Starting phenix.real_space_refine
on Thu Feb  5 07:24:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v0s_64670/02_2026/9v0s_64670.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v0s_64670/02_2026/9v0s_64670.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v0s_64670/02_2026/9v0s_64670.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v0s_64670/02_2026/9v0s_64670.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v0s_64670/02_2026/9v0s_64670.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v0s_64670/02_2026/9v0s_64670.map"
  }
  resolution = 3.78
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.004 sd=   0.038
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      93      5.16       5
     C    9870      2.51       5
     N    2619      2.21       5
     O    3069      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15651
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "B"
      Number of atoms: 3482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3482
          Classifications: {'peptide': 449}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 908
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "E"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 827
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 3482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3482
          Classifications: {'peptide': 449}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 908
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "H"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 827
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 3482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3482
          Classifications: {'peptide': 449}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436}
          Chain breaks: 1
    Chain: "G"
      Number of atoms: 908
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 908
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
    Chain: "I"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 827
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 101}
  Time building chain proxies: 3.73, per 1000 atoms: 0.24
  Number of scatterers: 15651
  At special positions: 0
  Unit cell: (148, 139, 125, 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      93     16.00
     O    3069      8.00
     N    2619      7.00
     C    9870      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=28, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  37 " - pdb=" SG  CYS B 439 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  69 " - pdb=" SG  CYS B 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 313 " - pdb=" SG  CYS B 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 322 " - pdb=" SG  CYS B 333 " distance=1.57
    Simple disulfide: pdb=" SG  CYS B 358 " - pdb=" SG  CYS B 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 382 " - pdb=" SG  CYS B 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 416 " - pdb=" SG  CYS B 422 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  37 " - pdb=" SG  CYS A 439 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  69 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 155 " - pdb=" SG  CYS A 290 " distance=2.24
    Simple disulfide: pdb=" SG  CYS A 313 " - pdb=" SG  CYS A 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 322 " - pdb=" SG  CYS A 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 358 " - pdb=" SG  CYS A 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 416 " - pdb=" SG  CYS A 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  90 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  37 " - pdb=" SG  CYS C 439 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  69 " - pdb=" SG  CYS C 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 313 " - pdb=" SG  CYS C 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 322 " - pdb=" SG  CYS C 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 358 " - pdb=" SG  CYS C 367 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 382 " - pdb=" SG  CYS C 393 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 416 " - pdb=" SG  CYS C 422 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  22 " - pdb=" SG  CYS G  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  22 " - pdb=" SG  CYS I  90 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.38
  Conformation dependent library (CDL) restraints added in 756.7 milliseconds
  

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3762

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 33 sheets defined
      24.0% alpha, 20.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'B' and resid 73 through 95
    Processing helix  chain 'B' and resid 148 through 160
      removed outlier: 3.850A  pdb=" N   LEU B 160 " --> pdb=" O   LYS B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 162 through 171
    Processing helix  chain 'B' and resid 194 through 200
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 217 through 240
      removed outlier: 4.104A  pdb=" N   ILE B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   ARG B 229 " --> pdb=" O   GLN B 225 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   LEU B 230 " --> pdb=" O   LYS B 226 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ASN B 240 " --> pdb=" O   GLU B 236 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 263
    Processing helix  chain 'B' and resid 267 through 277
    Processing helix  chain 'B' and resid 277 through 285
      removed outlier: 3.724A  pdb=" N   VAL B 281 " --> pdb=" O   ASN B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 372
    Processing helix  chain 'B' and resid 376 through 381
    Processing helix  chain 'B' and resid 473 through 478
      removed outlier: 3.502A  pdb=" N   ASN B 476 " --> pdb=" O   PRO B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 512
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.745A  pdb=" N   ASP D  90 " --> pdb=" O   ARG D  87 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   THR D  91 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 87 through 91'
    Processing helix  chain 'E' and resid 81 through 85
      removed outlier: 3.837A  pdb=" N   GLU E  85 " --> pdb=" O   PRO E  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 95
    Processing helix  chain 'A' and resid 148 through 159
    Processing helix  chain 'A' and resid 162 through 171
    Processing helix  chain 'A' and resid 194 through 200
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 217 through 240
      removed outlier: 4.127A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   ARG A 229 " --> pdb=" O   GLN A 225 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   LEU A 230 " --> pdb=" O   LYS A 226 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   ASN A 240 " --> pdb=" O   GLU A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 263
    Processing helix  chain 'A' and resid 267 through 277
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.782A  pdb=" N   VAL A 281 " --> pdb=" O   ASN A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 372
    Processing helix  chain 'A' and resid 376 through 383
    Processing helix  chain 'A' and resid 473 through 478
      removed outlier: 3.533A  pdb=" N   ASN A 476 " --> pdb=" O   PRO A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 512
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.705A  pdb=" N   THR F  91 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 81 through 85
      removed outlier: 3.895A  pdb=" N   GLU H  85 " --> pdb=" O   PRO H  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 96
    Processing helix  chain 'C' and resid 148 through 160
      removed outlier: 3.844A  pdb=" N   LEU C 160 " --> pdb=" O   LYS C 156 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 162 through 171
    Processing helix  chain 'C' and resid 194 through 200
    Processing helix  chain 'C' and resid 203 through 208
    Processing helix  chain 'C' and resid 217 through 240
      removed outlier: 4.318A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 217 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ARG C 229 " --> pdb=" O   GLN C 225 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU C 230 " --> pdb=" O   LYS C 226 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN C 240 " --> pdb=" O   GLU C 236 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 253 through 263
    Processing helix  chain 'C' and resid 267 through 277
    Processing helix  chain 'C' and resid 277 through 283
      removed outlier: 3.727A  pdb=" N   VAL C 281 " --> pdb=" O   ASN C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 368 through 372
    Processing helix  chain 'C' and resid 376 through 379
    Processing helix  chain 'C' and resid 380 through 385
      removed outlier: 4.041A  pdb=" N   VAL C 384 " --> pdb=" O   ASN C 380 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 473 through 478
    Processing helix  chain 'C' and resid 492 through 512
    Processing helix  chain 'G' and resid 87 through 91
      removed outlier: 3.825A  pdb=" N   ASP G  90 " --> pdb=" O   ARG G  87 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   THR G  91 " --> pdb=" O   VAL G  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 87 through 91'
    Processing helix  chain 'I' and resid 81 through 85
      removed outlier: 3.808A  pdb=" N   GLU I  85 " --> pdb=" O   PRO I  82 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 373 through 375
      removed outlier: 6.515A  pdb=" N   GLU B  30 " --> pdb=" O   LEU B 467 " (cutoff:3.500A)
      removed outlier: 7.490A  pdb=" N   VAL B 469 " --> pdb=" O   GLU B  30 " (cutoff:3.500A)
      removed outlier: 6.272A  pdb=" N   PHE B  32 " --> pdb=" O   VAL B 469 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 47
      removed outlier: 3.689A  pdb=" N   THR B 311 " --> pdb=" O   SER B  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 53
      removed outlier: 3.622A  pdb=" N   SER B  55 " --> pdb=" O   VAL B 301 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE B 190 " --> pdb=" O   VAL B  56 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR B  58 " --> pdb=" O   PHE B 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 53
    Processing sheet with id=AA5, first strand: chain 'B' and resid 321 through 322
    Processing sheet with id=AA6, first strand: chain 'B' and resid 404 through 407
      removed outlier: 4.191A  pdb=" N   CYS B 416 " --> pdb=" O   GLY B 438 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLY B 438 " --> pdb=" O   CYS B 416 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 430 through 431
    Processing sheet with id=AA8, first strand: chain 'D' and resid 6 through 7
      removed outlier: 3.538A  pdb=" N   SER D  21 " --> pdb=" O   SER D   7 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 10 through 11
      removed outlier: 6.334A  pdb=" N   GLY D  10 " --> pdb=" O   THR D 119 " (cutoff:3.500A)
      removed outlier: 5.681A  pdb=" N   ARG D  38 " --> pdb=" O   TRP D  47 " (cutoff:3.500A)
      removed outlier: 4.910A  pdb=" N   TRP D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   SER D  59 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 18 through 23
    Processing sheet with id=AB2, first strand: chain 'E' and resid 37 through 39
      removed outlier: 6.346A  pdb=" N   GLN E  39 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   VAL E  48 " --> pdb=" O   GLN E  39 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 86 through 88
    Processing sheet with id=AB4, first strand: chain 'A' and resid 373 through 375
      removed outlier: 6.507A  pdb=" N   GLU A  30 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 7.454A  pdb=" N   VAL A 469 " --> pdb=" O   GLU A  30 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   PHE A  32 " --> pdb=" O   VAL A 469 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 51 through 53
      removed outlier: 3.594A  pdb=" N   SER A  55 " --> pdb=" O   VAL A 301 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 190 " --> pdb=" O   VAL A  56 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   THR A  58 " --> pdb=" O   PHE A 190 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A 187 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A 179 " --> pdb=" O   VAL A 187 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 51 through 53
      removed outlier: 3.544A  pdb=" N   SER A 287 " --> pdb=" O   THR A 244 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 333 through 335
    Processing sheet with id=AB8, first strand: chain 'A' and resid 404 through 406
      removed outlier: 3.707A  pdb=" N   CYS A 416 " --> pdb=" O   GLY A 438 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 430 through 431
    Processing sheet with id=AC1, first strand: chain 'F' and resid 6 through 7
      removed outlier: 3.536A  pdb=" N   SER F   7 " --> pdb=" O   SER F  21 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   SER F  21 " --> pdb=" O   SER F   7 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'F' and resid 10 through 11
      removed outlier: 6.264A  pdb=" N   GLY F  10 " --> pdb=" O   THR F 119 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   ARG F  38 " --> pdb=" O   TRP F  47 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   TRP F  47 " --> pdb=" O   ARG F  38 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER F  59 " --> pdb=" O   SER F  50 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'H' and resid 18 through 23
    Processing sheet with id=AC4, first strand: chain 'H' and resid 37 through 39
      removed outlier: 6.541A  pdb=" N   GLN H  39 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   VAL H  48 " --> pdb=" O   GLN H  39 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'H' and resid 86 through 88
    Processing sheet with id=AC6, first strand: chain 'C' and resid 373 through 375
    Processing sheet with id=AC7, first strand: chain 'C' and resid 178 through 179
      removed outlier: 3.819A  pdb=" N   VAL C 179 " --> pdb=" O   VAL C 187 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL C 187 " --> pdb=" O   VAL C 179 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   LEU C 188 " --> pdb=" O   THR C  54 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 333 through 335
    Processing sheet with id=AC9, first strand: chain 'C' and resid 404 through 407
      removed outlier: 4.125A  pdb=" N   CYS C 416 " --> pdb=" O   GLY C 438 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   GLY C 438 " --> pdb=" O   CYS C 416 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 430 through 431
    Processing sheet with id=AD2, first strand: chain 'G' and resid 6 through 7
      removed outlier: 3.640A  pdb=" N   SER G  21 " --> pdb=" O   SER G   7 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11
      removed outlier: 6.287A  pdb=" N   GLY G  10 " --> pdb=" O   THR G 119 " (cutoff:3.500A)
      removed outlier: 5.832A  pdb=" N   ARG G  38 " --> pdb=" O   TRP G  47 " (cutoff:3.500A)
      removed outlier: 5.255A  pdb=" N   TRP G  47 " --> pdb=" O   ARG G  38 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER G  59 " --> pdb=" O   SER G  50 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'I' and resid 18 through 23
    Processing sheet with id=AD5, first strand: chain 'I' and resid 37 through 39
      removed outlier: 6.404A  pdb=" N   GLN I  39 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL I  48 " --> pdb=" O   GLN I  39 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'I' and resid 86 through 88

    630 hydrogen bonds defined for protein.
    1584 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: 3.17

  Time building geometry restraints manager: 1.84 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: 5045
        1.34 -     1.47: 3712
        1.47 -     1.59: 7041
        1.59 -     1.72: 0
        1.72 -     1.84: 126
  Bond restraints: 15924
  Sorted by residual:
  bond pdb=" N   SER F  85 "
       pdb=" CA  SER F  85 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.034 1.17e-02 7.31e+03 8.61e+00
  bond pdb=" N   SER F  84 "
       pdb=" CA  SER F  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.16e-02 7.43e+03 7.35e+00
  bond pdb=" N   PHE F  68 "
       pdb=" CA  PHE F  68 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.25e-02 6.40e+03 5.86e+00
  bond pdb=" N   ARG F  67 "
       pdb=" CA  ARG F  67 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.19e-02 7.06e+03 5.05e+00
  bond pdb=" C   GLN C 302 "
       pdb=" N   LEU C 303 "
    ideal  model  delta    sigma   weight residual
    1.331  1.284  0.047 2.07e-02 2.33e+03 5.05e+00
  ... (remaining 15919 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.40: 21279
        3.40 -     6.80: 266
        6.80 -    10.20: 28
       10.20 -    13.60: 7
       13.60 -    17.00: 2
  Bond angle restraints: 21582
  Sorted by residual:
  angle pdb=" CA  GLN E  39 "
        pdb=" CB  GLN E  39 "
        pdb=" CG  GLN E  39 "
      ideal   model   delta    sigma   weight residual
     114.10  124.00   -9.90 2.00e+00 2.50e-01 2.45e+01
  angle pdb=" C   LEU A 193 "
        pdb=" N   ASP A 194 "
        pdb=" CA  ASP A 194 "
      ideal   model   delta    sigma   weight residual
     121.54  129.54   -8.00 1.91e+00 2.74e-01 1.76e+01
  angle pdb=" N   ILE A 217 "
        pdb=" CA  ILE A 217 "
        pdb=" C   ILE A 217 "
      ideal   model   delta    sigma   weight residual
     113.53  109.43    4.10 9.80e-01 1.04e+00 1.75e+01
  angle pdb=" N   ILE B 217 "
        pdb=" CA  ILE B 217 "
        pdb=" C   ILE B 217 "
      ideal   model   delta    sigma   weight residual
     113.53  109.45    4.08 9.80e-01 1.04e+00 1.73e+01
  angle pdb=" CA  GLN A 202 "
        pdb=" CB  GLN A 202 "
        pdb=" CG  GLN A 202 "
      ideal   model   delta    sigma   weight residual
     114.10  122.39   -8.29 2.00e+00 2.50e-01 1.72e+01
  ... (remaining 21577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 8249
       17.95 -    35.91: 1067
       35.91 -    53.86: 271
       53.86 -    71.82: 40
       71.82 -    89.77: 15
  Dihedral angle restraints: 9642
    sinusoidal: 3771
      harmonic: 5871
  Sorted by residual:
  dihedral pdb=" CB  CYS C  37 "
           pdb=" SG  CYS C  37 "
           pdb=" SG  CYS C 439 "
           pdb=" CB  CYS C 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    0.45  -86.45     1      1.00e+01 1.00e-02 9.01e+01
  dihedral pdb=" CB  CYS B  37 "
           pdb=" SG  CYS B  37 "
           pdb=" SG  CYS B 439 "
           pdb=" CB  CYS B 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   10.49   82.51     1      1.00e+01 1.00e-02 8.35e+01
  dihedral pdb=" CB  CYS A  37 "
           pdb=" SG  CYS A  37 "
           pdb=" SG  CYS A 439 "
           pdb=" CB  CYS A 439 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   16.04   76.96     1      1.00e+01 1.00e-02 7.43e+01
  ... (remaining 9639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 2330
       0.097 -    0.194: 174
       0.194 -    0.290: 7
       0.290 -    0.387: 1
       0.387 -    0.484: 2
  Chirality restraints: 2514
  Sorted by residual:
  chirality pdb=" CB  VAL C 360 "
            pdb=" CA  VAL C 360 "
            pdb=" CG1 VAL C 360 "
            pdb=" CG2 VAL C 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.15   -0.48 2.00e-01 2.50e+01 5.86e+00
  chirality pdb=" CB  VAL A 360 "
            pdb=" CA  VAL A 360 "
            pdb=" CG1 VAL A 360 "
            pdb=" CG2 VAL A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.15   -0.48 2.00e-01 2.50e+01 5.74e+00
  chirality pdb=" CB  VAL B 482 "
            pdb=" CA  VAL B 482 "
            pdb=" CG1 VAL B 482 "
            pdb=" CG2 VAL B 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.58e+00
  ... (remaining 2511 not shown)

  Planarity restraints: 2736
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  67 "   -0.329 9.50e-02 1.11e+02   1.48e-01 1.34e+01
        pdb=" NE  ARG F  67 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  67 "    0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  67 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  67 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 296 "   -0.014 2.00e-02 2.50e+03   2.90e-02 8.39e+00
        pdb=" C   VAL B 296 "    0.050 2.00e-02 2.50e+03
        pdb=" O   VAL B 296 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LEU B 297 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP I  94 "    0.014 2.00e-02 2.50e+03   2.89e-02 8.38e+00
        pdb=" CG  ASP I  94 "   -0.050 2.00e-02 2.50e+03
        pdb=" OD1 ASP I  94 "    0.018 2.00e-02 2.50e+03
        pdb=" OD2 ASP I  94 "    0.018 2.00e-02 2.50e+03
  ... (remaining 2733 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 18
        2.42 -     3.04: 8972
        3.04 -     3.66: 23352
        3.66 -     4.28: 33642
        4.28 -     4.90: 56239
  Nonbonded interactions: 122223
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 254 "
            pdb=" OE1 GLU A  92 "
     model   vdw
     1.799 3.120
  nonbonded pdb=" OD2 ASP A 338 "
            pdb=" OH  TYR A 342 "
     model   vdw
     1.977 3.040
  nonbonded pdb=" OD2 ASP B 338 "
            pdb=" OH  TYR B 342 "
     model   vdw
     2.034 3.040
  nonbonded pdb=" CE1 PHE D  29 "
            pdb=" CE  MET D  34 "
     model   vdw
     2.071 3.760
  nonbonded pdb=" OD1 ASP D  46 "
            pdb=" N   TRP D  47 "
     model   vdw
     2.102 3.120
  ... (remaining 122218 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'H'
  selection = chain 'I'
}

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:             1.660
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.060
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
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   0.458  15952  Z= 0.313
  Angle     :  1.046  53.943  21638  Z= 0.547
  Chirality :  0.054   0.484   2514
  Planarity :  0.007   0.148   2736
  Dihedral  : 16.592  89.772   5796
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.66 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 25.57 %
    Favored  : 72.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.34 (0.17), residues: 2016
  helix: -0.81 (0.23), residues: 426
  sheet: -1.06 (0.22), residues: 519
  loop : -2.15 (0.17), residues: 1071

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 507 
 TYR   0.034   0.002   TYR A 417 
 PHE   0.045   0.002   PHE D  29 
 TRP   0.026   0.002   TRP G 108 
 HIS   0.015   0.003   HIS B 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00539 (15924)
  covalent geometry    : angle       0.96418 (21582)
  SS BOND              : bond        0.09521 (   28)
  SS BOND              : angle       8.03909 (   56)
  hydrogen bonds       : bond        0.12538 (  622)
  hydrogen bonds       : angle       6.46008 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 251
  time to evaluate  : 0.621 
Fit side-chains
REVERT: B  448 ASP cc_start: 0.8144 (p0) cc_final: 0.7664 (m-30)
REVERT: D   36 TRP cc_start: 0.8428 (m100) cc_final: 0.7826 (m100)
REVERT: D   64 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8442 (m)
REVERT: D   83 MET cc_start: 0.8110 (mmt) cc_final: 0.7908 (mmp)
REVERT: A  251 MET cc_start: 0.8459 (tpp) cc_final: 0.7854 (ttm)
REVERT: A  264 MET cc_start: 0.7762 (ptt) cc_final: 0.7524 (ptt)
REVERT: A  454 ASN cc_start: 0.8467 (p0) cc_final: 0.7970 (p0)
REVERT: A  486 ASP cc_start: 0.5943 (m-30) cc_final: 0.5250 (t0)
REVERT: F   36 TRP cc_start: 0.8487 (m100) cc_final: 0.7962 (m-10)
REVERT: H   44 LYS cc_start: 0.8115 (tptt) cc_final: 0.7608 (tttt)
REVERT: C  332 ILE cc_start: 0.8933 (mp) cc_final: 0.8507 (pt)
REVERT: C  400 THR cc_start: 0.7931 (OUTLIER) cc_final: 0.7710 (p)
REVERT: G   28 MET cc_start: 0.8237 (tpp) cc_final: 0.7972 (tpt)
REVERT: G   36 TRP cc_start: 0.8427 (m-10) cc_final: 0.7813 (m-10)
REVERT: G   64 VAL cc_start: 0.8738 (OUTLIER) cc_final: 0.8479 (p)
REVERT: I   77 ILE cc_start: 0.7974 (mt) cc_final: 0.7577 (mt)
  outliers start: 42
  outliers final: 34
  residues processed: 280
  average time/residue: 0.1239
  time to fit residues: 52.4541
Evaluate side-chains
  264 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 227
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 TYR
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  400 THR
Chi-restraints excluded: chain B residue  407 ILE
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue  107 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  174 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  349 VAL
Chi-restraints excluded: chain C residue  400 THR
Chi-restraints excluded: chain C residue  442 VAL
Chi-restraints excluded: chain C residue  475 ILE
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain I residue   10 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 194 optimal weight:    8.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 200 optimal weight:    5.9990
   chunk 77 optimal weight:    0.1980
   chunk 122 optimal weight:    4.9990
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
** D  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
E  55 HIS
A 283 GLN
A 331 ASN
A 454 ASN
F 114 GLN
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 197 ASN
C 345 ASN
** G  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  55 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.167719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.131439 restraints weight = 22483.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.134914 restraints weight = 14025.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137165 restraints weight = 10540.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.138479 restraints weight = 8910.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.138969 restraints weight = 8093.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15952  Z= 0.179
  Angle     :  0.646  13.938  21638  Z= 0.331
  Chirality :  0.043   0.196   2514
  Planarity :  0.004   0.038   2736
  Dihedral  :  6.494  65.696   2228
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 24.07 %
    Favored  : 70.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.92 (0.17), residues: 2016
  helix:  0.28 (0.25), residues: 414
  sheet: -0.98 (0.21), residues: 555
  loop : -2.13 (0.17), residues: 1047

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  63 
 TYR   0.033   0.002   TYR C 417 
 PHE   0.013   0.002   PHE B 505 
 TRP   0.016   0.002   TRP G 108 
 HIS   0.007   0.002   HIS B 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (15924)
  covalent geometry    : angle       0.64349 (21582)
  SS BOND              : bond        0.00375 (   28)
  SS BOND              : angle       1.38105 (   56)
  hydrogen bonds       : bond        0.03462 (  622)
  hydrogen bonds       : angle       5.58403 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 106
    poor density    : 243
  time to evaluate  : 0.538 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7878 (mm)
REVERT: B  244 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8958 (t)
REVERT: B  383 ASN cc_start: 0.8196 (t0) cc_final: 0.7576 (m-40)
REVERT: B  448 ASP cc_start: 0.8115 (p0) cc_final: 0.7749 (m-30)
REVERT: D   36 TRP cc_start: 0.8478 (m100) cc_final: 0.7861 (m100)
REVERT: E   55 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.6846 (m90)
REVERT: A   59 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.8000 (mm)
REVERT: A  251 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7834 (ttm)
REVERT: A  454 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.7494 (m110)
REVERT: A  486 ASP cc_start: 0.6025 (m-30) cc_final: 0.5359 (t0)
REVERT: F   36 TRP cc_start: 0.8326 (m100) cc_final: 0.7882 (m-10)
REVERT: H   44 LYS cc_start: 0.8345 (tptt) cc_final: 0.7883 (tttt)
REVERT: C   49 ARG cc_start: 0.8918 (ttp80) cc_final: 0.8600 (ttp80)
REVERT: C  217 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7646 (mt)
REVERT: C  332 ILE cc_start: 0.8929 (mp) cc_final: 0.8429 (pt)
REVERT: C  383 ASN cc_start: 0.8117 (t0) cc_final: 0.7495 (m-40)
REVERT: G   36 TRP cc_start: 0.8545 (m100) cc_final: 0.7851 (m-10)
REVERT: I   77 ILE cc_start: 0.8083 (mt) cc_final: 0.7670 (mt)
  outliers start: 106
  outliers final: 65
  residues processed: 320
  average time/residue: 0.1068
  time to fit residues: 51.7683
Evaluate side-chains
  301 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 229
  time to evaluate  : 0.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  267 THR
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  279 GLN
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   11 LEU
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   55 HIS
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue   94 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  267 THR
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  370 MET
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  454 ASN
Chi-restraints excluded: chain A residue  475 ILE
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  349 VAL
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  440 ASP
Chi-restraints excluded: chain C residue  469 VAL
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain G residue  119 THR
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 109 optimal weight:    0.0770
   chunk 16 optimal weight:    0.0980
   chunk 80 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 142 optimal weight:    0.0050
   chunk 2 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 115 optimal weight:    5.9990
   chunk 59 optimal weight:    0.9980
   chunk 170 optimal weight:    0.9980
   overall best weight:    0.4352

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

Flipped N/Q/H residues before XYZ refinement:
B 202 GLN
** D  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 GLN
E   1 GLN
E  55 HIS
** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 114 GLN
** H   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.171510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.135392 restraints weight = 22758.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.139216 restraints weight = 13626.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.141630 restraints weight = 9997.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.142786 restraints weight = 8317.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.143949 restraints weight = 7540.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  15952  Z= 0.112
  Angle     :  0.599  12.339  21638  Z= 0.307
  Chirality :  0.042   0.213   2514
  Planarity :  0.003   0.033   2736
  Dihedral  :  5.866  58.420   2209
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.93 %
    Favored  : 91.07 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 25.62 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.75 (0.18), residues: 2016
  helix:  0.71 (0.26), residues: 414
  sheet: -0.99 (0.21), residues: 588
  loop : -2.11 (0.17), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  76 
 TYR   0.014   0.001   TYR A 417 
 PHE   0.012   0.001   PHE F  29 
 TRP   0.011   0.001   TRP G 108 
 HIS   0.005   0.001   HIS B 317 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (15924)
  covalent geometry    : angle       0.59651 (21582)
  SS BOND              : bond        0.00224 (   28)
  SS BOND              : angle       1.27478 (   56)
  hydrogen bonds       : bond        0.03070 (  622)
  hydrogen bonds       : angle       5.40345 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  341 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 95
    poor density    : 246
  time to evaluate  : 0.524 
Fit side-chains
REVERT: B  167 ILE cc_start: 0.7415 (OUTLIER) cc_final: 0.7184 (tp)
REVERT: B  244 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8837 (t)
REVERT: B  383 ASN cc_start: 0.8160 (t0) cc_final: 0.7601 (m-40)
REVERT: B  448 ASP cc_start: 0.8088 (p0) cc_final: 0.7671 (m-30)
REVERT: D   36 TRP cc_start: 0.8295 (m100) cc_final: 0.7709 (m100)
REVERT: E   63 ARG cc_start: 0.7362 (ttm110) cc_final: 0.6785 (mtm110)
REVERT: E   81 GLN cc_start: 0.8207 (pp30) cc_final: 0.7757 (pp30)
REVERT: A  244 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8889 (t)
REVERT: A  251 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7698 (ttm)
REVERT: A  486 ASP cc_start: 0.5834 (m-30) cc_final: 0.5351 (t0)
REVERT: F   36 TRP cc_start: 0.8279 (m100) cc_final: 0.7605 (m100)
REVERT: H   44 LYS cc_start: 0.8364 (tptt) cc_final: 0.7859 (tttt)
REVERT: C  217 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7595 (mt)
REVERT: C  332 ILE cc_start: 0.8949 (mp) cc_final: 0.8478 (pt)
REVERT: C  383 ASN cc_start: 0.8244 (t0) cc_final: 0.7550 (m-40)
REVERT: G   36 TRP cc_start: 0.8331 (m100) cc_final: 0.7783 (m-10)
REVERT: G   64 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8507 (p)
REVERT: I   77 ILE cc_start: 0.7979 (mt) cc_final: 0.7557 (mt)
  outliers start: 95
  outliers final: 56
  residues processed: 317
  average time/residue: 0.1062
  time to fit residues: 51.4704
Evaluate side-chains
  295 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 233
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  244 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  396 MET
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 182 optimal weight:    0.7980
   chunk 145 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 164 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 121 optimal weight:    0.8980
   chunk 40 optimal weight:    6.9990
   chunk 183 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
D   3 GLN
** D  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN
F 114 GLN
H   1 GLN
** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 388 ASN
G 114 GLN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.168492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.133383 restraints weight = 22336.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.137124 restraints weight = 13246.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.139414 restraints weight = 9687.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.140889 restraints weight = 8067.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.141548 restraints weight = 7229.480|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.1453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15952  Z= 0.123
  Angle     :  0.591  12.176  21638  Z= 0.302
  Chirality :  0.042   0.213   2514
  Planarity :  0.003   0.033   2736
  Dihedral  :  5.623  47.389   2201
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 25.68 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.61 (0.18), residues: 2016
  helix:  0.98 (0.26), residues: 414
  sheet: -0.70 (0.22), residues: 552
  loop : -2.21 (0.17), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  76 
 TYR   0.012   0.001   TYR C 417 
 PHE   0.013   0.001   PHE F  29 
 TRP   0.013   0.001   TRP D 108 
 HIS   0.009   0.001   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (15924)
  covalent geometry    : angle       0.58928 (21582)
  SS BOND              : bond        0.00232 (   28)
  SS BOND              : angle       1.12869 (   56)
  hydrogen bonds       : bond        0.02994 (  622)
  hydrogen bonds       : angle       5.26922 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 253
  time to evaluate  : 0.404 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8064 (OUTLIER) cc_final: 0.7794 (mm)
REVERT: B  167 ILE cc_start: 0.7486 (OUTLIER) cc_final: 0.7210 (tp)
REVERT: B  334 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7441 (mm)
REVERT: B  383 ASN cc_start: 0.8202 (t0) cc_final: 0.7562 (m-40)
REVERT: B  448 ASP cc_start: 0.8137 (p0) cc_final: 0.7673 (m-30)
REVERT: D   36 TRP cc_start: 0.8333 (m100) cc_final: 0.7721 (m100)
REVERT: D   64 VAL cc_start: 0.8748 (OUTLIER) cc_final: 0.8427 (m)
REVERT: D  114 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7911 (mm-40)
REVERT: E   81 GLN cc_start: 0.8131 (pp30) cc_final: 0.7820 (pp30)
REVERT: A  225 GLN cc_start: 0.8536 (mm-40) cc_final: 0.8116 (mm-40)
REVERT: A  251 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.7772 (ttm)
REVERT: A  486 ASP cc_start: 0.5768 (m-30) cc_final: 0.5370 (t0)
REVERT: F   36 TRP cc_start: 0.8250 (m100) cc_final: 0.7612 (m100)
REVERT: F   74 ASN cc_start: 0.7692 (t0) cc_final: 0.7378 (t0)
REVERT: H   44 LYS cc_start: 0.8338 (tptt) cc_final: 0.7836 (tttt)
REVERT: C  141 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7408 (tt)
REVERT: C  217 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7615 (mt)
REVERT: C  332 ILE cc_start: 0.8985 (mp) cc_final: 0.8503 (pt)
REVERT: C  383 ASN cc_start: 0.8405 (t0) cc_final: 0.7729 (m-40)
REVERT: G   36 TRP cc_start: 0.8385 (m100) cc_final: 0.7821 (m-10)
REVERT: G   64 VAL cc_start: 0.8745 (OUTLIER) cc_final: 0.8514 (p)
REVERT: I   77 ILE cc_start: 0.8020 (mt) cc_final: 0.7607 (mt)
REVERT: I   93 TYR cc_start: 0.7402 (t80) cc_final: 0.7141 (t80)
  outliers start: 107
  outliers final: 67
  residues processed: 329
  average time/residue: 0.1035
  time to fit residues: 51.8126
Evaluate side-chains
  304 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 229
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  290 CYS
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  396 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain C residue  141 LEU
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  267 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  290 CYS
Chi-restraints excluded: chain C residue  407 ILE
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 158 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 95 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 132 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 186 optimal weight:    5.9990
   chunk 166 optimal weight:    0.0060
   chunk 133 optimal weight:    0.2980
   chunk 47 optimal weight:    5.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 114 GLN
** F  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 114 GLN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 ASN
G 114 GLN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.172258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.136284 restraints weight = 22764.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.140114 restraints weight = 13612.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.142446 restraints weight = 9997.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.143954 restraints weight = 8376.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.144517 restraints weight = 7512.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.1556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15952  Z= 0.116
  Angle     :  0.592  12.070  21638  Z= 0.301
  Chirality :  0.042   0.225   2514
  Planarity :  0.003   0.038   2736
  Dihedral  :  5.446  45.126   2201
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.63 %
    Favored  : 91.37 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 25.90 %
    Favored  : 68.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.18), residues: 2016
  helix:  1.14 (0.26), residues: 414
  sheet: -0.66 (0.22), residues: 552
  loop : -2.18 (0.17), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  76 
 TYR   0.012   0.001   TYR C 417 
 PHE   0.012   0.001   PHE C 505 
 TRP   0.017   0.001   TRP D 108 
 HIS   0.008   0.001   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (15924)
  covalent geometry    : angle       0.58907 (21582)
  SS BOND              : bond        0.00233 (   28)
  SS BOND              : angle       1.23139 (   56)
  hydrogen bonds       : bond        0.02855 (  622)
  hydrogen bonds       : angle       5.20183 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 253
  time to evaluate  : 0.613 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7812 (mm)
REVERT: B  334 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7401 (mm)
REVERT: B  383 ASN cc_start: 0.8205 (t0) cc_final: 0.7539 (m-40)
REVERT: B  448 ASP cc_start: 0.8113 (p0) cc_final: 0.7645 (m-30)
REVERT: D   36 TRP cc_start: 0.8250 (m100) cc_final: 0.7717 (m100)
REVERT: D   64 VAL cc_start: 0.8741 (OUTLIER) cc_final: 0.8451 (m)
REVERT: D  104 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6679 (pmm)
REVERT: E   38 TYR cc_start: 0.6918 (m-10) cc_final: 0.6698 (m-10)
REVERT: E   81 GLN cc_start: 0.8176 (pp30) cc_final: 0.7731 (pp30)
REVERT: A   59 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7916 (mm)
REVERT: A  225 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8091 (mm-40)
REVERT: A  244 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8896 (t)
REVERT: A  251 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7730 (ttm)
REVERT: A  486 ASP cc_start: 0.5648 (m-30) cc_final: 0.5259 (t0)
REVERT: F   36 TRP cc_start: 0.8285 (m100) cc_final: 0.7779 (m100)
REVERT: F   74 ASN cc_start: 0.7568 (t0) cc_final: 0.7290 (t0)
REVERT: H   44 LYS cc_start: 0.8322 (tptt) cc_final: 0.7812 (tttt)
REVERT: C  217 ILE cc_start: 0.8078 (OUTLIER) cc_final: 0.7605 (mt)
REVERT: C  332 ILE cc_start: 0.9019 (mp) cc_final: 0.8594 (pt)
REVERT: C  383 ASN cc_start: 0.8362 (t0) cc_final: 0.7666 (m-40)
REVERT: G   36 TRP cc_start: 0.8294 (m100) cc_final: 0.7781 (m-10)
REVERT: G   64 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8453 (p)
REVERT: I   77 ILE cc_start: 0.8009 (mt) cc_final: 0.7612 (mt)
  outliers start: 102
  outliers final: 66
  residues processed: 327
  average time/residue: 0.1015
  time to fit residues: 50.8455
Evaluate side-chains
  310 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 235
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  396 MET
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain D residue  106 VAL
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  159 HIS
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  244 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  407 ILE
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain G residue  107 THR
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 93 optimal weight:    0.7980
   chunk 112 optimal weight:    9.9990
   chunk 1 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 195 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 178 optimal weight:    9.9990
   chunk 100 optimal weight:    8.9990
   chunk 127 optimal weight:    0.0030
   chunk 134 optimal weight:    6.9990
   chunk 138 optimal weight:    6.9990
   overall best weight:    1.5596

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

Flipped N/Q/H residues before XYZ refinement:
B 283 GLN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  82 GLN
E  55 HIS
F  82 GLN
I   1 GLN
** I   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.165342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.130294 restraints weight = 22378.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.133665 restraints weight = 13829.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.135823 restraints weight = 10361.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.136975 restraints weight = 8753.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.137872 restraints weight = 7963.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15952  Z= 0.178
  Angle     :  0.641  12.974  21638  Z= 0.327
  Chirality :  0.043   0.241   2514
  Planarity :  0.003   0.032   2736
  Dihedral  :  5.415  44.318   2196
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.07 %
    Favored  : 89.93 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 26.40 %
    Favored  : 67.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.52 (0.18), residues: 2016
  helix:  1.11 (0.26), residues: 414
  sheet: -0.63 (0.22), residues: 519
  loop : -2.15 (0.17), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 507 
 TYR   0.013   0.001   TYR B 417 
 PHE   0.018   0.002   PHE D  29 
 TRP   0.020   0.001   TRP D 108 
 HIS   0.013   0.002   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (15924)
  covalent geometry    : angle       0.63814 (21582)
  SS BOND              : bond        0.00344 (   28)
  SS BOND              : angle       1.30344 (   56)
  hydrogen bonds       : bond        0.03142 (  622)
  hydrogen bonds       : angle       5.26428 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  356 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 107
    poor density    : 249
  time to evaluate  : 0.422 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.7937 (mm)
REVERT: B  334 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7646 (mm)
REVERT: B  383 ASN cc_start: 0.8303 (t0) cc_final: 0.7667 (m-40)
REVERT: D   28 MET cc_start: 0.8156 (tpp) cc_final: 0.7873 (tpp)
REVERT: D   36 TRP cc_start: 0.8512 (m100) cc_final: 0.7908 (m100)
REVERT: E   38 TYR cc_start: 0.6990 (m-10) cc_final: 0.6790 (m-10)
REVERT: E   55 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7405 (m90)
REVERT: E   81 GLN cc_start: 0.8050 (pp30) cc_final: 0.7551 (pp30)
REVERT: A   59 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.8056 (mm)
REVERT: A  251 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7748 (ttm)
REVERT: A  396 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8037 (ptm)
REVERT: F   36 TRP cc_start: 0.8379 (m100) cc_final: 0.7857 (m100)
REVERT: H   44 LYS cc_start: 0.8316 (tptt) cc_final: 0.7828 (tttt)
REVERT: C   49 ARG cc_start: 0.8818 (ttp80) cc_final: 0.8455 (ttp80)
REVERT: C  217 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7478 (mt)
REVERT: C  383 ASN cc_start: 0.8484 (t0) cc_final: 0.7731 (m-40)
REVERT: G   36 TRP cc_start: 0.8547 (m100) cc_final: 0.7827 (m-10)
REVERT: G   64 VAL cc_start: 0.8712 (OUTLIER) cc_final: 0.8438 (p)
REVERT: I   56 ARG cc_start: 0.7116 (mtp85) cc_final: 0.6898 (mtp180)
  outliers start: 107
  outliers final: 75
  residues processed: 325
  average time/residue: 0.0998
  time to fit residues: 48.8039
Evaluate side-chains
  320 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 237
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  318 THR
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   55 HIS
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue   94 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  164 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  334 LEU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   62 ASP
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   98 ASP
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain C residue   36 THR
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  440 ASP
Chi-restraints excluded: chain C residue  442 VAL
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue   87 ARG
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   50 ILE
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 131 optimal weight:   10.0000
   chunk 28 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 81 optimal weight:    9.9990
   chunk 185 optimal weight:    0.8980
   chunk 123 optimal weight:    0.9980
   chunk 132 optimal weight:    7.9990
   chunk 161 optimal weight:    1.9990
   chunk 179 optimal weight:    0.0870
   chunk 104 optimal weight:    0.8980
   chunk 192 optimal weight:   10.0000
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
D   3 GLN
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** 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 = 0.4078 r_free = 0.4078 target = 0.169856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.133590 restraints weight = 22542.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137270 restraints weight = 13513.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.139661 restraints weight = 10028.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.141087 restraints weight = 8394.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.141706 restraints weight = 7561.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15952  Z= 0.124
  Angle     :  0.617  13.092  21638  Z= 0.312
  Chirality :  0.043   0.256   2514
  Planarity :  0.003   0.039   2736
  Dihedral  :  5.311  44.838   2196
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.88 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 26.90 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.48 (0.18), residues: 2016
  helix:  1.15 (0.26), residues: 414
  sheet: -0.61 (0.22), residues: 519
  loop : -2.12 (0.17), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG F  76 
 TYR   0.013   0.001   TYR C 417 
 PHE   0.012   0.001   PHE C 505 
 TRP   0.018   0.001   TRP D 108 
 HIS   0.013   0.003   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (15924)
  covalent geometry    : angle       0.61475 (21582)
  SS BOND              : bond        0.00223 (   28)
  SS BOND              : angle       1.14533 (   56)
  hydrogen bonds       : bond        0.02921 (  622)
  hydrogen bonds       : angle       5.22585 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 238
  time to evaluate  : 0.547 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7845 (mm)
REVERT: B  167 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7154 (tp)
REVERT: B  334 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7554 (mm)
REVERT: B  383 ASN cc_start: 0.8287 (t0) cc_final: 0.7667 (m-40)
REVERT: B  448 ASP cc_start: 0.8096 (p0) cc_final: 0.7619 (m-30)
REVERT: D   28 MET cc_start: 0.8024 (tpp) cc_final: 0.7705 (tpp)
REVERT: D   34 MET cc_start: 0.7235 (mmm) cc_final: 0.6898 (mtt)
REVERT: D   36 TRP cc_start: 0.8309 (m100) cc_final: 0.7690 (m100)
REVERT: E   81 GLN cc_start: 0.8026 (pp30) cc_final: 0.7377 (pp30)
REVERT: A   59 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.7960 (mm)
REVERT: A  251 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7768 (ttm)
REVERT: A  486 ASP cc_start: 0.5806 (m-30) cc_final: 0.5347 (t0)
REVERT: F   36 TRP cc_start: 0.8302 (m100) cc_final: 0.7844 (m100)
REVERT: F   74 ASN cc_start: 0.7725 (t0) cc_final: 0.7413 (t0)
REVERT: F   83 MET cc_start: 0.7302 (OUTLIER) cc_final: 0.7000 (mtp)
REVERT: H   44 LYS cc_start: 0.8317 (tptt) cc_final: 0.7797 (tttt)
REVERT: C   49 ARG cc_start: 0.8616 (ttp80) cc_final: 0.8287 (ttp80)
REVERT: C  217 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7580 (mt)
REVERT: C  295 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7803 (pt0)
REVERT: C  297 LEU cc_start: 0.7323 (tt) cc_final: 0.6877 (tp)
REVERT: C  383 ASN cc_start: 0.8473 (t0) cc_final: 0.7714 (m-40)
REVERT: G   64 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8446 (p)
  outliers start: 93
  outliers final: 70
  residues processed: 301
  average time/residue: 0.1079
  time to fit residues: 49.1235
Evaluate side-chains
  313 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 234
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  442 VAL
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    3 GLN
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   71 SER
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue   94 ASP
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   39 GLN
Chi-restraints excluded: chain F residue   62 ASP
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  290 CYS
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  370 MET
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  442 VAL
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    2 VAL
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 116 optimal weight:    0.3980
   chunk 135 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 127 optimal weight:    5.9990
   chunk 20 optimal weight:    8.9990
   chunk 9 optimal weight:    0.7980
   chunk 157 optimal weight:    0.9990
   chunk 192 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 388 ASN
** D   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 388 ASN
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 388 ASN
** I   6 GLN ** 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 = 0.4083 r_free = 0.4083 target = 0.170330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.133851 restraints weight = 22681.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.137650 restraints weight = 13568.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.140061 restraints weight = 10006.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.141517 restraints weight = 8367.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.142095 restraints weight = 7533.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15952  Z= 0.126
  Angle     :  0.617  13.367  21638  Z= 0.312
  Chirality :  0.043   0.274   2514
  Planarity :  0.003   0.037   2736
  Dihedral  :  5.225  44.048   2194
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 26.96 %
    Favored  : 67.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.18), residues: 2016
  helix:  1.23 (0.26), residues: 414
  sheet: -0.59 (0.22), residues: 519
  loop : -2.11 (0.17), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 507 
 TYR   0.012   0.001   TYR C 417 
 PHE   0.011   0.001   PHE B 505 
 TRP   0.018   0.001   TRP G  36 
 HIS   0.012   0.002   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (15924)
  covalent geometry    : angle       0.61484 (21582)
  SS BOND              : bond        0.00318 (   28)
  SS BOND              : angle       1.12584 (   56)
  hydrogen bonds       : bond        0.02901 (  622)
  hydrogen bonds       : angle       5.17649 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 244
  time to evaluate  : 0.622 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8109 (OUTLIER) cc_final: 0.7833 (mm)
REVERT: B  167 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.7222 (tp)
REVERT: B  334 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7536 (mm)
REVERT: B  383 ASN cc_start: 0.8217 (t0) cc_final: 0.7609 (m-40)
REVERT: D   28 MET cc_start: 0.8095 (tpp) cc_final: 0.7848 (tpp)
REVERT: D   36 TRP cc_start: 0.8302 (m100) cc_final: 0.7716 (m100)
REVERT: E   81 GLN cc_start: 0.7952 (pp30) cc_final: 0.7284 (pp30)
REVERT: A   59 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7969 (mm)
REVERT: A  251 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7965 (ttm)
REVERT: A  396 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.8003 (ptm)
REVERT: A  486 ASP cc_start: 0.5785 (m-30) cc_final: 0.5350 (t0)
REVERT: F   36 TRP cc_start: 0.8204 (m100) cc_final: 0.7744 (m100)
REVERT: F   74 ASN cc_start: 0.7665 (t0) cc_final: 0.7337 (t0)
REVERT: F   83 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6969 (mtp)
REVERT: H   44 LYS cc_start: 0.8295 (tptt) cc_final: 0.7760 (tttt)
REVERT: C   49 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8344 (ttp80)
REVERT: C  217 ILE cc_start: 0.8072 (OUTLIER) cc_final: 0.7583 (mt)
REVERT: C  295 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7795 (pt0)
REVERT: C  297 LEU cc_start: 0.7268 (tt) cc_final: 0.6784 (tp)
REVERT: C  332 ILE cc_start: 0.8105 (OUTLIER) cc_final: 0.7905 (mm)
REVERT: C  383 ASN cc_start: 0.8480 (t0) cc_final: 0.7709 (m-40)
REVERT: G   36 TRP cc_start: 0.8130 (m100) cc_final: 0.7874 (m-10)
REVERT: G   64 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8435 (p)
REVERT: I   56 ARG cc_start: 0.7044 (mtp180) cc_final: 0.6778 (mtp85)
REVERT: I   93 TYR cc_start: 0.7318 (t80) cc_final: 0.6992 (t80)
  outliers start: 92
  outliers final: 70
  residues processed: 308
  average time/residue: 0.1117
  time to fit residues: 51.8330
Evaluate side-chains
  316 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 235
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue   94 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   62 ASP
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   64 ILE
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  290 CYS
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  440 ASP
Chi-restraints excluded: chain C residue  442 VAL
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    2 VAL
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue   87 ARG
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 172 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 179 optimal weight:    9.9990
   chunk 37 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 119 optimal weight:    0.5980
   chunk 161 optimal weight:    0.7980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 331 ASN
G 114 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.166834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.129757 restraints weight = 22738.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.133563 restraints weight = 13494.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.135953 restraints weight = 9923.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.137392 restraints weight = 8317.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.137931 restraints weight = 7506.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  15952  Z= 0.174
  Angle     :  0.661  13.822  21638  Z= 0.337
  Chirality :  0.044   0.282   2514
  Planarity :  0.004   0.039   2736
  Dihedral  :  5.337  43.006   2194
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 27.18 %
    Favored  : 67.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.18), residues: 2016
  helix:  1.18 (0.26), residues: 414
  sheet: -0.63 (0.22), residues: 519
  loop : -2.15 (0.17), residues: 1083

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 507 
 TYR   0.013   0.001   TYR C 417 
 PHE   0.014   0.001   PHE G  29 
 TRP   0.020   0.002   TRP G  36 
 HIS   0.011   0.002   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (15924)
  covalent geometry    : angle       0.65790 (21582)
  SS BOND              : bond        0.00317 (   28)
  SS BOND              : angle       1.47408 (   56)
  hydrogen bonds       : bond        0.03135 (  622)
  hydrogen bonds       : angle       5.25518 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 247
  time to evaluate  : 0.573 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7913 (mm)
REVERT: B  167 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7228 (tp)
REVERT: B  334 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7709 (mm)
REVERT: B  383 ASN cc_start: 0.8151 (t0) cc_final: 0.7619 (m-40)
REVERT: D   28 MET cc_start: 0.8072 (tpp) cc_final: 0.7859 (tpp)
REVERT: D   36 TRP cc_start: 0.8436 (m100) cc_final: 0.7819 (m100)
REVERT: E   56 ARG cc_start: 0.7368 (mtp180) cc_final: 0.7134 (mtp180)
REVERT: E   63 ARG cc_start: 0.7275 (ttm110) cc_final: 0.6771 (mtm110)
REVERT: E   81 GLN cc_start: 0.8044 (pp30) cc_final: 0.7377 (pp30)
REVERT: A   59 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7961 (mm)
REVERT: A  251 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7879 (ttm)
REVERT: A  396 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.8055 (ptm)
REVERT: A  486 ASP cc_start: 0.5829 (m-30) cc_final: 0.5424 (t0)
REVERT: F   36 TRP cc_start: 0.8369 (m100) cc_final: 0.7865 (m100)
REVERT: F   83 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.6950 (mtp)
REVERT: H   44 LYS cc_start: 0.8323 (tptt) cc_final: 0.7771 (tttt)
REVERT: C   49 ARG cc_start: 0.8781 (ttp80) cc_final: 0.8413 (ttp80)
REVERT: C  217 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7591 (mt)
REVERT: C  295 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7770 (pt0)
REVERT: C  383 ASN cc_start: 0.8433 (t0) cc_final: 0.7731 (m-40)
REVERT: C  454 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8013 (p0)
REVERT: G   64 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8465 (p)
REVERT: I   56 ARG cc_start: 0.7149 (mtp180) cc_final: 0.6893 (mtp85)
  outliers start: 89
  outliers final: 73
  residues processed: 307
  average time/residue: 0.1108
  time to fit residues: 50.8840
Evaluate side-chains
  327 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 243
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  475 ILE
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue   94 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   62 ASP
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain H residue   10 VAL
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  290 CYS
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  370 MET
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  440 ASP
Chi-restraints excluded: chain C residue  454 ASN
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    2 VAL
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   62 ASP
Chi-restraints excluded: chain G residue   64 VAL
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue   87 ARG
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain G residue  106 VAL
Chi-restraints excluded: chain G residue  114 GLN
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 197 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9980
   chunk 166 optimal weight:    3.9990
   chunk 74 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 134 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 177 optimal weight:   10.0000
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
D   3 GLN
** D  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 270 GLN
** G 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I   6 GLN ** 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 = 0.4063 r_free = 0.4063 target = 0.167457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.132426 restraints weight = 22690.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.136335 restraints weight = 15884.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.136537 restraints weight = 12697.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.136989 restraints weight = 10494.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.137086 restraints weight = 9642.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
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      :  0.005   0.069  15952  Z= 0.195
  Angle     :  0.683  14.081  21638  Z= 0.348
  Chirality :  0.044   0.291   2514
  Planarity :  0.004   0.043   2736
  Dihedral  :  5.466  43.164   2194
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.02 %
    Favored  : 89.98 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 27.57 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.18), residues: 2016
  helix:  1.12 (0.26), residues: 414
  sheet: -0.71 (0.22), residues: 549
  loop : -2.20 (0.17), residues: 1053

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 507 
 TYR   0.020   0.002   TYR C 417 
 PHE   0.017   0.002   PHE G  29 
 TRP   0.036   0.002   TRP G  36 
 HIS   0.013   0.002   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 (15924)
  covalent geometry    : angle       0.67884 (21582)
  SS BOND              : bond        0.00329 (   28)
  SS BOND              : angle       1.70244 (   56)
  hydrogen bonds       : bond        0.03259 (  622)
  hydrogen bonds       : angle       5.35121 ( 1584)

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

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

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4032 Ramachandran restraints generated.
    2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 237
  time to evaluate  : 0.611 
Fit side-chains
REVERT: B   59 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8020 (mm)
REVERT: B  334 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7742 (mm)
REVERT: B  383 ASN cc_start: 0.8193 (t0) cc_final: 0.7628 (m-40)
REVERT: D   36 TRP cc_start: 0.8566 (m100) cc_final: 0.7999 (m100)
REVERT: E   63 ARG cc_start: 0.7292 (ttm110) cc_final: 0.6770 (mtm110)
REVERT: E   81 GLN cc_start: 0.8055 (pp30) cc_final: 0.7382 (pp30)
REVERT: E   93 TYR cc_start: 0.7534 (t80) cc_final: 0.7290 (t80)
REVERT: A   59 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8060 (mm)
REVERT: A  251 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7931 (ttm)
REVERT: A  396 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8081 (ptm)
REVERT: A  486 ASP cc_start: 0.5940 (m-30) cc_final: 0.5545 (t0)
REVERT: F   36 TRP cc_start: 0.8384 (m100) cc_final: 0.7942 (m100)
REVERT: F   83 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6985 (mtp)
REVERT: H   44 LYS cc_start: 0.8277 (tptt) cc_final: 0.7817 (tttt)
REVERT: C  217 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7654 (mt)
REVERT: C  295 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7749 (pt0)
REVERT: C  383 ASN cc_start: 0.8405 (t0) cc_final: 0.7694 (m-40)
REVERT: C  445 LYS cc_start: 0.8441 (mttt) cc_final: 0.7491 (pttm)
REVERT: C  454 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7970 (p0)
  outliers start: 91
  outliers final: 75
  residues processed: 299
  average time/residue: 0.1210
  time to fit residues: 53.8975
Evaluate side-chains
  313 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 84
    poor density    : 229
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   59 ILE
Chi-restraints excluded: chain B residue   96 LEU
Chi-restraints excluded: chain B residue  138 LEU
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  159 HIS
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain B residue  171 LEU
Chi-restraints excluded: chain B residue  174 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  278 VAL
Chi-restraints excluded: chain B residue  308 VAL
Chi-restraints excluded: chain B residue  309 ILE
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  420 THR
Chi-restraints excluded: chain B residue  423 THR
Chi-restraints excluded: chain B residue  432 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  475 ILE
Chi-restraints excluded: chain B residue  492 ILE
Chi-restraints excluded: chain D residue    3 GLN
Chi-restraints excluded: chain D residue    5 VAL
Chi-restraints excluded: chain D residue   24 VAL
Chi-restraints excluded: chain D residue   97 VAL
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  104 MET
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   49 ILE
Chi-restraints excluded: chain E residue   60 VAL
Chi-restraints excluded: chain E residue   94 ASP
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue   59 ILE
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  157 VAL
Chi-restraints excluded: chain A residue  171 LEU
Chi-restraints excluded: chain A residue  174 THR
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  249 THR
Chi-restraints excluded: chain A residue  250 TYR
Chi-restraints excluded: chain A residue  251 MET
Chi-restraints excluded: chain A residue  290 CYS
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  400 THR
Chi-restraints excluded: chain A residue  422 CYS
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  452 VAL
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain F residue   62 ASP
Chi-restraints excluded: chain F residue   71 SER
Chi-restraints excluded: chain F residue   83 MET
Chi-restraints excluded: chain F residue  100 LEU
Chi-restraints excluded: chain F residue  106 VAL
Chi-restraints excluded: chain F residue  116 THR
Chi-restraints excluded: chain H residue   48 VAL
Chi-restraints excluded: chain H residue   60 VAL
Chi-restraints excluded: chain H residue   77 ILE
Chi-restraints excluded: chain H residue  100 VAL
Chi-restraints excluded: chain C residue  138 LEU
Chi-restraints excluded: chain C residue  144 VAL
Chi-restraints excluded: chain C residue  159 HIS
Chi-restraints excluded: chain C residue  164 VAL
Chi-restraints excluded: chain C residue  217 ILE
Chi-restraints excluded: chain C residue  249 THR
Chi-restraints excluded: chain C residue  250 TYR
Chi-restraints excluded: chain C residue  253 THR
Chi-restraints excluded: chain C residue  278 VAL
Chi-restraints excluded: chain C residue  290 CYS
Chi-restraints excluded: chain C residue  295 GLU
Chi-restraints excluded: chain C residue  370 MET
Chi-restraints excluded: chain C residue  422 CYS
Chi-restraints excluded: chain C residue  423 THR
Chi-restraints excluded: chain C residue  440 ASP
Chi-restraints excluded: chain C residue  454 ASN
Chi-restraints excluded: chain C residue  492 ILE
Chi-restraints excluded: chain G residue    2 VAL
Chi-restraints excluded: chain G residue    5 VAL
Chi-restraints excluded: chain G residue   62 ASP
Chi-restraints excluded: chain G residue   71 SER
Chi-restraints excluded: chain G residue   87 ARG
Chi-restraints excluded: chain G residue  100 LEU
Chi-restraints excluded: chain I residue   10 VAL
Chi-restraints excluded: chain I residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 201
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 165 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 184 optimal weight:    0.3980
   chunk 28 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 177 optimal weight:    3.9990
   chunk 195 optimal weight:    0.0030
   chunk 141 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.8192

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

Flipped N/Q/H residues before XYZ refinement:
D   3 GLN
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   3 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.171456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.136782 restraints weight = 22705.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.139075 restraints weight = 15088.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.140290 restraints weight = 11434.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.140794 restraints weight = 9827.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.141035 restraints weight = 9425.037|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.2014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  15952  Z= 0.143
  Angle     :  0.669  13.811  21638  Z= 0.341
  Chirality :  0.044   0.281   2514
  Planarity :  0.004   0.046   2736
  Dihedral  :  5.448  47.221   2193
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.47 %
    Favored  : 90.53 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 28.18 %
    Favored  : 67.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.18), residues: 2016
  helix:  1.18 (0.26), residues: 414
  sheet: -0.61 (0.22), residues: 543
  loop : -2.19 (0.17), residues: 1059

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 507 
 TYR   0.022   0.001   TYR A 417 
 PHE   0.015   0.001   PHE C 483 
 TRP   0.042   0.002   TRP G  36 
 HIS   0.014   0.002   HIS F  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15924)
  covalent geometry    : angle       0.66278 (21582)
  SS BOND              : bond        0.00334 (   28)
  SS BOND              : angle       1.93439 (   56)
  hydrogen bonds       : bond        0.03092 (  622)
  hydrogen bonds       : angle       5.34569 ( 1584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2388.70 seconds
wall clock time: 42 minutes 19.81 seconds (2539.81 seconds total)