Starting phenix.real_space_refine
on Sun May 18 17:10:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8szl_40920/05_2025/8szl_40920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8szl_40920/05_2025/8szl_40920.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8szl_40920/05_2025/8szl_40920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8szl_40920/05_2025/8szl_40920.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8szl_40920/05_2025/8szl_40920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8szl_40920/05_2025/8szl_40920.cif"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2706 atoms to isotropic.
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     124      5.16       5
     C    9573      2.51       5
     N    2600      2.21       5
     O    2784      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15081
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3759
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 488, 3750
          Classifications: {'peptide': 488}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 470}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
      Conformer: "B"
        Number of residues, atoms: 488, 3750
          Classifications: {'peptide': 488}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 470}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 3813
    Chain: "B"
      Number of atoms: 3780
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 492, 3780
          Classifications: {'peptide': 492}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 18, 'TRANS': 473}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "C"
      Number of atoms: 3771
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 490, 3765
          Classifications: {'peptide': 490}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 472}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
      Conformer: "B"
        Number of residues, atoms: 490, 3765
          Classifications: {'peptide': 490}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 472}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 3832
    Chain: "D"
      Number of atoms: 3771
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 490, 3765
          Classifications: {'peptide': 490}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 472}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 46
          Unresolved non-hydrogen angles: 54
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
      Conformer: "B"
        Number of residues, atoms: 490, 3762
          Classifications: {'peptide': 490}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 17, 'TRANS': 472}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved chain link dihedrals: 4
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 3828
  Time building chain proxies: 17.05, per 1000 atoms: 1.13
  Number of scatterers: 15081
  At special positions: 0
  Unit cell: (164.205, 171.585, 77.49, 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     124     16.00
     O    2784      8.00
     N    2600      7.00
     C    9573      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: 4.23
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3656

  Finding SS restraints...
    Secondary structure from input PDB file:
      98 helices and 12 sheets defined
      55.5% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.11
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 81
    Processing helix  chain 'A' and resid 89 through 94
      removed outlier: 3.593A  pdb=" N   THR A  94 " --> pdb=" O   HIS A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 122
      removed outlier: 3.532A  pdb=" N   VAL A 118 " --> pdb=" O   GLU A 114 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   GLN A 120 " --> pdb=" O   HIS A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.960A  pdb=" N   PHE A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LYS A 135 " --> pdb=" O   ASP A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 149
      removed outlier: 3.538A  pdb=" N   GLN A 146 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   PHE A 148 " --> pdb=" O   LEU A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 171
    Processing helix  chain 'A' and resid 220 through 234
      removed outlier: 4.415A  pdb=" N   LEU A 224 " --> pdb=" O   CYS A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 234 through 239
      removed outlier: 3.612A  pdb=" N   HIS A 239 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 276
    Processing helix  chain 'A' and resid 283 through 299
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 318 through 331
    Processing helix  chain 'A' and resid 339 through 352
      removed outlier: 3.537A  pdb=" N   ALA A 343 " --> pdb=" O   ASP A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 363
    Processing helix  chain 'A' and resid 382 through 397
      removed outlier: 3.628A  pdb=" N   VAL A 386 " --> pdb=" O   SER A 382 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ARG A 387 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ASN A 388 " --> pdb=" O   GLU A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 409
    Processing helix  chain 'A' and resid 444 through 459
      removed outlier: 3.699A  pdb=" N   LEU A 457 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASN A 459 " --> pdb=" O   VAL A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 496
      removed outlier: 3.581A  pdb=" N   ALA A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 508
      removed outlier: 3.718A  pdb=" N   ARG A 504 " --> pdb=" O   SER A 500 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A 505 " --> pdb=" O   ALA A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 530
    Processing helix  chain 'A' and resid 531 through 541
      removed outlier: 3.554A  pdb=" N   PHE A 537 " --> pdb=" O   GLU A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 564
      removed outlier: 3.530A  pdb=" N   ALA A 560 " --> pdb=" O   PRO A 556 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A 561 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 574
      removed outlier: 3.730A  pdb=" N   LYS A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   LEU A 571 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 81
    Processing helix  chain 'B' and resid 89 through 94
    Processing helix  chain 'B' and resid 105 through 107
      No H-bonds generated for 'chain 'B' and resid 105 through 107'
    Processing helix  chain 'B' and resid 108 through 122
      removed outlier: 3.604A  pdb=" N   SER B 113 " --> pdb=" O   ARG B 109 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   GLU B 114 " --> pdb=" O   ASP B 110 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   MET B 115 " --> pdb=" O   CYS B 111 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ARG B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   VAL B 119 " --> pdb=" O   MET B 115 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   GLN B 120 " --> pdb=" O   HIS B 116 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   GLU B 121 " --> pdb=" O   ARG B 117 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 137
      removed outlier: 3.667A  pdb=" N   PHE B 133 " --> pdb=" O   ASP B 129 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG B 134 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LYS B 135 " --> pdb=" O   ASP B 131 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   CYS B 136 " --> pdb=" O   LEU B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 149
      removed outlier: 3.791A  pdb=" N   PHE B 148 " --> pdb=" O   LEU B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 171
    Processing helix  chain 'B' and resid 221 through 234
    Processing helix  chain 'B' and resid 237 through 241
      removed outlier: 3.665A  pdb=" N   PHE B 241 " --> pdb=" O   VAL B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 276
    Processing helix  chain 'B' and resid 283 through 295
    Processing helix  chain 'B' and resid 308 through 313
    Processing helix  chain 'B' and resid 318 through 332
    Processing helix  chain 'B' and resid 339 through 352
      removed outlier: 3.639A  pdb=" N   ALA B 343 " --> pdb=" O   ASP B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 363
    Processing helix  chain 'B' and resid 364 through 369
    Processing helix  chain 'B' and resid 382 through 397
    Processing helix  chain 'B' and resid 398 through 400
      No H-bonds generated for 'chain 'B' and resid 398 through 400'
    Processing helix  chain 'B' and resid 401 through 409
    Processing helix  chain 'B' and resid 445 through 459
      removed outlier: 3.866A  pdb=" N   LEU B 457 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASN B 459 " --> pdb=" O   VAL B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 492
      removed outlier: 3.798A  pdb=" N   VAL B 487 " --> pdb=" O   ARG B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 508
      removed outlier: 4.122A  pdb=" N   LEU B 502 " --> pdb=" O   ASP B 498 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   ARG B 503 " --> pdb=" O   VAL B 499 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ARG B 504 " --> pdb=" O   SER B 500 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE B 505 " --> pdb=" O   ALA B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 521 through 528
    Processing helix  chain 'B' and resid 531 through 541
      removed outlier: 3.916A  pdb=" N   VAL B 535 " --> pdb=" O   HIS B 531 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   PHE B 537 " --> pdb=" O   GLU B 533 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   LEU B 538 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 563
      removed outlier: 3.507A  pdb=" N   ASP B 559 " --> pdb=" O   ILE B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 573
      removed outlier: 3.882A  pdb=" N   LYS B 570 " --> pdb=" O   LEU B 566 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   LEU B 571 " --> pdb=" O   GLU B 567 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 73
      No H-bonds generated for 'chain 'C' and resid 71 through 73'
    Processing helix  chain 'C' and resid 74 through 82
      removed outlier: 3.890A  pdb=" N   TYR C  78 " --> pdb=" O   ASP C  74 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 88 through 98
      removed outlier: 4.082A  pdb=" N   PHE C  92 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 122
      removed outlier: 3.659A  pdb=" N   VAL C 118 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 129 through 137
      removed outlier: 3.565A  pdb=" N   LYS C 135 " --> pdb=" O   ASP C 131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 140 through 149
    Processing helix  chain 'C' and resid 156 through 174
      removed outlier: 3.529A  pdb=" N   VAL C 164 " --> pdb=" O   PHE C 160 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ARG C 166 " --> pdb=" O   GLY C 162 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LYS C 172 " --> pdb=" O   PHE C 168 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLU C 173 " --> pdb=" O   GLU C 169 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   LEU C 174 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 233
      removed outlier: 4.092A  pdb=" N   LEU C 224 " --> pdb=" O   CYS C 220 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   THR C 232 " --> pdb=" O   ILE C 228 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 234 through 239
    Processing helix  chain 'C' and resid 267 through 278
      removed outlier: 3.610A  pdb=" N   VAL C 273 " --> pdb=" O   ALA C 269 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE C 278 " --> pdb=" O   VAL C 274 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 283 through 300
    Processing helix  chain 'C' and resid 307 through 316
      removed outlier: 3.875A  pdb=" N   SER C 313 " --> pdb=" O   ALA C 309 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 318 through 331
    Processing helix  chain 'C' and resid 339 through 352
      removed outlier: 3.590A  pdb=" N   PHE C 348 " --> pdb=" O   LEU C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 356 through 369
    Processing helix  chain 'C' and resid 382 through 397
      removed outlier: 3.512A  pdb=" N   VAL C 386 " --> pdb=" O   SER C 382 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 398 through 400
      No H-bonds generated for 'chain 'C' and resid 398 through 400'
    Processing helix  chain 'C' and resid 401 through 409
    Processing helix  chain 'C' and resid 444 through 456
    Processing helix  chain 'C' and resid 486 through 497
      removed outlier: 4.399A  pdb=" N   LEU C 490 " --> pdb=" O   THR C 486 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU C 491 " --> pdb=" O   VAL C 487 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 498 through 508
      removed outlier: 3.511A  pdb=" N   LEU C 502 " --> pdb=" O   ASP C 498 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   SER C 508 " --> pdb=" O   ARG C 504 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 522 through 530
    Processing helix  chain 'C' and resid 531 through 542
    Processing helix  chain 'C' and resid 555 through 563
      removed outlier: 3.569A  pdb=" N   GLN C 562 " --> pdb=" O   ASP C 558 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   PHE C 563 " --> pdb=" O   ASP C 559 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 565 through 574
    Processing helix  chain 'D' and resid 72 through 82
      removed outlier: 3.672A  pdb=" N   LEU D  76 " --> pdb=" O   LEU D  72 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE D  77 " --> pdb=" O   GLY D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 89 through 98
    Processing helix  chain 'D' and resid 105 through 107
      No H-bonds generated for 'chain 'D' and resid 105 through 107'
    Processing helix  chain 'D' and resid 108 through 120
      removed outlier: 3.550A  pdb=" N   VAL D 119 " --> pdb=" O   MET D 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 129 through 138
    Processing helix  chain 'D' and resid 140 through 149
      removed outlier: 3.557A  pdb=" N   GLN D 146 " --> pdb=" O   VAL D 142 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 156 through 172
      removed outlier: 3.644A  pdb=" N   GLY D 162 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL D 164 " --> pdb=" O   PHE D 160 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ARG D 166 " --> pdb=" O   GLY D 162 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 220 through 233
      removed outlier: 4.247A  pdb=" N   LEU D 224 " --> pdb=" O   CYS D 220 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR D 232 " --> pdb=" O   ILE D 228 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 234 through 239
    Processing helix  chain 'D' and resid 267 through 278
      removed outlier: 3.581A  pdb=" N   VAL D 273 " --> pdb=" O   ALA D 269 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ILE D 278 " --> pdb=" O   VAL D 274 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 283 through 300
    Processing helix  chain 'D' and resid 307 through 316
      removed outlier: 3.719A  pdb=" N   SER D 313 " --> pdb=" O   ALA D 309 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 318 through 331
      removed outlier: 3.513A  pdb=" N   LYS D 329 " --> pdb=" O   GLY D 325 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 339 through 352
    Processing helix  chain 'D' and resid 356 through 369
    Processing helix  chain 'D' and resid 382 through 397
      removed outlier: 3.509A  pdb=" N   VAL D 386 " --> pdb=" O   SER D 382 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   SER D 395 " --> pdb=" O   SER D 391 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 401 through 409
    Processing helix  chain 'D' and resid 444 through 456
      removed outlier: 3.762A  pdb=" N   PHE D 450 " --> pdb=" O   ARG D 446 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 486 through 497
      removed outlier: 4.175A  pdb=" N   LEU D 490 " --> pdb=" O   THR D 486 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU D 491 " --> pdb=" O   VAL D 487 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 498 through 507
      removed outlier: 3.551A  pdb=" N   LEU D 502 " --> pdb=" O   ASP D 498 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 521 through 530
      removed outlier: 3.808A  pdb=" N   VAL D 525 " --> pdb=" O   THR D 521 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 531 through 542
      removed outlier: 3.604A  pdb=" N   CYS D 542 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 555 through 564
    Processing helix  chain 'D' and resid 565 through 574
      removed outlier: 3.562A  pdb=" N   LYS D 570 " --> pdb=" O   LEU D 566 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   LEU D 571 " --> pdb=" O   GLU D 567 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 209
    Processing sheet with id=AA3, first strand: chain 'A' and resid 215 through 216
    Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 88
      removed outlier: 3.652A  pdb=" N   ILE B  87 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LEU B 128 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 205 through 209
    Processing sheet with id=AA6, first strand: chain 'B' and resid 215 through 216
    Processing sheet with id=AA7, first strand: chain 'B' and resid 438 through 439
      removed outlier: 3.748A  pdb=" N   ASN B 443 " --> pdb=" O   ASP B 439 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 205 through 209
    Processing sheet with id=AA9, first strand: chain 'C' and resid 215 through 216
    Processing sheet with id=AB1, first strand: chain 'D' and resid 87 through 88
      removed outlier: 4.253A  pdb=" N   ILE D  87 " --> pdb=" O   LEU D 128 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LEU D 128 " --> pdb=" O   ILE D  87 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'D' and resid 205 through 209
    Processing sheet with id=AB3, first strand: chain 'D' and resid 215 through 216

    696 hydrogen bonds defined for protein.
    2026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.77

  Time building geometry restraints manager: 5.00 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: 3257
        1.33 -     1.45: 3329
        1.45 -     1.57: 8608
        1.57 -     1.69: 0
        1.69 -     1.81: 188
  Bond restraints: 15382
  Sorted by residual:
  bond pdb=" C   ARG D 320 "
       pdb=" N   ASN D 321 "
    ideal  model  delta    sigma   weight residual
    1.335  1.303  0.031 1.36e-02 5.41e+03 5.30e+00
  bond pdb=" C   ARG D 320 "
       pdb=" O   ARG D 320 "
    ideal  model  delta    sigma   weight residual
    1.237  1.210  0.027 1.19e-02 7.06e+03 5.13e+00
  bond pdb=" CA  ARG D 320 "
       pdb=" C   ARG D 320 "
    ideal  model  delta    sigma   weight residual
    1.524  1.500  0.024 1.29e-02 6.01e+03 3.44e+00
  bond pdb=" N   LEU C  69 "
       pdb=" CA  LEU C  69 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.20e+00
  bond pdb=" N   LEU D  69 "
       pdb=" CA  LEU D  69 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.03e+00
  ... (remaining 15377 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.18: 19468
        1.18 -     2.36: 1080
        2.36 -     3.54: 164
        3.54 -     4.72: 68
        4.72 -     5.89: 14
  Bond angle restraints: 20794
  Sorted by residual:
  angle pdb=" C   TYR B 399 "
        pdb=" CA  TYR B 399 "
        pdb=" CB  TYR B 399 "
      ideal   model   delta    sigma   weight residual
     117.23  111.34    5.89 1.36e+00 5.41e-01 1.88e+01
  angle pdb=" N   ALA D 480 "
        pdb=" CA  ALA D 480 "
        pdb=" C   ALA D 480 "
      ideal   model   delta    sigma   weight residual
     110.43  115.50   -5.07 1.31e+00 5.83e-01 1.50e+01
  angle pdb=" CA  GLY D 234 "
        pdb=" C   GLY D 234 "
        pdb=" N   THR D 235 "
      ideal   model   delta    sigma   weight residual
     114.23  116.97   -2.74 8.80e-01 1.29e+00 9.71e+00
  angle pdb=" N   LYS B 297 "
        pdb=" CA  LYS B 297 "
        pdb=" C   LYS B 297 "
      ideal   model   delta    sigma   weight residual
     113.12  109.30    3.82 1.25e+00 6.40e-01 9.35e+00
  angle pdb=" N   ALA B 364 "
        pdb=" CA  ALA B 364 "
        pdb=" CB  ALA B 364 "
      ideal   model   delta    sigma   weight residual
     114.17  110.74    3.43 1.14e+00 7.69e-01 9.03e+00
  ... (remaining 20789 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 8408
       17.54 -    35.08: 685
       35.08 -    52.62: 111
       52.62 -    70.16: 25
       70.16 -    87.69: 11
  Dihedral angle restraints: 9240
    sinusoidal: 3572
      harmonic: 5668
  Sorted by residual:
  dihedral pdb=" CA  LEU A 367 "
           pdb=" C   LEU A 367 "
           pdb=" N   ALA A 368 "
           pdb=" CA  ALA A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.97   24.03     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  TYR D 463 "
           pdb=" C   TYR D 463 "
           pdb=" N   ASP D 464 "
           pdb=" CA  ASP D 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.20   21.80     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  TYR C 463 "
           pdb=" C   TYR C 463 "
           pdb=" N   ASP C 464 "
           pdb=" CA  ASP C 464 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.71   19.29     0      5.00e+00 4.00e-02 1.49e+01
  ... (remaining 9237 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 2112
       0.062 -    0.125: 229
       0.125 -    0.187: 15
       0.187 -    0.250: 1
       0.250 -    0.312: 1
  Chirality restraints: 2358
  Sorted by residual:
  chirality pdb=" CA  ALA D 480 "
            pdb=" N   ALA D 480 "
            pdb=" C   ALA D 480 "
            pdb=" CB  ALA D 480 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.17    0.31 2.00e-01 2.50e+01 2.44e+00
  chirality pdb=" CA  VAL B 499 "
            pdb=" N   VAL B 499 "
            pdb=" C   VAL B 499 "
            pdb=" CB  VAL B 499 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.19    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  ILE A 555 "
            pdb=" N   ILE A 555 "
            pdb=" C   ILE A 555 "
            pdb=" CB  ILE A 555 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.94e-01
  ... (remaining 2355 not shown)

  Planarity restraints: 2681
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C 105 "    0.037 5.00e-02 4.00e+02   5.63e-02 5.07e+00
        pdb=" N   PRO C 106 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C 106 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 106 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 555 "    0.031 5.00e-02 4.00e+02   4.72e-02 3.56e+00
        pdb=" N   PRO C 556 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 556 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 556 "    0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 105 "   -0.031 5.00e-02 4.00e+02   4.63e-02 3.42e+00
        pdb=" N   PRO D 106 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO D 106 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO D 106 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 2678 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 183
        2.61 -     3.18: 14306
        3.18 -     3.76: 22665
        3.76 -     4.33: 32987
        4.33 -     4.90: 52737
  Nonbonded interactions: 122878
  Sorted by model distance:
  nonbonded pdb=" O   SER C 395 "
            pdb=" OG  SER C 402 "
     model   vdw
     2.040 3.040
  nonbonded pdb=" OE2 GLU A 529 "
            pdb=" OH  TYR D 517 "
     model   vdw
     2.084 3.040
  nonbonded pdb=" ND2 ASN B 427 "
            pdb=" OD1 ASN C 465 "
     model   vdw
     2.121 3.120
  nonbonded pdb=" OG1 THR A 211 "
            pdb=" OE2 GLU A 358 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" OH  TYR B 517 "
            pdb=" OD1 ASP C 518 "
     model   vdw
     2.131 3.040
  ... (remaining 122873 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 69 through 119 or resid 121 through 378 or resid 380 throu \ 
gh 576))
  selection = (chain 'B' and (resid 69 through 119 or resid 121 through 173 or resid 192 throu \ 
gh 378 or resid 380 through 576))
  selection = (chain 'C' and (resid 69 through 119 or resid 121 through 173 or resid 192 throu \ 
gh 378 or resid 380 through 576))
  selection = (chain 'D' and (resid 69 through 119 or resid 121 through 173 or resid 192 throu \ 
gh 378 or resid 380 through 576))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.06 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:             12.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.130
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.760
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     46.950
  Find NCS groups from input model:        0.860
  Set up NCS constraints:                  0.090
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   64.290
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5643
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15382  Z= 0.164
  Angle     :  0.650   5.894  20794  Z= 0.363
  Chirality :  0.040   0.312   2358
  Planarity :  0.005   0.056   2681
  Dihedral  : 13.639  87.695   5584
  Min Nonbonded Distance : 2.040

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.19), residues: 1940
  helix: -0.36 (0.17), residues: 948
  sheet: -1.04 (0.46), residues: 117
  loop : -0.74 (0.22), residues: 875

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 552 
 HIS   0.007   0.002   HIS B 461 
 PHE   0.017   0.002   PHE D 152 
 TYR   0.015   0.001   TYR A 303 
 ARG   0.006   0.001   ARG D 476 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27323 (  696)
  hydrogen bonds       : angle       8.57076 ( 2026)
  covalent geometry    : bond        0.00367 (15382)
  covalent geometry    : angle       0.65028 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.876 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.3287
  time to fit residues: 115.1662
Evaluate side-chains
  145 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 2.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 164 optimal weight:    3.9990
   chunk 147 optimal weight:    0.9990
   chunk 82 optimal weight:    0.9980
   chunk 50 optimal weight:    0.4980
   chunk 99 optimal weight:    3.9990
   chunk 78 optimal weight:    0.6980
   chunk 152 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 92 optimal weight:   10.0000
   chunk 113 optimal weight:    5.9990
   chunk 177 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 263 HIS
A 321 ASN
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 HIS
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 462 ASN
B 468 HIS
D 404 GLN
D 443 ASN
D 445 HIS
D 459 ASN
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 531 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.106451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.081701 restraints weight = 81854.235|
|-----------------------------------------------------------------------------|
r_work (start): 0.3662 rms_B_bonded: 5.63
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3660
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3660 r_free = 0.3660    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3660
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  15382  Z= 0.148
  Angle     :  0.697  11.881  20794  Z= 0.358
  Chirality :  0.043   0.231   2358
  Planarity :  0.005   0.052   2681
  Dihedral  :  4.925  25.127   2100
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  :  6.74 %
    Favored  : 92.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.19), residues: 1940
  helix:  0.09 (0.16), residues: 988
  sheet: -0.97 (0.45), residues: 122
  loop : -0.53 (0.22), residues: 830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP C 194 
 HIS   0.005   0.001   HIS D 468 
 PHE   0.041   0.002   PHE D 505 
 TYR   0.033   0.002   TYR A 347 
 ARG   0.010   0.001   ARG D 503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04814 (  696)
  hydrogen bonds       : angle       5.67738 ( 2026)
  covalent geometry    : bond        0.00327 (15382)
  covalent geometry    : angle       0.69686 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 1.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 LEU cc_start: 0.8307 (mp) cc_final: 0.8081 (mp)
REVERT: A  507 LEU cc_start: 0.9092 (tp) cc_final: 0.8839 (mp)
REVERT: A  511 ASP cc_start: 0.9030 (t0) cc_final: 0.8814 (t0)
REVERT: B  266 MET cc_start: 0.8894 (mmt) cc_final: 0.8231 (mmm)
REVERT: B  478 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6838 (tm-30)
REVERT: C  115 MET cc_start: 0.8255 (tpp) cc_final: 0.8005 (tpp)
REVERT: C  495 TYR cc_start: 0.8921 (t80) cc_final: 0.8645 (t80)
REVERT: C  523 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8148 (pp)
  outliers start: 15
  outliers final: 10
  residues processed: 193
  average time/residue: 0.2728
  time to fit residues: 78.2780
Evaluate side-chains
  151 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 1.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  154 ILE
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  154 ILE
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  232 THR
Chi-restraints excluded: chain C residue  523 LEU
Chi-restraints excluded: chain D residue  144 LEU
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  232 THR
Chi-restraints excluded: chain D residue  249 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 134 optimal weight:    5.9990
   chunk 101 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 174 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 48 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   chunk 179 optimal weight:    5.9990
   chunk 151 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 408 HIS
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 445 HIS
B 524 HIS
B 531 HIS
C 408 HIS
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 531 HIS
D 573 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.105685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.080209 restraints weight = 83916.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3588 rms_B_bonded: 5.88
r_work: 0.3423 rms_B_bonded: 5.77 restraints_weight: 2.0000
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3421 r_free = 0.3421    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.2992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15382  Z= 0.137
  Angle     :  0.642  12.570  20794  Z= 0.328
  Chirality :  0.042   0.145   2358
  Planarity :  0.004   0.052   2681
  Dihedral  :  4.748  24.709   2100
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  8.21 %
    Favored  : 90.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.19), residues: 1940
  helix:  0.21 (0.16), residues: 1009
  sheet: -0.64 (0.45), residues: 123
  loop : -0.39 (0.23), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 194 
 HIS   0.008   0.001   HIS C 524 
 PHE   0.033   0.001   PHE D 505 
 TYR   0.027   0.002   TYR A  78 
 ARG   0.008   0.001   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  696)
  hydrogen bonds       : angle       5.18776 ( 2026)
  covalent geometry    : bond        0.00309 (15382)
  covalent geometry    : angle       0.64238 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 1.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8618 (m-80) cc_final: 0.8272 (m-80)
REVERT: A  200 THR cc_start: 0.8851 (m) cc_final: 0.8491 (p)
REVERT: A  507 LEU cc_start: 0.9053 (tp) cc_final: 0.8838 (mp)
REVERT: A  573 GLN cc_start: 0.9105 (tp-100) cc_final: 0.8876 (mm-40)
REVERT: B  294 TYR cc_start: 0.8654 (OUTLIER) cc_final: 0.7814 (t80)
REVERT: B  431 MET cc_start: 0.8424 (ttp) cc_final: 0.7981 (ttt)
REVERT: B  432 MET cc_start: 0.8389 (ttm) cc_final: 0.7899 (tpp)
REVERT: D  340 MET cc_start: 0.8329 (tmm) cc_final: 0.8037 (tmm)
REVERT: D  510 MET cc_start: 0.5439 (ppp) cc_final: 0.5141 (ppp)
REVERT: D  529 GLU cc_start: 0.8634 (tp30) cc_final: 0.7951 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 172
  average time/residue: 0.2699
  time to fit residues: 68.2826
Evaluate side-chains
  158 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  523 LEU
Chi-restraints excluded: chain D residue  320 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 141 optimal weight:    2.9990
   chunk 150 optimal weight:    4.9990
   chunk 186 optimal weight:    1.9990
   chunk 151 optimal weight:   20.0000
   chunk 164 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   chunk 172 optimal weight:    0.4980
   chunk 129 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 120 GLN    B
C 443 ASN
** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 573 GLN
D 408 HIS
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.104978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.078819 restraints weight = 115372.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3558 rms_B_bonded: 6.96
r_work: 0.3380 rms_B_bonded: 6.46 restraints_weight: 2.0000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  15382  Z= 0.127
  Angle     :  0.631  10.711  20794  Z= 0.320
  Chirality :  0.041   0.149   2358
  Planarity :  0.004   0.053   2681
  Dihedral  :  4.627  24.772   2100
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.68 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.19), residues: 1940
  helix:  0.34 (0.16), residues: 1011
  sheet: -0.37 (0.45), residues: 119
  loop : -0.30 (0.23), residues: 810

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 
 PHE   0.039   0.001   PHE C 505 
 TYR   0.033   0.002   TYR A  78 
 ARG   0.005   0.000   ARG C 205 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  696)
  hydrogen bonds       : angle       5.04182 ( 2026)
  covalent geometry    : bond        0.00287 (15382)
  covalent geometry    : angle       0.63141 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 1.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8635 (m-80) cc_final: 0.8299 (m-80)
REVERT: A  200 THR cc_start: 0.8873 (m) cc_final: 0.8559 (p)
REVERT: A  573 GLN cc_start: 0.9177 (tp-100) cc_final: 0.8896 (mm-40)
REVERT: B  200 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8403 (p)
REVERT: B  266 MET cc_start: 0.8375 (mmm) cc_final: 0.8140 (mmm)
REVERT: B  294 TYR cc_start: 0.8678 (OUTLIER) cc_final: 0.7956 (t80)
REVERT: D  510 MET cc_start: 0.5554 (ppp) cc_final: 0.5264 (ppp)
  outliers start: 22
  outliers final: 19
  residues processed: 167
  average time/residue: 0.2742
  time to fit residues: 68.7834
Evaluate side-chains
  161 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 1.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  319 ASP
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  523 LEU
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Chi-restraints excluded: chain D residue  552 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 122 optimal weight:    6.9990
   chunk 101 optimal weight:    0.8980
   chunk 174 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 136 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 163 optimal weight:    0.0770
   chunk 82 optimal weight:    0.7980
   chunk 158 optimal weight:    1.9990
   chunk 131 optimal weight:    1.9990
   overall best weight:    1.1542

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.103212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.077249 restraints weight = 103300.884|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 6.53
r_work: 0.3352 rms_B_bonded: 6.18 restraints_weight: 2.0000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15382  Z= 0.141
  Angle     :  0.630  12.461  20794  Z= 0.319
  Chirality :  0.041   0.203   2358
  Planarity :  0.004   0.048   2681
  Dihedral  :  4.643  23.939   2100
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.15 %
    Favored  : 87.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.19), residues: 1940
  helix:  0.34 (0.17), residues: 1017
  sheet: -0.32 (0.45), residues: 123
  loop : -0.22 (0.23), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 
 PHE   0.039   0.001   PHE C 505 
 TYR   0.029   0.002   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03531 (  696)
  hydrogen bonds       : angle       4.98372 ( 2026)
  covalent geometry    : bond        0.00323 (15382)
  covalent geometry    : angle       0.63027 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 161
  time to evaluate  : 1.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 THR cc_start: 0.8864 (m) cc_final: 0.8574 (p)
REVERT: A  573 GLN cc_start: 0.9296 (tp-100) cc_final: 0.8954 (mm-40)
REVERT: B  200 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8481 (p)
REVERT: B  294 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8075 (t80)
REVERT: B  431 MET cc_start: 0.8448 (ttp) cc_final: 0.8153 (ttt)
REVERT: B  432 MET cc_start: 0.8398 (ttm) cc_final: 0.7949 (tpp)
REVERT: C  112 MET cc_start: 0.8523 (mmp) cc_final: 0.8283 (mmm)
REVERT: D  112 MET cc_start: 0.9012 (mmp) cc_final: 0.8661 (mmm)
REVERT: D  115 MET cc_start: 0.8403 (tpp) cc_final: 0.8122 (tpp)
REVERT: D  340 MET cc_start: 0.8263 (tmm) cc_final: 0.7975 (tmm)
REVERT: D  510 MET cc_start: 0.5806 (ppp) cc_final: 0.5497 (ppp)
REVERT: D  529 GLU cc_start: 0.8646 (tp30) cc_final: 0.7989 (tm-30)
  outliers start: 25
  outliers final: 18
  residues processed: 176
  average time/residue: 0.2807
  time to fit residues: 72.9418
Evaluate side-chains
  169 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 1.829 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  525 VAL
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  411 LEU
Chi-restraints excluded: chain D residue  459 ASN
Chi-restraints excluded: chain D residue  552 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 187 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 173 optimal weight:    2.9990
   chunk 185 optimal weight:   10.0000
   chunk 14 optimal weight:    0.6980
   chunk 183 optimal weight:    0.0770
   chunk 43 optimal weight:    9.9990
   chunk 139 optimal weight:    5.9990
   chunk 127 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.6938

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.104010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.078236 restraints weight = 94999.931|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 6.24
r_work: 0.3388 rms_B_bonded: 5.98 restraints_weight: 2.0000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3386
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3386 r_free = 0.3386    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3386
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  15382  Z= 0.118
  Angle     :  0.626  12.584  20794  Z= 0.314
  Chirality :  0.040   0.158   2358
  Planarity :  0.004   0.046   2681
  Dihedral  :  4.501  24.217   2100
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.81 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.20), residues: 1940
  helix:  0.38 (0.17), residues: 1020
  sheet: -0.19 (0.45), residues: 123
  loop : -0.15 (0.23), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 194 
 HIS   0.004   0.001   HIS D 468 
 PHE   0.042   0.001   PHE C 505 
 TYR   0.028   0.001   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03258 (  696)
  hydrogen bonds       : angle       4.89805 ( 2026)
  covalent geometry    : bond        0.00270 (15382)
  covalent geometry    : angle       0.62556 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 160
  time to evaluate  : 1.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 THR cc_start: 0.8862 (m) cc_final: 0.8554 (p)
REVERT: A  398 MET cc_start: 0.8383 (mmm) cc_final: 0.7408 (mmm)
REVERT: A  573 GLN cc_start: 0.9310 (tp-100) cc_final: 0.8936 (mm-40)
REVERT: B  200 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8466 (p)
REVERT: B  294 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8061 (t80)
REVERT: B  432 MET cc_start: 0.8327 (ttm) cc_final: 0.7915 (tpp)
REVERT: B  507 LEU cc_start: 0.9258 (mt) cc_final: 0.9054 (mp)
REVERT: C  112 MET cc_start: 0.8579 (mmp) cc_final: 0.8332 (mmm)
REVERT: D  112 MET cc_start: 0.9001 (mmp) cc_final: 0.8669 (mmm)
REVERT: D  340 MET cc_start: 0.8262 (tmm) cc_final: 0.7942 (tmm)
REVERT: D  510 MET cc_start: 0.5828 (ppp) cc_final: 0.5611 (ppp)
  outliers start: 15
  outliers final: 12
  residues processed: 172
  average time/residue: 0.2848
  time to fit residues: 72.4348
Evaluate side-chains
  161 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 147
  time to evaluate  : 1.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Chi-restraints excluded: chain D residue  552 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 165 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 189 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 155 optimal weight:    0.9990
   chunk 179 optimal weight:    1.9990
   chunk 185 optimal weight:    0.6980
   chunk 135 optimal weight:    0.0170
   overall best weight:    0.7422

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 554 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.103900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.078062 restraints weight = 102189.501|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 6.50
r_work: 0.3377 rms_B_bonded: 6.17 restraints_weight: 2.0000
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15382  Z= 0.121
  Angle     :  0.635  10.697  20794  Z= 0.318
  Chirality :  0.041   0.228   2358
  Planarity :  0.004   0.048   2681
  Dihedral  :  4.477  24.030   2100
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 13.36 %
    Favored  : 85.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.20), residues: 1940
  helix:  0.43 (0.17), residues: 1024
  sheet: -0.07 (0.46), residues: 123
  loop : -0.14 (0.23), residues: 793

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 194 
 HIS   0.004   0.001   HIS D 468 
 PHE   0.042   0.001   PHE C 505 
 TYR   0.026   0.001   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03191 (  696)
  hydrogen bonds       : angle       4.85650 ( 2026)
  covalent geometry    : bond        0.00278 (15382)
  covalent geometry    : angle       0.63541 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 151
  time to evaluate  : 1.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 THR cc_start: 0.8855 (m) cc_final: 0.8557 (p)
REVERT: A  398 MET cc_start: 0.8359 (mmm) cc_final: 0.7363 (mmm)
REVERT: A  573 GLN cc_start: 0.9300 (tp-100) cc_final: 0.8951 (mm-40)
REVERT: B  200 THR cc_start: 0.8757 (OUTLIER) cc_final: 0.8459 (p)
REVERT: B  245 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8746 (mt-10)
REVERT: B  294 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8077 (t80)
REVERT: B  320 ARG cc_start: 0.8816 (mpp80) cc_final: 0.8566 (mtm-85)
REVERT: B  431 MET cc_start: 0.8469 (ttp) cc_final: 0.8169 (ttt)
REVERT: B  432 MET cc_start: 0.8276 (ttm) cc_final: 0.7879 (tpp)
REVERT: C  112 MET cc_start: 0.8646 (mmp) cc_final: 0.8384 (mmm)
REVERT: D  112 MET cc_start: 0.9007 (mmp) cc_final: 0.8688 (mmm)
REVERT: D  340 MET cc_start: 0.8321 (tmm) cc_final: 0.8036 (tmm)
REVERT: D  523 LEU cc_start: 0.9433 (tt) cc_final: 0.9088 (mp)
  outliers start: 18
  outliers final: 14
  residues processed: 163
  average time/residue: 0.2712
  time to fit residues: 67.0725
Evaluate side-chains
  161 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  200 THR
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Chi-restraints excluded: chain D residue  552 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 156 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 143 optimal weight:    0.4980
   chunk 132 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 158 optimal weight:    0.9980
   chunk 112 optimal weight:    0.6980
   chunk 176 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.102730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.077541 restraints weight = 80764.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3539 rms_B_bonded: 5.68
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3539
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3539 r_free = 0.3539    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3539
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15382  Z= 0.135
  Angle     :  0.642  10.827  20794  Z= 0.323
  Chirality :  0.041   0.173   2358
  Planarity :  0.004   0.049   2681
  Dihedral  :  4.531  23.460   2100
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 13.79 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.20), residues: 1940
  helix:  0.41 (0.17), residues: 1026
  sheet:  0.04 (0.46), residues: 122
  loop : -0.09 (0.24), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 
 PHE   0.043   0.001   PHE C 505 
 TYR   0.025   0.001   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  696)
  hydrogen bonds       : angle       4.87222 ( 2026)
  covalent geometry    : bond        0.00314 (15382)
  covalent geometry    : angle       0.64243 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 149
  time to evaluate  : 1.803 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  200 THR cc_start: 0.8748 (m) cc_final: 0.8532 (p)
REVERT: A  573 GLN cc_start: 0.9413 (tp-100) cc_final: 0.9024 (mm-40)
REVERT: B  115 MET cc_start: 0.8288 (mmt) cc_final: 0.7829 (mpp)
REVERT: B  245 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8394 (mt-10)
REVERT: B  294 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7812 (t80)
REVERT: B  320 ARG cc_start: 0.8450 (mpp80) cc_final: 0.8134 (mtm-85)
REVERT: C  112 MET cc_start: 0.8677 (mmp) cc_final: 0.8444 (mmm)
REVERT: D  112 MET cc_start: 0.8993 (mmp) cc_final: 0.8724 (mmm)
REVERT: D  340 MET cc_start: 0.8275 (tmm) cc_final: 0.7978 (tmm)
REVERT: D  341 MET cc_start: 0.6776 (mmm) cc_final: 0.6574 (mmm)
REVERT: D  523 LEU cc_start: 0.9442 (tt) cc_final: 0.9123 (mp)
REVERT: D  529 GLU cc_start: 0.8677 (tp30) cc_final: 0.8073 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 158
  average time/residue: 0.2795
  time to fit residues: 66.3678
Evaluate side-chains
  160 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 1.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 40 optimal weight:   10.0000
   chunk 182 optimal weight:    0.0570
   chunk 139 optimal weight:    8.9990
   chunk 194 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 124 optimal weight:    2.9990
   chunk 125 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 128 optimal weight:    0.3980
   overall best weight:    1.0502

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 388 ASN
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 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 = 0.4096 r_free = 0.4096 target = 0.102206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.076763 restraints weight = 88998.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 5.98
r_work: 0.3357 rms_B_bonded: 5.94 restraints_weight: 2.0000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3359
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3359 r_free = 0.3359    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3359
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.4298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15382  Z= 0.136
  Angle     :  0.645  11.093  20794  Z= 0.325
  Chirality :  0.041   0.175   2358
  Planarity :  0.004   0.050   2681
  Dihedral  :  4.523  23.202   2100
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 14.03 %
    Favored  : 84.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.20), residues: 1940
  helix:  0.42 (0.17), residues: 1027
  sheet:  0.05 (0.46), residues: 123
  loop : -0.08 (0.24), residues: 790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 194 
 HIS   0.004   0.001   HIS D 468 
 PHE   0.044   0.001   PHE C 505 
 TYR   0.025   0.001   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03217 (  696)
  hydrogen bonds       : angle       4.85484 ( 2026)
  covalent geometry    : bond        0.00316 (15382)
  covalent geometry    : angle       0.64460 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 1.864 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8579 (m-80) cc_final: 0.8273 (m-80)
REVERT: A  200 THR cc_start: 0.8870 (m) cc_final: 0.8601 (p)
REVERT: A  573 GLN cc_start: 0.9439 (tp-100) cc_final: 0.9031 (mm-40)
REVERT: B  115 MET cc_start: 0.8305 (mmt) cc_final: 0.7758 (mpp)
REVERT: B  245 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8702 (mt-10)
REVERT: B  294 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.8085 (t80)
REVERT: B  320 ARG cc_start: 0.8859 (mpp80) cc_final: 0.8588 (mtm-85)
REVERT: B  398 MET cc_start: 0.8102 (mmm) cc_final: 0.6964 (mmm)
REVERT: C  112 MET cc_start: 0.8804 (mmp) cc_final: 0.8479 (mmm)
REVERT: D  112 MET cc_start: 0.9050 (mmp) cc_final: 0.8706 (mmm)
REVERT: D  340 MET cc_start: 0.8345 (tmm) cc_final: 0.8061 (tmm)
REVERT: D  523 LEU cc_start: 0.9445 (tt) cc_final: 0.9105 (mp)
REVERT: D  529 GLU cc_start: 0.8606 (tp30) cc_final: 0.8164 (tm-30)
  outliers start: 18
  outliers final: 14
  residues processed: 158
  average time/residue: 0.2716
  time to fit residues: 65.8618
Evaluate side-chains
  156 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  245 GLU
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 169 optimal weight:    5.9990
   chunk 49 optimal weight:    0.9990
   chunk 181 optimal weight:    0.9980
   chunk 167 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    0.2980
   chunk 134 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 162 optimal weight:    7.9990
   chunk 180 optimal weight:    3.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.102830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.077820 restraints weight = 78313.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 5.61
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3554
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3554 r_free = 0.3554    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3554
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15382  Z= 0.120
  Angle     :  0.643  11.072  20794  Z= 0.322
  Chirality :  0.040   0.167   2358
  Planarity :  0.004   0.049   2681
  Dihedral  :  4.460  23.407   2100
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 14.46 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.20), residues: 1940
  helix:  0.46 (0.17), residues: 1022
  sheet:  0.12 (0.46), residues: 122
  loop : -0.09 (0.23), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 194 
 HIS   0.004   0.001   HIS C 524 
 PHE   0.043   0.001   PHE C 505 
 TYR   0.025   0.001   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03102 (  696)
  hydrogen bonds       : angle       4.82209 ( 2026)
  covalent geometry    : bond        0.00277 (15382)
  covalent geometry    : angle       0.64263 (20794)

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

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

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3880 Ramachandran restraints generated.
    1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 1.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8488 (m-80) cc_final: 0.8190 (m-80)
REVERT: A  401 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7830 (t80)
REVERT: A  432 MET cc_start: 0.8036 (ttm) cc_final: 0.7711 (tpp)
REVERT: A  573 GLN cc_start: 0.9440 (tp-100) cc_final: 0.9009 (mm-40)
REVERT: B  115 MET cc_start: 0.8288 (mmt) cc_final: 0.7804 (mpp)
REVERT: B  294 TYR cc_start: 0.8364 (OUTLIER) cc_final: 0.7729 (t80)
REVERT: B  398 MET cc_start: 0.7811 (mmm) cc_final: 0.6720 (mmm)
REVERT: B  432 MET cc_start: 0.7750 (ttm) cc_final: 0.7447 (tpp)
REVERT: C  112 MET cc_start: 0.8743 (mmp) cc_final: 0.8453 (mmm)
REVERT: C  280 MET cc_start: 0.9086 (pmm) cc_final: 0.8750 (pmm)
REVERT: D  112 MET cc_start: 0.9008 (mmp) cc_final: 0.8723 (mmm)
REVERT: D  115 MET cc_start: 0.8398 (tpp) cc_final: 0.8178 (tpp)
REVERT: D  340 MET cc_start: 0.8248 (tmm) cc_final: 0.7941 (tmm)
REVERT: D  523 LEU cc_start: 0.9439 (tt) cc_final: 0.9108 (mp)
  outliers start: 15
  outliers final: 11
  residues processed: 157
  average time/residue: 0.2576
  time to fit residues: 60.7519
Evaluate side-chains
  153 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 CYS
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain B residue  108 LEU
Chi-restraints excluded: chain B residue  294 TYR
Chi-restraints excluded: chain B residue  319 ASP
Chi-restraints excluded: chain B residue  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain C residue  216 CYS
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 181 optimal weight:    3.9990
   chunk 175 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 138 optimal weight:    6.9990
   chunk 139 optimal weight:    7.9990
   chunk 189 optimal weight:    5.9990
   chunk 96 optimal weight:    0.0040
   chunk 41 optimal weight:    4.9990
   chunk 153 optimal weight:    0.9980
   overall best weight:    1.3994

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

Flipped N/Q/H residues before XYZ refinement:
** A 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.102380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.076394 restraints weight = 113353.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 6.94
r_work: 0.3331 rms_B_bonded: 6.49 restraints_weight: 2.0000
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3331
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3331 r_free = 0.3331    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3331
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15382  Z= 0.157
  Angle     :  0.665  11.715  20794  Z= 0.336
  Chirality :  0.041   0.167   2358
  Planarity :  0.004   0.052   2681
  Dihedral  :  4.597  22.820   2100
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 14.58 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.20), residues: 1940
  helix:  0.34 (0.16), residues: 1035
  sheet: -0.04 (0.46), residues: 122
  loop : -0.07 (0.24), residues: 783

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 
 PHE   0.044   0.001   PHE C 505 
 TYR   0.026   0.001   TYR A  78 
 ARG   0.007   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03324 (  696)
  hydrogen bonds       : angle       4.87268 ( 2026)
  covalent geometry    : bond        0.00365 (15382)
  covalent geometry    : angle       0.66515 (20794)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12011.22 seconds
wall clock time: 208 minutes 18.83 seconds (12498.83 seconds total)