Starting phenix.real_space_refine
on Wed Mar  4 08:52:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dmp_30766/03_2026/7dmp_30766.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dmp_30766/03_2026/7dmp_30766.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dmp_30766/03_2026/7dmp_30766.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dmp_30766/03_2026/7dmp_30766.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dmp_30766/03_2026/7dmp_30766.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dmp_30766/03_2026/7dmp_30766.map"
  }
  resolution = 3.2
  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=   0.000 sd=   0.001
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      38      5.16       5
     C    7866      2.51       5
     N    2090      2.21       5
     O    2314      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 59 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12308
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 2704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2704
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 31, 'TRANS': 304}
          Chain breaks: 4
    Chain: "b"
      Number of atoms: 2704
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2704
          Classifications: {'peptide': 336}
          Link IDs: {'PTRANS': 31, 'TRANS': 304}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1521
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 4, 'TRANS': 181}
    Chain: "a"
      Number of atoms: 1521
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1521
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 4, 'TRANS': 181}
    Chain: "C"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1929
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 12, 'TRANS': 229}
          Chain breaks: 2
    Chain: "c"
      Number of atoms: 1929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1929
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 12, 'TRANS': 229}
          Chain breaks: 2
  Time building chain proxies: 2.80, per 1000 atoms: 0.23
  Number of scatterers: 12308
  At special positions: 0
  Unit cell: (110.16, 84.66, 223.38, 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      38     16.00
     O    2314      8.00
     N    2090      7.00
     C    7866      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 680.2 milliseconds
  

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2780

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 16 sheets defined
      17.1% alpha, 28.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid 277 through 291
      removed outlier: 3.720A  pdb=" N   GLU B 281 " --> pdb=" O   LEU B 277 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   THR B 285 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
      removed outlier: 5.113A  pdb=" N   ALA B 288 " --> pdb=" O   GLU B 284 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LEU B 289 " --> pdb=" O   THR B 285 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   PHE B 290 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 313 through 325
      removed outlier: 3.652A  pdb=" N   TYR B 320 " --> pdb=" O   GLU B 316 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE B 321 " --> pdb=" O   SER B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 345
      removed outlier: 3.576A  pdb=" N   ASP B 345 " --> pdb=" O   LYS B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 492
      removed outlier: 3.769A  pdb=" N   ARG B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 538
      removed outlier: 3.551A  pdb=" N   LEU B 535 " --> pdb=" O   GLN B 531 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 599
      removed outlier: 3.963A  pdb=" N   GLU B 598 " --> pdb=" O   PRO B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 688
      removed outlier: 3.542A  pdb=" N   GLU B 687 " --> pdb=" O   SER B 683 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 278 through 285
      removed outlier: 3.551A  pdb=" N   THR b 285 " --> pdb=" O   GLU b 281 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 286 through 289
    Processing helix  chain 'b' and resid 314 through 325
    Processing helix  chain 'b' and resid 334 through 345
    Processing helix  chain 'b' and resid 479 through 494
      removed outlier: 3.589A  pdb=" N   LEU b 483 " --> pdb=" O   GLU b 479 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 533 through 538
      removed outlier: 3.647A  pdb=" N   SER b 538 " --> pdb=" O   ASP b 534 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 595 through 599
      removed outlier: 4.077A  pdb=" N   GLU b 598 " --> pdb=" O   PRO b 595 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ASP b 599 " --> pdb=" O   ILE b 596 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'b' and resid 595 through 599'
    Processing helix  chain 'b' and resid 683 through 690
      removed outlier: 3.561A  pdb=" N   PHE b 690 " --> pdb=" O   GLU b 686 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 5 through 9
    Processing helix  chain 'C' and resid 24 through 39
      removed outlier: 4.150A  pdb=" N   MET C  33 " --> pdb=" O   LEU C  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 96
      removed outlier: 3.785A  pdb=" N   ALA C  93 " --> pdb=" O   THR C  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 99
      No H-bonds generated for 'chain 'C' and resid 97 through 99'
    Processing helix  chain 'C' and resid 135 through 149
    Processing helix  chain 'C' and resid 177 through 181
      removed outlier: 3.580A  pdb=" N   GLU C 180 " --> pdb=" O   PRO C 177 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   VAL C 181 " --> pdb=" O   LEU C 178 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 177 through 181'
    Processing helix  chain 'C' and resid 271 through 276
    Processing helix  chain 'c' and resid 24 through 39
      removed outlier: 3.504A  pdb=" N   LEU c  28 " --> pdb=" O   ARG c  24 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   MET c  33 " --> pdb=" O   LEU c  29 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 64 through 68
      removed outlier: 4.050A  pdb=" N   GLN c  67 " --> pdb=" O   SER c  64 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   LEU c  68 " --> pdb=" O   GLU c  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'c' and resid 64 through 68'
    Processing helix  chain 'c' and resid 89 through 96
      removed outlier: 3.912A  pdb=" N   ILE c  96 " --> pdb=" O   MET c  92 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 136 through 151
    Processing helix  chain 'c' and resid 183 through 187
      removed outlier: 3.627A  pdb=" N   SER c 186 " --> pdb=" O   LYS c 183 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 271 through 276
    Processing sheet with id=AA1, first strand: chain 'B' and resid 441 through 442
      removed outlier: 5.839A  pdb=" N   GLU B 369 " --> pdb=" O   PHE B 354 " (cutoff:3.500A)
      removed outlier: 5.123A  pdb=" N   PHE B 354 " --> pdb=" O   GLU B 369 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   TRP B 355 " --> pdb=" O   ASN B 644 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   SER B 637 " --> pdb=" O   ALA B 623 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ALA B 623 " --> pdb=" O   SER B 637 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 496 through 498
    Processing sheet with id=AA3, first strand: chain 'b' and resid 441 through 442
      removed outlier: 3.614A  pdb=" N   PHE b 431 " --> pdb=" O   ALA b 368 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU b 369 " --> pdb=" O   PHE b 354 " (cutoff:3.500A)
      removed outlier: 5.537A  pdb=" N   PHE b 354 " --> pdb=" O   GLU b 369 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   GLU b 371 " --> pdb=" O   CYS b 352 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   CYS b 352 " --> pdb=" O   GLU b 371 " (cutoff:3.500A)
      removed outlier: 15.264A  pdb=" N   PHE b 642 " --> pdb=" O   ARG b 351 " (cutoff:3.500A)
      removed outlier: 10.789A  pdb=" N   ARG b 353 " --> pdb=" O   PHE b 642 " (cutoff:3.500A)
      removed outlier: 9.937A  pdb=" N   ASN b 644 " --> pdb=" O   ARG b 353 " (cutoff:3.500A)
      removed outlier: 6.107A  pdb=" N   TRP b 355 " --> pdb=" O   ASN b 644 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   TYR b 646 " --> pdb=" O   TRP b 355 " (cutoff:3.500A)
      removed outlier: 5.370A  pdb=" N   ALA b 633 " --> pdb=" O   SER b 627 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'b' and resid 497 through 498
    Processing sheet with id=AA5, first strand: chain 'A' and resid 19 through 20
      removed outlier: 5.854A  pdb=" N   GLN A  56 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLU A  49 " --> pdb=" O   HIS A  54 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   HIS A  54 " --> pdb=" O   GLU A  49 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   GLN A  79 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   VAL A  72 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   HIS A  77 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ARG A  89 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A 104 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   GLU A  91 " --> pdb=" O   GLN A 102 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   GLN A 102 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   GLU A  93 " --> pdb=" O   HIS A 100 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR A 114 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR A 127 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLU A 116 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLN A 125 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 19 through 20
      removed outlier: 5.854A  pdb=" N   GLN A  56 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLU A  49 " --> pdb=" O   HIS A  54 " (cutoff:3.500A)
      removed outlier: 4.937A  pdb=" N   HIS A  54 " --> pdb=" O   GLU A  49 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   GLN A  79 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   VAL A  72 " --> pdb=" O   HIS A  77 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   HIS A  77 " --> pdb=" O   VAL A  72 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ARG A  89 " --> pdb=" O   VAL A 104 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   VAL A 104 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
      removed outlier: 7.144A  pdb=" N   GLU A  91 " --> pdb=" O   GLN A 102 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   GLN A 102 " --> pdb=" O   GLU A  91 " (cutoff:3.500A)
      removed outlier: 4.915A  pdb=" N   GLU A  93 " --> pdb=" O   HIS A 100 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   THR A 114 " --> pdb=" O   THR A 127 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   THR A 127 " --> pdb=" O   THR A 114 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLU A 116 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 5.373A  pdb=" N   GLN A 125 " --> pdb=" O   GLU A 116 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   CYS A 180 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   GLU A 197 " --> pdb=" O   HIS A 183 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'a' and resid 34 through 37
      removed outlier: 3.574A  pdb=" N   SER a  47 " --> pdb=" O   GLN a  56 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   GLN a  56 " --> pdb=" O   SER a  47 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU a  49 " --> pdb=" O   HIS a  54 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   HIS a  54 " --> pdb=" O   GLU a  49 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   GLN a  79 " --> pdb=" O   ASP a  70 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL a  72 " --> pdb=" O   HIS a  77 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   HIS a  77 " --> pdb=" O   VAL a  72 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   GLN a 102 " --> pdb=" O   GLU a  93 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ALA a  95 " --> pdb=" O   HIS a 100 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   HIS a 100 " --> pdb=" O   ALA a  95 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   GLN a 125 " --> pdb=" O   GLU a 116 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'a' and resid 34 through 37
      removed outlier: 3.574A  pdb=" N   SER a  47 " --> pdb=" O   GLN a  56 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   GLN a  56 " --> pdb=" O   SER a  47 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   GLU a  49 " --> pdb=" O   HIS a  54 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   HIS a  54 " --> pdb=" O   GLU a  49 " (cutoff:3.500A)
      removed outlier: 5.793A  pdb=" N   GLN a  79 " --> pdb=" O   ASP a  70 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   VAL a  72 " --> pdb=" O   HIS a  77 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   HIS a  77 " --> pdb=" O   VAL a  72 " (cutoff:3.500A)
      removed outlier: 5.407A  pdb=" N   GLN a 102 " --> pdb=" O   GLU a  93 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ALA a  95 " --> pdb=" O   HIS a 100 " (cutoff:3.500A)
      removed outlier: 5.316A  pdb=" N   HIS a 100 " --> pdb=" O   ALA a  95 " (cutoff:3.500A)
      removed outlier: 5.581A  pdb=" N   GLN a 125 " --> pdb=" O   GLU a 116 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   CYS a 180 " --> pdb=" O   PHE a 176 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   GLU a 181 " --> pdb=" O   GLU a 198 " (cutoff:3.500A)
      removed outlier: 4.512A  pdb=" N   GLU a 198 " --> pdb=" O   GLU a 181 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'a' and resid 163 through 164
    Processing sheet with id=AB1, first strand: chain 'C' and resid 44 through 48
      removed outlier: 6.670A  pdb=" N   ILE C  59 " --> pdb=" O   TRP C  47 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LYS C  72 " --> pdb=" O   GLY C  62 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TYR C  75 " --> pdb=" O   SER C  83 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   SER C  83 " --> pdb=" O   TYR C  75 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 153 through 154
    Processing sheet with id=AB3, first strand: chain 'C' and resid 226 through 230
      removed outlier: 5.109A  pdb=" N   LEU C 247 " --> pdb=" O   SER C 241 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'c' and resid 43 through 48
      removed outlier: 5.442A  pdb=" N   VAL c  44 " --> pdb=" O   LEU c  63 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   LEU c  63 " --> pdb=" O   VAL c  44 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE c  46 " --> pdb=" O   GLN c  61 " (cutoff:3.500A)
      removed outlier: 5.688A  pdb=" N   GLN c  61 " --> pdb=" O   PHE c  46 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'c' and resid 110 through 113
    Processing sheet with id=AB6, first strand: chain 'c' and resid 153 through 154
    Processing sheet with id=AB7, first strand: chain 'c' and resid 226 through 230
      removed outlier: 4.815A  pdb=" N   LEU c 247 " --> pdb=" O   SER c 241 " (cutoff:3.500A)

    455 hydrogen bonds defined for protein.
    1203 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.35 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3461
        1.33 -     1.45: 2386
        1.45 -     1.57: 6734
        1.57 -     1.69: 1
        1.69 -     1.81: 64
  Bond restraints: 12646
  Sorted by residual:
  bond pdb=" C   ILE C 221 "
       pdb=" N   PRO C 222 "
    ideal  model  delta    sigma   weight residual
    1.332  1.372 -0.040 8.20e-03 1.49e+04 2.38e+01
  bond pdb=" C   ILE c 221 "
       pdb=" N   PRO c 222 "
    ideal  model  delta    sigma   weight residual
    1.337  1.376 -0.039 1.24e-02 6.50e+03 9.85e+00
  bond pdb=" C   TRP b 630 "
       pdb=" O   TRP b 630 "
    ideal  model  delta    sigma   weight residual
    1.246  1.225  0.021 9.20e-03 1.18e+04 5.37e+00
  bond pdb=" C   VAL B 314 "
       pdb=" O   VAL B 314 "
    ideal  model  delta    sigma   weight residual
    1.237  1.213  0.024 1.17e-02 7.31e+03 4.17e+00
  bond pdb=" C   SER c  21 "
       pdb=" N   PRO c  22 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.82e+00
  ... (remaining 12641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 16583
        1.83 -     3.65: 467
        3.65 -     5.48: 65
        5.48 -     7.31: 25
        7.31 -     9.14: 12
  Bond angle restraints: 17152
  Sorted by residual:
  angle pdb=" N   VAL a  27 "
        pdb=" CA  VAL a  27 "
        pdb=" C   VAL a  27 "
      ideal   model   delta    sigma   weight residual
     113.71  109.11    4.60 9.50e-01 1.11e+00 2.34e+01
  angle pdb=" C   ALA a  95 "
        pdb=" N   ASP a  96 "
        pdb=" CA  ASP a  96 "
      ideal   model   delta    sigma   weight residual
     121.54  130.68   -9.14 1.91e+00 2.74e-01 2.29e+01
  angle pdb=" C   ILE b 617 "
        pdb=" N   PRO b 618 "
        pdb=" CA  PRO b 618 "
      ideal   model   delta    sigma   weight residual
     119.05  124.17   -5.12 1.11e+00 8.12e-01 2.13e+01
  angle pdb=" C   ASN B 478 "
        pdb=" N   GLU B 479 "
        pdb=" CA  GLU B 479 "
      ideal   model   delta    sigma   weight residual
     121.54  129.83   -8.29 1.91e+00 2.74e-01 1.89e+01
  angle pdb=" N   TYR b 620 "
        pdb=" CA  TYR b 620 "
        pdb=" C   TYR b 620 "
      ideal   model   delta    sigma   weight residual
     109.11  115.08   -5.97 1.42e+00 4.96e-01 1.77e+01
  ... (remaining 17147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.01: 6672
       18.01 -    36.01: 603
       36.01 -    54.02: 100
       54.02 -    72.03: 29
       72.03 -    90.03: 22
  Dihedral angle restraints: 7426
    sinusoidal: 3038
      harmonic: 4388
  Sorted by residual:
  dihedral pdb=" CA  SER C  21 "
           pdb=" C   SER C  21 "
           pdb=" N   PRO C  22 "
           pdb=" CA  PRO C  22 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.33   22.67     0      5.00e+00 4.00e-02 2.06e+01
  dihedral pdb=" C   ASN a 165 "
           pdb=" N   ASN a 165 "
           pdb=" CA  ASN a 165 "
           pdb=" CB  ASN a 165 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.48   10.88     0      2.50e+00 1.60e-01 1.90e+01
  dihedral pdb=" CA  PRO C  22 "
           pdb=" C   PRO C  22 "
           pdb=" N   ASP C  23 "
           pdb=" CA  ASP C  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.32  -20.68     0      5.00e+00 4.00e-02 1.71e+01
  ... (remaining 7423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1502
       0.072 -    0.144: 244
       0.144 -    0.217: 16
       0.217 -    0.289: 3
       0.289 -    0.361: 1
  Chirality restraints: 1766
  Sorted by residual:
  chirality pdb=" CA  ASN a 165 "
            pdb=" N   ASN a 165 "
            pdb=" C   ASN a 165 "
            pdb=" CB  ASN a 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" CA  LYS a 166 "
            pdb=" N   LYS a 166 "
            pdb=" C   LYS a 166 "
            pdb=" CB  LYS a 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.04e+00
  chirality pdb=" CA  ASP a  96 "
            pdb=" N   ASP a  96 "
            pdb=" C   ASP a  96 "
            pdb=" CB  ASP a  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.41e+00
  ... (remaining 1763 not shown)

  Planarity restraints: 2248
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 435 "   -0.040 5.00e-02 4.00e+02   5.99e-02 5.74e+00
        pdb=" N   PRO B 436 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO B 436 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B 436 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA c  69 "    0.038 5.00e-02 4.00e+02   5.72e-02 5.24e+00
        pdb=" N   PRO c  70 "   -0.099 5.00e-02 4.00e+02
        pdb=" CA  PRO c  70 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO c  70 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER c  21 "    0.035 5.00e-02 4.00e+02   5.37e-02 4.62e+00
        pdb=" N   PRO c  22 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO c  22 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO c  22 "    0.030 5.00e-02 4.00e+02
  ... (remaining 2245 not shown)

  Histogram of nonbonded interaction distances:
        1.02 -     1.80: 1
        1.80 -     2.57: 111
        2.57 -     3.35: 14164
        3.35 -     4.12: 31027
        4.12 -     4.90: 55617
  Nonbonded interactions: 100920
  Sorted by model distance:
  nonbonded pdb=" OH  TYR b 634 "
            pdb=" CG  GLN c  18 "
     model   vdw
     1.020 3.440
  nonbonded pdb=" OH  TYR b 634 "
            pdb=" CD  GLN c  18 "
     model   vdw
     1.948 3.270
  nonbonded pdb=" OD1 ASN b 615 "
            pdb=" OD2 ASP c  23 "
     model   vdw
     1.987 3.040
  nonbonded pdb=" CG2 VAL b 326 "
            pdb=" CE1 TYR b 634 "
     model   vdw
     2.052 3.760
  nonbonded pdb=" OE2 GLU B 316 "
            pdb=" NZ  LYS B 641 "
     model   vdw
     2.119 3.120
  ... (remaining 100915 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 'a'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'b'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'c'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.890
  Find NCS groups from input model:        0.140
  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:1.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12646  Z= 0.190
  Angle     :  0.758   9.135  17152  Z= 0.438
  Chirality :  0.052   0.361   1766
  Planarity :  0.006   0.060   2248
  Dihedral  : 14.924  90.032   4646
  Min Nonbonded Distance : 1.020

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  7.12 %
    Favored  : 91.27 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -4.33 (0.17), residues: 1492
  helix: -3.09 (0.24), residues: 218
  sheet: -2.68 (0.23), residues: 372
  loop : -3.01 (0.16), residues: 902

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG b 484 
 TYR   0.014   0.001   TYR b 334 
 PHE   0.015   0.001   PHE B 636 
 TRP   0.013   0.001   TRP B 542 
 HIS   0.004   0.001   HIS A 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12646)
  covalent geometry    : angle       0.75772 (17152)
  hydrogen bonds       : bond        0.16127 (  363)
  hydrogen bonds       : angle       8.03617 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  318 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 297
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  351 ARG cc_start: 0.6407 (ttp80) cc_final: 0.5807 (ttp80)
REVERT: b  619 GLN cc_start: 0.6054 (OUTLIER) cc_final: 0.5829 (tt0)
REVERT: A   89 ARG cc_start: 0.8233 (ptt90) cc_final: 0.7690 (ptt-90)
REVERT: A  102 GLN cc_start: 0.7474 (mm-40) cc_final: 0.7204 (mm110)
REVERT: A  155 LEU cc_start: 0.8164 (mt) cc_final: 0.7933 (mt)
REVERT: a  109 ASN cc_start: 0.8196 (p0) cc_final: 0.7904 (p0)
REVERT: a  110 ASN cc_start: 0.6173 (t0) cc_final: 0.5917 (t0)
REVERT: a  164 MET cc_start: 0.7802 (mmm) cc_final: 0.7601 (mmm)
REVERT: C   20 LEU cc_start: 0.6258 (mt) cc_final: 0.5969 (mt)
REVERT: C  270 MET cc_start: 0.5713 (mmt) cc_final: 0.5376 (mmt)
REVERT: c   94 MET cc_start: 0.6584 (ptp) cc_final: 0.6109 (mtm)
REVERT: c  104 MET cc_start: 0.7583 (tpt) cc_final: 0.7337 (tpp)
REVERT: c  134 ILE cc_start: 0.6809 (tp) cc_final: 0.6397 (tp)
REVERT: c  230 MET cc_start: 0.6623 (mmm) cc_final: 0.6269 (mmt)
REVERT: c  270 MET cc_start: 0.5249 (mmm) cc_final: 0.4925 (mmm)
  outliers start: 21
  outliers final: 12
  residues processed: 314
  average time/residue: 0.1353
  time to fit residues: 57.7917
Evaluate side-chains
  203 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 190
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  315 MET
Chi-restraints excluded: chain B residue  616 LEU
Chi-restraints excluded: chain B residue  617 ILE
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain b residue  310 SER
Chi-restraints excluded: chain b residue  612 LEU
Chi-restraints excluded: chain b residue  619 GLN
Chi-restraints excluded: chain b residue  622 ILE
Chi-restraints excluded: chain b residue  625 LEU
Chi-restraints excluded: chain b residue  627 SER
Chi-restraints excluded: chain b residue  636 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.5980
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.3980
   chunk 149 optimal weight:    0.3980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
B 323 GLN
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 495 HIS
B 541 ASN
b 478 ASN
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 619 GLN
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  31 HIS
A 100 HIS
A 110 ASN
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 157 HIS
A 160 GLN
a 123 HIS
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
c 189 HIS
c 251 HIS
c 257 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.143315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.112389 restraints weight = 18472.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3674 rms_B_bonded: 2.86
r_work: 0.3539 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12646  Z= 0.240
  Angle     :  0.691   7.460  17152  Z= 0.357
  Chirality :  0.047   0.182   1766
  Planarity :  0.005   0.047   2248
  Dihedral  :  6.141  59.104   1717
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 14.24 %
    Favored  : 83.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.70 (0.18), residues: 1492
  helix: -1.76 (0.29), residues: 220
  sheet: -2.69 (0.23), residues: 368
  loop : -2.62 (0.17), residues: 904

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG b 438 
 TYR   0.021   0.002   TYR C 262 
 PHE   0.018   0.002   PHE b 645 
 TRP   0.017   0.002   TRP A 141 
 HIS   0.006   0.001   HIS b 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 (12646)
  covalent geometry    : angle       0.69065 (17152)
  hydrogen bonds       : bond        0.03931 (  363)
  hydrogen bonds       : angle       6.22935 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 221
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  428 TYR cc_start: 0.8232 (m-80) cc_final: 0.8031 (m-10)
REVERT: A   66 ARG cc_start: 0.7815 (ttp80) cc_final: 0.7537 (mtp-110)
REVERT: a   37 ARG cc_start: 0.7510 (ttm110) cc_final: 0.6584 (mtm110)
REVERT: a   38 LEU cc_start: 0.7657 (mm) cc_final: 0.6984 (mp)
REVERT: a  109 ASN cc_start: 0.8168 (p0) cc_final: 0.7578 (p0)
REVERT: a  111 ASP cc_start: 0.7891 (m-30) cc_final: 0.7612 (m-30)
REVERT: C   75 TYR cc_start: 0.8401 (p90) cc_final: 0.7748 (p90)
REVERT: c   92 MET cc_start: 0.7614 (ptm) cc_final: 0.7116 (ttp)
REVERT: c   94 MET cc_start: 0.7304 (ptp) cc_final: 0.6565 (mtm)
REVERT: c  146 GLN cc_start: 0.8507 (mt0) cc_final: 0.8190 (mt0)
REVERT: c  230 MET cc_start: 0.7632 (mmm) cc_final: 0.7348 (mmt)
REVERT: c  250 TYR cc_start: 0.7379 (p90) cc_final: 0.6565 (p90)
  outliers start: 29
  outliers final: 15
  residues processed: 237
  average time/residue: 0.1220
  time to fit residues: 40.5856
Evaluate side-chains
  194 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 179
  time to evaluate  : 0.474 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  452 VAL
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain b residue  457 ILE
Chi-restraints excluded: chain b residue  478 ASN
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue  168 HIS
Chi-restraints excluded: chain c residue  214 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9980
   chunk 125 optimal weight:    0.3980
   chunk 78 optimal weight:    1.9990
   chunk 121 optimal weight:    0.4980
   chunk 2 optimal weight:    0.5980
   chunk 25 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 143 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 495 HIS
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 110 ASN
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** 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 = 0.4040 r_free = 0.4040 target = 0.139442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.109153 restraints weight = 18992.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 2.82
r_work: 0.3491 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12646  Z= 0.170
  Angle     :  0.609   8.205  17152  Z= 0.311
  Chirality :  0.044   0.164   1766
  Planarity :  0.004   0.041   2248
  Dihedral  :  4.522  22.193   1692
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.08 %
    Favored  : 81.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.23 (0.19), residues: 1492
  helix: -1.07 (0.32), residues: 222
  sheet: -2.54 (0.25), residues: 348
  loop : -2.33 (0.18), residues: 922

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG b 438 
 TYR   0.019   0.002   TYR B 365 
 PHE   0.021   0.002   PHE B 558 
 TRP   0.014   0.001   TRP b 440 
 HIS   0.012   0.001   HIS b 544 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12646)
  covalent geometry    : angle       0.60887 (17152)
  hydrogen bonds       : bond        0.03300 (  363)
  hydrogen bonds       : angle       5.80948 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 202
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: B  428 TYR cc_start: 0.8141 (m-80) cc_final: 0.7809 (m-80)
REVERT: b  522 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7146 (pm20)
REVERT: A   42 ASP cc_start: 0.5433 (m-30) cc_final: 0.5103 (m-30)
REVERT: A  185 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6924 (tm-30)
REVERT: a   37 ARG cc_start: 0.7540 (ttm110) cc_final: 0.6422 (mtm110)
REVERT: a   38 LEU cc_start: 0.7668 (mm) cc_final: 0.7011 (mp)
REVERT: a  109 ASN cc_start: 0.8267 (p0) cc_final: 0.7614 (p0)
REVERT: a  111 ASP cc_start: 0.7906 (m-30) cc_final: 0.7587 (m-30)
REVERT: C  188 PHE cc_start: 0.7171 (m-10) cc_final: 0.6876 (m-10)
REVERT: c   94 MET cc_start: 0.7364 (ptp) cc_final: 0.6828 (mtm)
REVERT: c  230 MET cc_start: 0.7590 (mmm) cc_final: 0.7305 (mmt)
REVERT: c  250 TYR cc_start: 0.7417 (p90) cc_final: 0.6626 (p90)
REVERT: c  256 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8205 (ptmt)
  outliers start: 35
  outliers final: 24
  residues processed: 225
  average time/residue: 0.1182
  time to fit residues: 37.6443
Evaluate side-chains
  203 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 179
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  457 ILE
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue   95 GLN
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  214 LEU
Chi-restraints excluded: chain c residue  221 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0870
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 544 HIS
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a 110 ASN
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 234 ASN
** C 251 HIS ** 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 = 0.3990 r_free = 0.3990 target = 0.135613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.104886 restraints weight = 18900.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 2.81
r_work: 0.3439 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.3788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  12646  Z= 0.210
  Angle     :  0.631   7.675  17152  Z= 0.323
  Chirality :  0.045   0.169   1766
  Planarity :  0.004   0.040   2248
  Dihedral  :  4.643  21.070   1692
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 17.23 %
    Favored  : 79.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.03 (0.20), residues: 1492
  helix: -0.89 (0.33), residues: 224
  sheet: -2.57 (0.25), residues: 352
  loop : -2.12 (0.18), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.019   0.002   TYR B 365 
 PHE   0.017   0.002   PHE B 558 
 TRP   0.013   0.002   TRP B 542 
 HIS   0.011   0.001   HIS b 544 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 (12646)
  covalent geometry    : angle       0.63111 (17152)
  hydrogen bonds       : bond        0.03368 (  363)
  hydrogen bonds       : angle       5.77600 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 197
  time to evaluate  : 0.471 
Fit side-chains
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8385 (mp)
REVERT: B  428 TYR cc_start: 0.8291 (m-80) cc_final: 0.7932 (m-80)
REVERT: A   66 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7603 (mtp-110)
REVERT: A  185 GLU cc_start: 0.7272 (tm-30) cc_final: 0.6932 (tm-30)
REVERT: a   37 ARG cc_start: 0.7616 (ttm110) cc_final: 0.6478 (mtm110)
REVERT: a   38 LEU cc_start: 0.7515 (mm) cc_final: 0.6856 (mp)
REVERT: a   90 TYR cc_start: 0.7983 (t80) cc_final: 0.7779 (t80)
REVERT: a  109 ASN cc_start: 0.8369 (p0) cc_final: 0.7749 (p0)
REVERT: a  111 ASP cc_start: 0.7979 (m-30) cc_final: 0.7616 (m-30)
REVERT: C   32 LEU cc_start: 0.7854 (mt) cc_final: 0.7639 (mt)
REVERT: c   12 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5091 (mp)
REVERT: c   92 MET cc_start: 0.7750 (ptm) cc_final: 0.7408 (ttp)
REVERT: c   94 MET cc_start: 0.7398 (ptp) cc_final: 0.6850 (mtm)
REVERT: c  149 LYS cc_start: 0.7740 (mmmt) cc_final: 0.7347 (mmtm)
REVERT: c  230 MET cc_start: 0.7793 (mmm) cc_final: 0.7501 (mmt)
REVERT: c  250 TYR cc_start: 0.7457 (p90) cc_final: 0.6584 (p90)
REVERT: c  270 MET cc_start: 0.7097 (mmm) cc_final: 0.6714 (mmm)
  outliers start: 46
  outliers final: 37
  residues processed: 227
  average time/residue: 0.1182
  time to fit residues: 38.2056
Evaluate side-chains
  218 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 179
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  593 LEU
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain b residue  331 ASP
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  457 ILE
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain b residue  545 HIS
Chi-restraints excluded: chain b residue  692 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain c residue   12 LEU
Chi-restraints excluded: chain c residue   45 LEU
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  153 ILE
Chi-restraints excluded: chain c residue  214 LEU
Chi-restraints excluded: chain c residue  221 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    0.8980
   chunk 137 optimal weight:    2.9990
   chunk 146 optimal weight:    1.9990
   chunk 109 optimal weight:    0.9990
   chunk 88 optimal weight:    3.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 657 ASN
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 680 ASN
** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
a 110 ASN
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** 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 = 0.3977 r_free = 0.3977 target = 0.134682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.104039 restraints weight = 18870.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3548 rms_B_bonded: 2.79
r_work: 0.3413 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7390
moved from start:          0.4105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12646  Z= 0.187
  Angle     :  0.619   8.011  17152  Z= 0.316
  Chirality :  0.044   0.169   1766
  Planarity :  0.004   0.042   2248
  Dihedral  :  4.670  21.268   1692
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.71 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.53 %
    Favored  : 78.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.97 (0.20), residues: 1492
  helix: -1.00 (0.32), residues: 236
  sheet: -2.59 (0.25), residues: 348
  loop : -2.02 (0.19), residues: 908

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 158 
 TYR   0.023   0.002   TYR C 258 
 PHE   0.017   0.002   PHE B 558 
 TRP   0.014   0.002   TRP c  82 
 HIS   0.014   0.001   HIS b 544 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (12646)
  covalent geometry    : angle       0.61859 (17152)
  hydrogen bonds       : bond        0.03230 (  363)
  hydrogen bonds       : angle       5.73810 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 199
  time to evaluate  : 0.489 
Fit side-chains
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8433 (mp)
REVERT: B  428 TYR cc_start: 0.8316 (m-80) cc_final: 0.7888 (m-80)
REVERT: B  692 MET cc_start: 0.4235 (pmm) cc_final: 0.4031 (pmm)
REVERT: A   66 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7611 (mtp-110)
REVERT: A  111 ASP cc_start: 0.8025 (m-30) cc_final: 0.7761 (m-30)
REVERT: A  155 LEU cc_start: 0.8118 (mt) cc_final: 0.7825 (mp)
REVERT: A  185 GLU cc_start: 0.7383 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: a   37 ARG cc_start: 0.7487 (ttm110) cc_final: 0.6616 (mtm110)
REVERT: a   38 LEU cc_start: 0.7503 (mm) cc_final: 0.6863 (mp)
REVERT: a  109 ASN cc_start: 0.8396 (p0) cc_final: 0.7744 (p0)
REVERT: a  111 ASP cc_start: 0.8047 (m-30) cc_final: 0.7711 (m-30)
REVERT: C   32 LEU cc_start: 0.7883 (mt) cc_final: 0.7635 (mt)
REVERT: C  168 HIS cc_start: 0.7078 (m170) cc_final: 0.6824 (m-70)
REVERT: c   12 LEU cc_start: 0.5647 (OUTLIER) cc_final: 0.5380 (mp)
REVERT: c   29 LEU cc_start: 0.8357 (mm) cc_final: 0.8110 (mm)
REVERT: c   92 MET cc_start: 0.7799 (ptm) cc_final: 0.7397 (ttp)
REVERT: c   94 MET cc_start: 0.7485 (ptp) cc_final: 0.6883 (mtm)
REVERT: c  149 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7484 (mmtm)
REVERT: c  230 MET cc_start: 0.7703 (mmm) cc_final: 0.7429 (mmt)
REVERT: c  250 TYR cc_start: 0.7445 (p90) cc_final: 0.6536 (p90)
REVERT: c  270 MET cc_start: 0.6894 (mmm) cc_final: 0.6487 (mmm)
  outliers start: 48
  outliers final: 35
  residues processed: 231
  average time/residue: 0.1138
  time to fit residues: 37.9748
Evaluate side-chains
  218 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 181
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  457 ILE
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  470 ILE
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain b residue  545 HIS
Chi-restraints excluded: chain b residue  692 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain a residue   31 HIS
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain a residue  185 GLU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain c residue   12 LEU
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  214 LEU
Chi-restraints excluded: chain c residue  221 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 106 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0670
   chunk 95 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 57 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   chunk 96 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
a 110 ASN
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** 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 = 0.3967 r_free = 0.3967 target = 0.133991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.104290 restraints weight = 18750.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 2.66
r_work: 0.3415 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.4312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12646  Z= 0.172
  Angle     :  0.619   9.614  17152  Z= 0.315
  Chirality :  0.044   0.169   1766
  Planarity :  0.004   0.042   2248
  Dihedral  :  4.658  20.975   1692
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.98 %
    Favored  : 92.02 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 18.22 %
    Favored  : 78.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.90 (0.20), residues: 1492
  helix: -0.87 (0.33), residues: 236
  sheet: -2.68 (0.25), residues: 330
  loop : -1.96 (0.19), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG a  30 
 TYR   0.020   0.002   TYR B 365 
 PHE   0.018   0.002   PHE B 558 
 TRP   0.011   0.001   TRP a 117 
 HIS   0.015   0.001   HIS a  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (12646)
  covalent geometry    : angle       0.61936 (17152)
  hydrogen bonds       : bond        0.03211 (  363)
  hydrogen bonds       : angle       5.68673 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 191
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8436 (mp)
REVERT: B  428 TYR cc_start: 0.8335 (m-80) cc_final: 0.7864 (m-80)
REVERT: A   66 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7528 (mtp-110)
REVERT: A  108 VAL cc_start: 0.8827 (m) cc_final: 0.8614 (p)
REVERT: A  185 GLU cc_start: 0.7399 (tm-30) cc_final: 0.7098 (tm-30)
REVERT: a   37 ARG cc_start: 0.7509 (ttm110) cc_final: 0.6831 (ttp-110)
REVERT: a   38 LEU cc_start: 0.7485 (OUTLIER) cc_final: 0.6928 (mp)
REVERT: a  109 ASN cc_start: 0.8369 (p0) cc_final: 0.7626 (p0)
REVERT: a  111 ASP cc_start: 0.8043 (m-30) cc_final: 0.7712 (m-30)
REVERT: C   20 LEU cc_start: 0.7063 (mt) cc_final: 0.6755 (mt)
REVERT: C  168 HIS cc_start: 0.7187 (m170) cc_final: 0.6927 (m90)
REVERT: c   29 LEU cc_start: 0.8370 (mm) cc_final: 0.8089 (mm)
REVERT: c   92 MET cc_start: 0.7790 (ptm) cc_final: 0.7401 (ttp)
REVERT: c   94 MET cc_start: 0.7490 (ptp) cc_final: 0.6874 (mtm)
REVERT: c  149 LYS cc_start: 0.7838 (mmmt) cc_final: 0.7512 (mmtm)
REVERT: c  230 MET cc_start: 0.7691 (mmm) cc_final: 0.7440 (mmt)
REVERT: c  250 TYR cc_start: 0.7423 (p90) cc_final: 0.6534 (p90)
REVERT: c  270 MET cc_start: 0.6858 (mmm) cc_final: 0.6545 (mmm)
REVERT: c  275 MET cc_start: 0.8719 (mmm) cc_final: 0.8400 (mmt)
  outliers start: 49
  outliers final: 37
  residues processed: 226
  average time/residue: 0.1135
  time to fit residues: 36.7790
Evaluate side-chains
  219 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 180
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain b residue  316 GLU
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  457 ILE
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain b residue  545 HIS
Chi-restraints excluded: chain b residue  692 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain a residue   31 HIS
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain a residue  185 GLU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   78 ASN
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  214 LEU
Chi-restraints excluded: chain c residue  221 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 141 optimal weight:    0.4980
   chunk 135 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 96 optimal weight:    0.4980
   chunk 31 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** B 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
a 110 ASN
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** 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 = 0.3945 r_free = 0.3945 target = 0.132290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.102414 restraints weight = 18755.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 2.65
r_work: 0.3398 rms_B_bonded: 3.30 restraints_weight: 0.5000
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.4531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  12646  Z= 0.200
  Angle     :  0.638   9.195  17152  Z= 0.324
  Chirality :  0.045   0.180   1766
  Planarity :  0.004   0.054   2248
  Dihedral  :  4.750  20.986   1692
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 18.53 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.86 (0.20), residues: 1492
  helix: -0.87 (0.32), residues: 236
  sheet: -2.63 (0.25), residues: 338
  loop : -1.93 (0.19), residues: 918

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG a  30 
 TYR   0.020   0.002   TYR B 667 
 PHE   0.018   0.002   PHE B 558 
 TRP   0.014   0.002   TRP c  82 
 HIS   0.012   0.001   HIS a  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12646)
  covalent geometry    : angle       0.63799 (17152)
  hydrogen bonds       : bond        0.03328 (  363)
  hydrogen bonds       : angle       5.70505 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 187
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8402 (mp)
REVERT: B  428 TYR cc_start: 0.8310 (m-80) cc_final: 0.7873 (m-80)
REVERT: A   66 ARG cc_start: 0.7842 (ttp80) cc_final: 0.7521 (mtp-110)
REVERT: a   37 ARG cc_start: 0.7534 (ttm110) cc_final: 0.6909 (ttp-110)
REVERT: a   38 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.6945 (mp)
REVERT: a  109 ASN cc_start: 0.8414 (p0) cc_final: 0.7667 (p0)
REVERT: a  111 ASP cc_start: 0.8055 (m-30) cc_final: 0.7682 (m-30)
REVERT: C  168 HIS cc_start: 0.7240 (m170) cc_final: 0.6991 (m90)
REVERT: c   29 LEU cc_start: 0.8403 (mm) cc_final: 0.8109 (mm)
REVERT: c   92 MET cc_start: 0.7827 (ptm) cc_final: 0.7491 (ttp)
REVERT: c   94 MET cc_start: 0.7453 (ptp) cc_final: 0.6841 (mtm)
REVERT: c  149 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7576 (mmtm)
REVERT: c  230 MET cc_start: 0.7725 (mmm) cc_final: 0.7460 (mmt)
REVERT: c  250 TYR cc_start: 0.7409 (p90) cc_final: 0.6510 (p90)
REVERT: c  270 MET cc_start: 0.6919 (mmm) cc_final: 0.6708 (mmm)
REVERT: c  272 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.8047 (tp)
REVERT: c  275 MET cc_start: 0.8733 (mmm) cc_final: 0.8239 (mmt)
  outliers start: 48
  outliers final: 44
  residues processed: 220
  average time/residue: 0.1067
  time to fit residues: 34.2383
Evaluate side-chains
  222 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 175
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  469 VAL
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  676 ILE
Chi-restraints excluded: chain b residue  316 GLU
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain b residue  545 HIS
Chi-restraints excluded: chain b residue  588 VAL
Chi-restraints excluded: chain b residue  655 VAL
Chi-restraints excluded: chain b residue  692 MET
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain a residue   31 HIS
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue  110 ASN
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain a residue  185 GLU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain C residue  255 THR
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  132 VAL
Chi-restraints excluded: chain c residue  153 ILE
Chi-restraints excluded: chain c residue  214 LEU
Chi-restraints excluded: chain c residue  221 ILE
Chi-restraints excluded: chain c residue  272 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 133 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 82 optimal weight:    0.2980
   chunk 121 optimal weight:    0.3980
   chunk 105 optimal weight:    0.6980
   chunk 48 optimal weight:    0.4980
   chunk 140 optimal weight:    0.0570
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
B 450 GLN
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b 544 HIS
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
a 110 ASN
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.134084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.103507 restraints weight = 18657.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.77
r_work: 0.3395 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12646  Z= 0.150
  Angle     :  0.617   9.154  17152  Z= 0.313
  Chirality :  0.044   0.167   1766
  Planarity :  0.004   0.050   2248
  Dihedral  :  4.672  19.771   1692
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 13.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.07 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.79 (0.20), residues: 1492
  helix: -0.75 (0.33), residues: 236
  sheet: -2.56 (0.24), residues: 356
  loop : -1.87 (0.19), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG c 171 
 TYR   0.023   0.002   TYR A 113 
 PHE   0.016   0.001   PHE B 558 
 TRP   0.014   0.001   TRP c  82 
 HIS   0.014   0.001   HIS a  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (12646)
  covalent geometry    : angle       0.61718 (17152)
  hydrogen bonds       : bond        0.03142 (  363)
  hydrogen bonds       : angle       5.59406 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 192
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8374 (mp)
REVERT: B  428 TYR cc_start: 0.8306 (m-80) cc_final: 0.7848 (m-80)
REVERT: B  619 GLN cc_start: 0.6134 (mt0) cc_final: 0.5774 (tt0)
REVERT: A   66 ARG cc_start: 0.7820 (ttp80) cc_final: 0.7482 (mtp-110)
REVERT: A  155 LEU cc_start: 0.8336 (mt) cc_final: 0.8080 (mp)
REVERT: a   37 ARG cc_start: 0.7618 (ttm110) cc_final: 0.6904 (ttp-110)
REVERT: a   38 LEU cc_start: 0.7447 (OUTLIER) cc_final: 0.6903 (mp)
REVERT: C   20 LEU cc_start: 0.7049 (mt) cc_final: 0.6753 (mt)
REVERT: C  168 HIS cc_start: 0.7274 (m170) cc_final: 0.6992 (m90)
REVERT: c   29 LEU cc_start: 0.8389 (mm) cc_final: 0.8112 (mm)
REVERT: c   92 MET cc_start: 0.7875 (ptm) cc_final: 0.7562 (ttp)
REVERT: c   94 MET cc_start: 0.7450 (ptp) cc_final: 0.6809 (mtm)
REVERT: c  149 LYS cc_start: 0.7932 (mmmt) cc_final: 0.7569 (mmtm)
REVERT: c  230 MET cc_start: 0.7731 (mmm) cc_final: 0.7488 (mmt)
REVERT: c  250 TYR cc_start: 0.7361 (p90) cc_final: 0.6495 (p90)
REVERT: c  270 MET cc_start: 0.6939 (mmm) cc_final: 0.6595 (mmm)
REVERT: c  272 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7948 (tp)
REVERT: c  275 MET cc_start: 0.8752 (mmm) cc_final: 0.8174 (mmt)
  outliers start: 46
  outliers final: 36
  residues processed: 225
  average time/residue: 0.1103
  time to fit residues: 35.6039
Evaluate side-chains
  216 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 177
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain b residue  316 GLU
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  544 HIS
Chi-restraints excluded: chain b residue  545 HIS
Chi-restraints excluded: chain b residue  655 VAL
Chi-restraints excluded: chain b residue  692 MET
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain a residue   31 HIS
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain a residue  185 GLU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue   89 THR
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  132 VAL
Chi-restraints excluded: chain c residue  221 ILE
Chi-restraints excluded: chain c residue  272 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 143 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 96 optimal weight:    0.1980
   chunk 80 optimal weight:    0.8980
   chunk 105 optimal weight:    0.5980
   chunk 60 optimal weight:    0.5980
   chunk 1 optimal weight:    0.1980
   chunk 102 optimal weight:    0.2980
   chunk 122 optimal weight:    0.5980
   chunk 39 optimal weight:    0.4980
   chunk 44 optimal weight:    0.4980
   overall best weight:    0.3380

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

Flipped N/Q/H residues before XYZ refinement:
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
a 110 ASN
** C 251 HIS ** 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 = 0.3975 r_free = 0.3975 target = 0.134661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.104189 restraints weight = 18702.807|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 2.78
r_work: 0.3417 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7385
moved from start:          0.4587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12646  Z= 0.140
  Angle     :  0.619   9.149  17152  Z= 0.312
  Chirality :  0.044   0.211   1766
  Planarity :  0.004   0.043   2248
  Dihedral  :  4.606  21.480   1692
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 13.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.06 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.72 (0.20), residues: 1492
  helix: -0.68 (0.33), residues: 236
  sheet: -2.52 (0.24), residues: 356
  loop : -1.83 (0.19), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 158 
 TYR   0.020   0.002   TYR A 113 
 PHE   0.015   0.001   PHE B 558 
 TRP   0.014   0.001   TRP c  82 
 HIS   0.010   0.001   HIS a  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (12646)
  covalent geometry    : angle       0.61851 (17152)
  hydrogen bonds       : bond        0.03100 (  363)
  hydrogen bonds       : angle       5.50934 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 180
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8392 (mp)
REVERT: B  428 TYR cc_start: 0.8313 (m-80) cc_final: 0.7846 (m-80)
REVERT: B  619 GLN cc_start: 0.6309 (mt0) cc_final: 0.5968 (tt0)
REVERT: A   66 ARG cc_start: 0.7819 (ttp80) cc_final: 0.7484 (mtp-110)
REVERT: A  155 LEU cc_start: 0.8324 (mt) cc_final: 0.8067 (mp)
REVERT: a   37 ARG cc_start: 0.7525 (ttm110) cc_final: 0.6849 (ttp-110)
REVERT: a   38 LEU cc_start: 0.7452 (mm) cc_final: 0.6880 (mp)
REVERT: C  168 HIS cc_start: 0.7364 (m170) cc_final: 0.7111 (m90)
REVERT: c   29 LEU cc_start: 0.8476 (mm) cc_final: 0.8216 (mm)
REVERT: c   92 MET cc_start: 0.7850 (ptm) cc_final: 0.7572 (ttp)
REVERT: c   94 MET cc_start: 0.7462 (ptp) cc_final: 0.6820 (mtm)
REVERT: c  149 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7557 (mmtm)
REVERT: c  230 MET cc_start: 0.7677 (mmm) cc_final: 0.7432 (mmt)
REVERT: c  250 TYR cc_start: 0.7358 (p90) cc_final: 0.6521 (p90)
REVERT: c  270 MET cc_start: 0.6869 (mmm) cc_final: 0.6553 (mmm)
REVERT: c  272 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7967 (tp)
REVERT: c  275 MET cc_start: 0.8753 (mmm) cc_final: 0.8179 (mmt)
  outliers start: 41
  outliers final: 34
  residues processed: 210
  average time/residue: 0.1089
  time to fit residues: 32.9990
Evaluate side-chains
  208 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  471 SER
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain b residue  316 GLU
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  588 VAL
Chi-restraints excluded: chain b residue  655 VAL
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain a residue   31 HIS
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain a residue  185 GLU
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   83 SER
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  132 VAL
Chi-restraints excluded: chain c residue  221 ILE
Chi-restraints excluded: chain c residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 133 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 124 optimal weight:    0.0970
   chunk 136 optimal weight:    0.5980
   chunk 11 optimal weight:    0.4980
   chunk 68 optimal weight:    3.9990
   chunk 107 optimal weight:    0.1980
   chunk 32 optimal weight:    0.6980
   chunk 123 optimal weight:    0.0980
   chunk 30 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.2978

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

Flipped N/Q/H residues before XYZ refinement:
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
a 110 ASN
C 133 GLN
** C 251 HIS ** 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 = 0.3984 r_free = 0.3984 target = 0.135307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.104961 restraints weight = 18685.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.78
r_work: 0.3433 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.4597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12646  Z= 0.136
  Angle     :  0.617   8.877  17152  Z= 0.312
  Chirality :  0.044   0.190   1766
  Planarity :  0.004   0.043   2248
  Dihedral  :  4.597  21.888   1692
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.77 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.37 %
    Favored  : 76.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.66 (0.20), residues: 1492
  helix: -0.64 (0.33), residues: 238
  sheet: -2.45 (0.24), residues: 356
  loop : -1.80 (0.19), residues: 898

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 158 
 TYR   0.026   0.002   TYR c 262 
 PHE   0.013   0.001   PHE B 558 
 TRP   0.012   0.001   TRP c  82 
 HIS   0.008   0.001   HIS b 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (12646)
  covalent geometry    : angle       0.61693 (17152)
  hydrogen bonds       : bond        0.03021 (  363)
  hydrogen bonds       : angle       5.46080 ( 1203)

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

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

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2984 Ramachandran restraints generated.
    1492 Oldfield, 0 Emsley, 1492 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 181
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: B  366 ILE cc_start: 0.8832 (OUTLIER) cc_final: 0.8387 (mp)
REVERT: B  428 TYR cc_start: 0.8299 (m-80) cc_final: 0.7990 (m-80)
REVERT: B  619 GLN cc_start: 0.6362 (mt0) cc_final: 0.6017 (tt0)
REVERT: b  441 VAL cc_start: 0.8603 (t) cc_final: 0.8353 (m)
REVERT: A   42 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5953 (m-30)
REVERT: A   66 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7480 (mtp-110)
REVERT: A  155 LEU cc_start: 0.8317 (mt) cc_final: 0.8058 (mp)
REVERT: a   37 ARG cc_start: 0.7519 (ttm110) cc_final: 0.6865 (ttp-110)
REVERT: a   38 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.6940 (mp)
REVERT: a  195 GLU cc_start: 0.7967 (tt0) cc_final: 0.7708 (tt0)
REVERT: C  168 HIS cc_start: 0.7335 (m170) cc_final: 0.7088 (m90)
REVERT: c   29 LEU cc_start: 0.8480 (mm) cc_final: 0.8225 (mm)
REVERT: c   92 MET cc_start: 0.7856 (ptm) cc_final: 0.7606 (ttp)
REVERT: c   94 MET cc_start: 0.7472 (ptp) cc_final: 0.6841 (mtm)
REVERT: c  149 LYS cc_start: 0.7918 (mmmt) cc_final: 0.7550 (mmtm)
REVERT: c  230 MET cc_start: 0.7630 (mmm) cc_final: 0.7381 (mmt)
REVERT: c  270 MET cc_start: 0.6794 (mmm) cc_final: 0.6412 (mmm)
REVERT: c  272 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.8005 (tp)
REVERT: c  275 MET cc_start: 0.8742 (mmm) cc_final: 0.8156 (mmt)
  outliers start: 40
  outliers final: 32
  residues processed: 209
  average time/residue: 0.1098
  time to fit residues: 32.9397
Evaluate side-chains
  208 residues out of total 1306 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 172
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 VAL
Chi-restraints excluded: chain B residue  366 ILE
Chi-restraints excluded: chain B residue  370 VAL
Chi-restraints excluded: chain B residue  435 VAL
Chi-restraints excluded: chain B residue  462 THR
Chi-restraints excluded: chain B residue  602 ILE
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain b residue  316 GLU
Chi-restraints excluded: chain b residue  370 VAL
Chi-restraints excluded: chain b residue  447 THR
Chi-restraints excluded: chain b residue  469 VAL
Chi-restraints excluded: chain b residue  501 PHE
Chi-restraints excluded: chain b residue  588 VAL
Chi-restraints excluded: chain b residue  655 VAL
Chi-restraints excluded: chain A residue   38 LEU
Chi-restraints excluded: chain A residue   42 ASP
Chi-restraints excluded: chain A residue   74 ASN
Chi-restraints excluded: chain A residue   97 ASP
Chi-restraints excluded: chain a residue   31 HIS
Chi-restraints excluded: chain a residue   38 LEU
Chi-restraints excluded: chain a residue  114 THR
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue   29 LEU
Chi-restraints excluded: chain C residue   45 LEU
Chi-restraints excluded: chain C residue   92 MET
Chi-restraints excluded: chain C residue   98 VAL
Chi-restraints excluded: chain C residue  131 VAL
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  153 ILE
Chi-restraints excluded: chain C residue  221 ILE
Chi-restraints excluded: chain c residue   51 LEU
Chi-restraints excluded: chain c residue   84 LEU
Chi-restraints excluded: chain c residue  130 VAL
Chi-restraints excluded: chain c residue  132 VAL
Chi-restraints excluded: chain c residue  221 ILE
Chi-restraints excluded: chain c residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 109 optimal weight:    0.9980
   chunk 102 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 145 optimal weight:    0.0980
   chunk 89 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** b 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
a  31 HIS
** a 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.133018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.102492 restraints weight = 18673.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 2.76
r_work: 0.3381 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.4776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12646  Z= 0.181
  Angle     :  0.642   9.078  17152  Z= 0.324
  Chirality :  0.045   0.168   1766
  Planarity :  0.004   0.045   2248
  Dihedral  :  4.677  21.573   1692
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.18 %
    Favored  : 91.82 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.21 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -2.67 (0.20), residues: 1492
  helix: -0.64 (0.33), residues: 236
  sheet: -2.46 (0.25), residues: 356
  loop : -1.81 (0.19), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 158 
 TYR   0.021   0.002   TYR c 262 
 PHE   0.015   0.002   PHE B 558 
 TRP   0.014   0.001   TRP c  82 
 HIS   0.015   0.001   HIS a  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (12646)
  covalent geometry    : angle       0.64168 (17152)
  hydrogen bonds       : bond        0.03195 (  363)
  hydrogen bonds       : angle       5.53608 ( 1203)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4039.44 seconds
wall clock time: 69 minutes 44.32 seconds (4184.32 seconds total)