 0.8091 (t0) cc_final: 0.7673 (t0)
REVERT: A  534 ILE cc_start: 0.6372 (OUTLIER) cc_final: 0.5992 (tp)
REVERT: B  214 TYR cc_start: 0.8772 (t80) cc_final: 0.8100 (t80)
REVERT: B  218 ASP cc_start: 0.7536 (m-30) cc_final: 0.7291 (m-30)
REVERT: B  315 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8318 (pt0)
REVERT: B  358 LEU cc_start: 0.6688 (tt) cc_final: 0.6331 (tp)
REVERT: B  534 ILE cc_start: 0.7083 (OUTLIER) cc_final: 0.6631 (tp)
REVERT: C    3 HIS cc_start: 0.7665 (m-70) cc_final: 0.7453 (m170)
REVERT: C  308 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7981 (m-80)
REVERT: C  419 ASP cc_start: 0.7515 (t0) cc_final: 0.7296 (t0)
REVERT: C  534 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6745 (tp)
  outliers start: 83
  outliers final: 71
  residues processed: 220
  average time/residue: 0.2217
  time to fit residues: 74.5164
Evaluate side-chains
  228 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 151
  time to evaluate  : 1.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  337 ASN
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  460 ILE
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  485 GLU
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue   94 LYS
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  308 TYR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  329 ILE
Chi-restraints excluded: chain C residue  337 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  439 MET
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 102 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 138 optimal weight:    5.9990
   chunk 135 optimal weight:    6.9990
   chunk 142 optimal weight:    6.9990
   chunk 58 optimal weight:    7.9990
   chunk 36 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   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 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 HIS
B 150 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.107686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.096314 restraints weight = 21099.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.097982 restraints weight = 14966.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.099156 restraints weight = 11554.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.3540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12807  Z= 0.191
  Angle     :  0.664   8.954  17316  Z= 0.334
  Chirality :  0.046   0.159   1977
  Planarity :  0.004   0.036   2226
  Dihedral  :  5.993  39.310   1707
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  6.36 %
    Allowed  : 23.79 %
    Favored  : 69.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.20), residues: 1593
  helix: -0.96 (0.39), residues: 183
  sheet: -1.57 (0.22), residues: 555
  loop : -1.94 (0.19), residues: 855

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 215 
 HIS   0.007   0.001   HIS A 162 
 PHE   0.014   0.002   PHE B 411 
 TYR   0.011   0.001   TYR A 354 
 ARG   0.003   0.000   ARG C 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03207 (  391)
  hydrogen bonds       : angle       6.55486 ( 1020)
  covalent geometry    : bond        0.00442 (12807)
  covalent geometry    : angle       0.66432 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  254 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 166
  time to evaluate  : 1.458 
Fit side-chains
REVERT: A  123 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8445 (mp0)
REVERT: A  153 MET cc_start: 0.8246 (tpt) cc_final: 0.7207 (tpp)
REVERT: A  315 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8131 (pt0)
REVERT: A  482 ASN cc_start: 0.7946 (t0) cc_final: 0.7428 (t0)
REVERT: A  534 ILE cc_start: 0.6112 (OUTLIER) cc_final: 0.5668 (tp)
REVERT: B  150 HIS cc_start: 0.7716 (OUTLIER) cc_final: 0.7370 (m90)
REVERT: B  214 TYR cc_start: 0.8728 (t80) cc_final: 0.8044 (t80)
REVERT: B  315 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8245 (pt0)
REVERT: B  534 ILE cc_start: 0.7032 (OUTLIER) cc_final: 0.6544 (tp)
REVERT: C  162 HIS cc_start: 0.7557 (m-70) cc_final: 0.7337 (m90)
REVERT: C  308 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.7977 (m-80)
REVERT: C  534 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6469 (tp)
  outliers start: 88
  outliers final: 71
  residues processed: 225
  average time/residue: 0.2115
  time to fit residues: 72.4779
Evaluate side-chains
  241 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 162
  time to evaluate  : 1.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  337 ASN
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    3 HIS
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  150 HIS
Chi-restraints excluded: chain B residue  159 SER
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  308 TYR
Chi-restraints excluded: chain C residue  321 SER
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  337 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  504 LEU
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 157 optimal weight:   10.0000
   chunk 129 optimal weight:    0.8980
   chunk 145 optimal weight:    0.0570
   chunk 71 optimal weight:    4.9990
   chunk 8 optimal weight:    8.9990
   chunk 6 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9990
   chunk 128 optimal weight:    9.9990
   overall best weight:    2.7904

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B   3 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.109472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.098229 restraints weight = 21034.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.099815 restraints weight = 14798.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.101157 restraints weight = 11393.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12807  Z= 0.149
  Angle     :  0.631   9.269  17316  Z= 0.316
  Chirality :  0.045   0.153   1977
  Planarity :  0.003   0.033   2226
  Dihedral  :  5.719  38.636   1707
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.65 %
    Favored  : 93.35 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 24.30 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.35 (0.20), residues: 1593
  helix: -0.76 (0.39), residues: 183
  sheet: -1.28 (0.23), residues: 537
  loop : -1.93 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 215 
 HIS   0.008   0.001   HIS B 150 
 PHE   0.015   0.001   PHE B 411 
 TYR   0.015   0.001   TYR C 372 
 ARG   0.003   0.000   ARG C 431 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02978 (  391)
  hydrogen bonds       : angle       6.24702 ( 1020)
  covalent geometry    : bond        0.00346 (12807)
  covalent geometry    : angle       0.63133 (17316)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 177
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
REVERT: A  123 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8461 (mp0)
REVERT: A  153 MET cc_start: 0.8207 (tpt) cc_final: 0.7548 (tpp)
REVERT: A  315 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8102 (pt0)
REVERT: A  482 ASN cc_start: 0.7791 (t0) cc_final: 0.7305 (t0)
REVERT: A  511 MET cc_start: 0.7903 (tmm) cc_final: 0.7565 (tmm)
REVERT: A  534 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5807 (tp)
REVERT: B  214 TYR cc_start: 0.8717 (t80) cc_final: 0.8010 (t80)
REVERT: B  272 SER cc_start: 0.9034 (t) cc_final: 0.8499 (p)
REVERT: B  315 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8209 (pt0)
REVERT: B  511 MET cc_start: 0.7999 (tmm) cc_final: 0.7772 (tmm)
REVERT: B  534 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6659 (tp)
REVERT: C  162 HIS cc_start: 0.7522 (m-70) cc_final: 0.7287 (m90)
REVERT: C  301 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8540 (tt)
REVERT: C  534 ILE cc_start: 0.6380 (OUTLIER) cc_final: 0.5969 (tp)
  outliers start: 76
  outliers final: 63
  residues processed: 227
  average time/residue: 0.2258
  time to fit residues: 77.5341
Evaluate side-chains
  236 residues out of total 1383 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 166
  time to evaluate  : 1.485 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   51 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  123 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  159 SER
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 TRP
Chi-restraints excluded: chain A residue  206 LYS
Chi-restraints excluded: chain A residue  210 VAL
Chi-restraints excluded: chain A residue  215 TRP
Chi-restraints excluded: chain A residue  301 LEU
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  315 GLN
Chi-restraints excluded: chain A residue  324 ASP
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  337 ASN
Chi-restraints excluded: chain A residue  345 THR
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  486 ASN
Chi-restraints excluded: chain A residue  504 LEU
Chi-restraints excluded: chain A residue  534 ILE
Chi-restraints excluded: chain B residue    5 LEU
Chi-restraints excluded: chain B residue   20 VAL
Chi-restraints excluded: chain B residue   68 LEU
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  115 SER
Chi-restraints excluded: chain B residue  123 GLU
Chi-restraints excluded: chain B residue  174 TRP
Chi-restraints excluded: chain B residue  206 LYS
Chi-restraints excluded: chain B residue  210 VAL
Chi-restraints excluded: chain B residue  215 TRP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  315 GLN
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  324 ASP
Chi-restraints excluded: chain B residue  329 ILE
Chi-restraints excluded: chain B residue  345 THR
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  460 ILE
Chi-restraints excluded: chain B residue  461 VAL
Chi-restraints excluded: chain B residue  486 ASN
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  534 ILE
Chi-restraints excluded: chain C residue    5 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue   68 LEU
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  136 ILE
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  174 TRP
Chi-restraints excluded: chain C residue  206 LYS
Chi-restraints excluded: chain C residue  215 TRP
Chi-restraints excluded: chain C residue  227 GLU
Chi-restraints excluded: chain C residue  301 LEU
Chi-restraints excluded: chain C residue  324 ASP
Chi-restraints excluded: chain C residue  337 ASN
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  346 VAL
Chi-restraints excluded: chain C residue  355 LEU
Chi-restraints excluded: chain C residue  386 LEU
Chi-restraints excluded: chain C residue  448 PHE
Chi-restraints excluded: chain C residue  461 VAL
Chi-restraints excluded: chain C residue  486 ASN
Chi-restraints excluded: chain C residue  534 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 135 optimal weight:   10.0000
   chunk 77 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9980
   chunk 143 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 94 optimal weight:    0.3980
   chunk 99 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 100 optimal weight:    6.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    3.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 150 HIS
** B 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 440 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C   3 HIS
** C 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.109002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.097726 restraints weight = 21189.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.099408 restraints weight = 14967.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.100573 restraints weight = 11509.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3107
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12807  Z= 0.180
  Angle     :  0.654   9.158  17316  Z= 0.327
  Chirality :  0.046   0.166   1977
  Planarity :  0.003   0.035   2226
  Dihedral  :  5.756  39.115   1707
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 24.51 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.20), residues: 1593
  helix: -0.72 (0.39), residues: 183
  sheet: -1.25 (0.23), residues: 537
  loop : -1.93 (0.19), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 215 
 HIS   0.007   0.001   HIS A 162 
 PHE   0.014   0.002   PHE B 411 
 TYR   0.014   0.001   TYR C 372 
 ARG   0.004   0.000   ARG B 243 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03105 (  391)
  hydrogen bonds       : angle       6.30269 ( 1020)
  covalent geometry    : bond        0.00418 (12807)
  covalent geometry    : angle       0.65422 (17316)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3301.30 seconds
wall clock time: 58 minutes 36.42 seconds (3516.42 seconds total)