Starting phenix.real_space_refine
on Sun Aug 24 05:18:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8szl_40920/08_2025/8szl_40920.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8szl_40920/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8szl_40920/08_2025/8szl_40920.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8szl_40920/08_2025/8szl_40920.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8szl_40920/08_2025/8szl_40920.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8szl_40920/08_2025/8szl_40920.map"
  }
  resolution = 3.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 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: {'GLU:plan': 6, 'ASP:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 3828
  Time building chain proxies: 6.08, per 1000 atoms: 0.40
  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: 1.45
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.55
  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: 2.43

  Time building geometry restraints manager: 1.89 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:             9.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     18.410
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.720
-------------------------------------------------------------------------------
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 : 5.50
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.006   0.001   ARG D 476 
 TYR   0.015   0.001   TYR A 303 
 PHE   0.017   0.002   PHE D 152 
 TRP   0.012   0.001   TRP D 552 
 HIS   0.007   0.002   HIS B 461 

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

*********************** 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  : 0.604 
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: 0.1625
  time to fit residues: 56.9053
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  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 194 optimal weight:    0.0980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    0.0370
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    9.9990
   overall best weight:    0.3858

-------------------------------------------------------------------------------
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 445 HIS
B 462 ASN
B 468 HIS
C 120 GLN    B
C 140 ASN
D 404 GLN
D 443 ASN
D 445 HIS
D 459 ASN
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 531 HIS
D 573 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.107764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.082146 restraints weight = 99384.973|
|-----------------------------------------------------------------------------|
r_work (start): 0.3672 rms_B_bonded: 6.46
r_work: 0.3504 rms_B_bonded: 6.28 restraints_weight: 2.0000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3508
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3508 r_free = 0.3508    target_work(ls_wunit_k1) = 0.073         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3508
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.2461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  15382  Z= 0.138
  Angle     :  0.696  13.840  20794  Z= 0.355
  Chirality :  0.043   0.209   2358
  Planarity :  0.005   0.054   2681
  Dihedral  :  4.898  25.279   2100
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  6.56 %
    Favored  : 92.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.48 (0.19), residues: 1940
  helix:  0.06 (0.16), residues: 990
  sheet: -0.74 (0.45), residues: 118
  loop : -0.56 (0.22), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D 503 
 TYR   0.035   0.002   TYR A 347 
 PHE   0.039   0.002   PHE D 505 
 TRP   0.011   0.002   TRP C 194 
 HIS   0.004   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (15382)
  covalent geometry    : angle       0.69580 (20794)
  hydrogen bonds       : bond        0.04591 (  696)
  hydrogen bonds       : angle       5.60483 ( 2026)

*********************** 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
  201 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 188
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8715 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  507 LEU cc_start: 0.9025 (tp) cc_final: 0.8765 (mp)
REVERT: B  266 MET cc_start: 0.8926 (mmt) cc_final: 0.8252 (mmm)
REVERT: B  478 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: C  115 MET cc_start: 0.8343 (tpp) cc_final: 0.8075 (tpp)
REVERT: C  495 TYR cc_start: 0.9003 (t80) cc_final: 0.8776 (t80)
REVERT: C  523 LEU cc_start: 0.8502 (pp) cc_final: 0.8213 (pp)
REVERT: D  112 MET cc_start: 0.8819 (mmp) cc_final: 0.8575 (mmm)
REVERT: D  529 GLU cc_start: 0.8622 (tp30) cc_final: 0.8415 (tp30)
  outliers start: 13
  outliers final: 8
  residues processed: 198
  average time/residue: 0.1222
  time to fit residues: 36.3534
Evaluate side-chains
  149 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 141
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
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 D residue  108 LEU
Chi-restraints excluded: chain D residue  144 LEU
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 40 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 145 optimal weight:    7.9990
   chunk 141 optimal weight:    3.9990
   chunk 82 optimal weight:    6.9990
   chunk 144 optimal weight:   10.0000
   chunk 194 optimal weight:    0.5980
   chunk 137 optimal weight:    0.0370
   chunk 61 optimal weight:    0.6980
   overall best weight:    1.2260

-------------------------------------------------------------------------------
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
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 524 HIS
B 531 HIS
C 408 HIS
C 443 ASN
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.104280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.077763 restraints weight = 119405.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 7.16
r_work: 0.3350 rms_B_bonded: 6.54 restraints_weight: 2.0000
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3350
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3350 r_free = 0.3350    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 = 0.3350 r_free = 0.3350    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3350
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15382  Z= 0.155
  Angle     :  0.659  13.095  20794  Z= 0.338
  Chirality :  0.042   0.146   2358
  Planarity :  0.004   0.055   2681
  Dihedral  :  4.807  24.525   2100
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  :  8.03 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.24 (0.19), residues: 1940
  helix:  0.24 (0.16), residues: 1009
  sheet: -0.74 (0.44), residues: 122
  loop : -0.39 (0.23), residues: 809

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 503 
 TYR   0.024   0.002   TYR D  78 
 PHE   0.032   0.002   PHE D 505 
 TRP   0.011   0.002   TRP C 194 
 HIS   0.007   0.001   HIS C 524 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (15382)
  covalent geometry    : angle       0.65888 (20794)
  hydrogen bonds       : bond        0.04051 (  696)
  hydrogen bonds       : angle       5.21743 ( 2026)

*********************** 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
  190 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 161
  time to evaluate  : 0.625 
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: 0.8665 (m-80) cc_final: 0.8263 (m-80)
REVERT: A  200 THR cc_start: 0.8886 (m) cc_final: 0.8559 (p)
REVERT: A  347 TYR cc_start: 0.8781 (t80) cc_final: 0.8506 (t80)
REVERT: A  432 MET cc_start: 0.8358 (ttm) cc_final: 0.8120 (tpp)
REVERT: A  507 LEU cc_start: 0.9097 (tp) cc_final: 0.8870 (mp)
REVERT: A  573 GLN cc_start: 0.9119 (tp-100) cc_final: 0.8888 (mm-40)
REVERT: B  200 THR cc_start: 0.8768 (m) cc_final: 0.8441 (p)
REVERT: B  266 MET cc_start: 0.9000 (mmt) cc_final: 0.8352 (mmm)
REVERT: B  294 TYR cc_start: 0.8766 (OUTLIER) cc_final: 0.7754 (t80)
REVERT: B  432 MET cc_start: 0.8391 (ttm) cc_final: 0.7858 (tpp)
REVERT: C  304 MET cc_start: 0.9011 (mtt) cc_final: 0.8797 (mtm)
REVERT: C  573 GLN cc_start: 0.9089 (mm110) cc_final: 0.8837 (mm110)
REVERT: D  112 MET cc_start: 0.8859 (mmp) cc_final: 0.8581 (mmm)
REVERT: D  340 MET cc_start: 0.8412 (tmm) cc_final: 0.8121 (tmm)
REVERT: D  510 MET cc_start: 0.5595 (ppp) cc_final: 0.5261 (ppp)
  outliers start: 29
  outliers final: 19
  residues processed: 182
  average time/residue: 0.1142
  time to fit residues: 30.8935
Evaluate side-chains
  166 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
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  132 LEU
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  174 LEU
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  108 LEU
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  459 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 93 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 179 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 51 optimal weight:    1.9990
   chunk 145 optimal weight:    7.9990
   chunk 75 optimal weight:    1.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    1.3586

-------------------------------------------------------------------------------
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**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 140 ASN
** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 408 HIS
** D 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 573 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.103035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.077824 restraints weight = 69940.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 5.23
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3541
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3541 r_free = 0.3541    target_work(ls_wunit_k1) = 0.075         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3541
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  15382  Z= 0.155
  Angle     :  0.650  11.948  20794  Z= 0.329
  Chirality :  0.042   0.198   2358
  Planarity :  0.004   0.056   2681
  Dihedral  :  4.764  24.597   2100
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 10.23 %
    Favored  : 88.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.19), residues: 1940
  helix:  0.27 (0.16), residues: 1024
  sheet: -0.53 (0.45), residues: 120
  loop : -0.35 (0.23), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 205 
 TYR   0.025   0.002   TYR D  78 
 PHE   0.036   0.001   PHE C 505 
 TRP   0.011   0.001   TRP C 194 
 HIS   0.006   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15382)
  covalent geometry    : angle       0.64961 (20794)
  hydrogen bonds       : bond        0.03651 (  696)
  hydrogen bonds       : angle       5.10289 ( 2026)

*********************** 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
  185 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8624 (m-80) cc_final: 0.8306 (m-80)
REVERT: A  200 THR cc_start: 0.8745 (m) cc_final: 0.8521 (p)
REVERT: A  347 TYR cc_start: 0.8520 (t80) cc_final: 0.8304 (t80)
REVERT: A  573 GLN cc_start: 0.9224 (tp-100) cc_final: 0.8907 (mm-40)
REVERT: B  294 TYR cc_start: 0.8557 (OUTLIER) cc_final: 0.7481 (t80)
REVERT: B  432 MET cc_start: 0.7962 (ttm) cc_final: 0.7476 (tpp)
REVERT: C  573 GLN cc_start: 0.9174 (mm110) cc_final: 0.8852 (mm110)
REVERT: D  112 MET cc_start: 0.8887 (mmp) cc_final: 0.8652 (mmm)
REVERT: D  510 MET cc_start: 0.5071 (ppp) cc_final: 0.4840 (ppp)
  outliers start: 22
  outliers final: 18
  residues processed: 178
  average time/residue: 0.1264
  time to fit residues: 33.3771
Evaluate side-chains
  166 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 147
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
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  469 CYS
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  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 D residue  319 ASP
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 140 optimal weight:    7.9990
   chunk 99 optimal weight:    0.8980
   chunk 131 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 170 optimal weight:    0.9990
   chunk 166 optimal weight:    0.9980
   chunk 115 optimal weight:    0.0370
   chunk 7 optimal weight:    8.9990
   chunk 95 optimal weight:    6.9990
   chunk 159 optimal weight:    1.9990
   overall best weight:    0.7260

-------------------------------------------------------------------------------
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 468 HIS
** B 427 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.104126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.078529 restraints weight = 84003.683|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 5.89
r_work: 0.3392 rms_B_bonded: 5.80 restraints_weight: 2.0000
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    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 = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.3709

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= 0.120
  Angle     :  0.629  12.992  20794  Z= 0.315
  Chirality :  0.041   0.161   2358
  Planarity :  0.004   0.054   2681
  Dihedral  :  4.582  24.270   2100
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 11.89 %
    Favored  : 86.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.03 (0.19), residues: 1940
  helix:  0.39 (0.17), residues: 1020
  sheet: -0.16 (0.46), residues: 118
  loop : -0.25 (0.23), residues: 802

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 551 
 TYR   0.021   0.001   TYR C 237 
 PHE   0.038   0.001   PHE C 505 
 TRP   0.013   0.002   TRP C 194 
 HIS   0.005   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (15382)
  covalent geometry    : angle       0.62938 (20794)
  hydrogen bonds       : bond        0.03376 (  696)
  hydrogen bonds       : angle       4.96330 ( 2026)

*********************** 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
  178 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8660 (m-80) cc_final: 0.8284 (m-80)
REVERT: A  200 THR cc_start: 0.8873 (m) cc_final: 0.8566 (p)
REVERT: A  398 MET cc_start: 0.8445 (mmm) cc_final: 0.7490 (mmm)
REVERT: A  431 MET cc_start: 0.8087 (ttt) cc_final: 0.7844 (ttt)
REVERT: A  573 GLN cc_start: 0.9287 (tp-100) cc_final: 0.8946 (mm-40)
REVERT: B  294 TYR cc_start: 0.8685 (OUTLIER) cc_final: 0.7909 (t80)
REVERT: B  432 MET cc_start: 0.8258 (ttm) cc_final: 0.7769 (tpp)
REVERT: C  573 GLN cc_start: 0.9162 (mm110) cc_final: 0.8830 (mm110)
REVERT: D  340 MET cc_start: 0.8282 (tmm) cc_final: 0.8026 (tmm)
REVERT: D  510 MET cc_start: 0.5749 (ppp) cc_final: 0.5542 (ppp)
  outliers start: 19
  outliers final: 16
  residues processed: 173
  average time/residue: 0.1319
  time to fit residues: 34.1619
Evaluate side-chains
  162 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 145
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  469 CYS
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  338 VAL
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  319 ASP
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  433 CYS
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 55 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 194 optimal weight:   10.0000
   chunk 192 optimal weight:    3.9990
   chunk 130 optimal weight:    7.9990
   chunk 188 optimal weight:    6.9990
   chunk 80 optimal weight:    0.9990
   chunk 65 optimal weight:    4.9990
   chunk 171 optimal weight:    4.9990
   chunk 66 optimal weight:    0.7980
   chunk 152 optimal weight:    0.0370
   overall best weight:    1.1664

-------------------------------------------------------------------------------
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**
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 264 ASN ** 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 = 0.4094 r_free = 0.4094 target = 0.102356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.076876 restraints weight = 87041.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 5.91
r_work: 0.3359 rms_B_bonded: 5.72 restraints_weight: 2.0000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3916

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= 0.143
  Angle     :  0.650  11.188  20794  Z= 0.326
  Chirality :  0.041   0.188   2358
  Planarity :  0.004   0.050   2681
  Dihedral  :  4.617  24.149   2100
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.75 %
    Favored  : 85.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.00 (0.19), residues: 1940
  helix:  0.31 (0.16), residues: 1031
  sheet: -0.21 (0.46), residues: 120
  loop : -0.19 (0.23), residues: 789

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 109 
 TYR   0.020   0.001   TYR C 237 
 PHE   0.035   0.001   PHE C 505 
 TRP   0.010   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (15382)
  covalent geometry    : angle       0.65005 (20794)
  hydrogen bonds       : bond        0.03447 (  696)
  hydrogen bonds       : angle       4.96159 ( 2026)

*********************** 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
  177 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 154
  time to evaluate  : 0.661 
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: 0.8619 (m-80) cc_final: 0.8234 (m-80)
REVERT: A  200 THR cc_start: 0.8887 (m) cc_final: 0.8603 (p)
REVERT: B  294 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7895 (t80)
REVERT: B  320 ARG cc_start: 0.8837 (mpp80) cc_final: 0.8584 (mtm-85)
REVERT: B  432 MET cc_start: 0.8352 (ttm) cc_final: 0.7860 (tpp)
REVERT: B  507 LEU cc_start: 0.9259 (mt) cc_final: 0.9057 (mp)
REVERT: C  573 GLN cc_start: 0.9173 (mm110) cc_final: 0.8836 (mm110)
REVERT: D  340 MET cc_start: 0.8345 (tmm) cc_final: 0.8053 (tmm)
REVERT: D  510 MET cc_start: 0.5691 (ppp) cc_final: 0.5469 (ppp)
REVERT: D  523 LEU cc_start: 0.9447 (tt) cc_final: 0.9113 (mp)
  outliers start: 23
  outliers final: 19
  residues processed: 171
  average time/residue: 0.1282
  time to fit residues: 33.0492
Evaluate side-chains
  167 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
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  469 CYS
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 C residue  338 VAL
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  319 ASP
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  433 CYS
Chi-restraints excluded: chain D residue  459 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 178 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9990
   chunk 107 optimal weight:    5.9990
   chunk 8 optimal weight:    2.9990
   chunk 150 optimal weight:    6.9990
   overall best weight:    1.0186

-------------------------------------------------------------------------------
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**
** B 427 ASN ** 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 = 0.4100 r_free = 0.4100 target = 0.102645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.077349 restraints weight = 84123.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 5.77
r_work: 0.3369 rms_B_bonded: 5.70 restraints_weight: 2.0000
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3369
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3369 r_free = 0.3369    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 = 0.3369 r_free = 0.3369    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3369
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4120

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= 0.132
  Angle     :  0.639  11.792  20794  Z= 0.319
  Chirality :  0.041   0.167   2358
  Planarity :  0.004   0.047   2681
  Dihedral  :  4.559  24.002   2100
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.19), residues: 1940
  helix:  0.39 (0.16), residues: 1027
  sheet:  0.03 (0.46), residues: 122
  loop : -0.14 (0.23), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 109 
 TYR   0.021   0.001   TYR C 237 
 PHE   0.043   0.001   PHE C 505 
 TRP   0.011   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (15382)
  covalent geometry    : angle       0.63938 (20794)
  hydrogen bonds       : bond        0.03310 (  696)
  hydrogen bonds       : angle       4.92687 ( 2026)

*********************** 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
  175 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 TYR cc_start: 0.8621 (m-80) cc_final: 0.8257 (m-80)
REVERT: A  200 THR cc_start: 0.8882 (m) cc_final: 0.8617 (p)
REVERT: A  573 GLN cc_start: 0.9353 (tp-100) cc_final: 0.8994 (mm-40)
REVERT: B  115 MET cc_start: 0.8306 (mmt) cc_final: 0.7774 (mpp)
REVERT: B  245 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8779 (mt-10)
REVERT: B  294 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7952 (t80)
REVERT: B  431 MET cc_start: 0.8397 (ttp) cc_final: 0.8077 (ttt)
REVERT: B  432 MET cc_start: 0.8313 (ttm) cc_final: 0.7824 (tpp)
REVERT: C  112 MET cc_start: 0.8872 (mmm) cc_final: 0.8663 (mmm)
REVERT: C  573 GLN cc_start: 0.9170 (mm110) cc_final: 0.8813 (mm110)
REVERT: D  340 MET cc_start: 0.8354 (tmm) cc_final: 0.8059 (tmm)
REVERT: D  523 LEU cc_start: 0.9446 (tt) cc_final: 0.9106 (mp)
REVERT: D  529 GLU cc_start: 0.8817 (tp30) cc_final: 0.8221 (tm-30)
  outliers start: 22
  outliers final: 18
  residues processed: 170
  average time/residue: 0.1290
  time to fit residues: 33.1787
Evaluate side-chains
  167 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 147
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  469 CYS
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  108 LEU
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  319 ASP
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  433 CYS
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 33 optimal weight:    1.9990
   chunk 158 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 103 optimal weight:    7.9990
   chunk 28 optimal weight:    0.7980
   chunk 80 optimal weight:    0.3980
   chunk 148 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   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 427 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 = 0.4109 r_free = 0.4109 target = 0.103101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.077495 restraints weight = 98063.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3542 rms_B_bonded: 6.29
r_work: 0.3367 rms_B_bonded: 6.08 restraints_weight: 2.0000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    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 = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.4255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15382  Z= 0.120
  Angle     :  0.640  11.991  20794  Z= 0.319
  Chirality :  0.041   0.247   2358
  Planarity :  0.004   0.047   2681
  Dihedral  :  4.467  24.059   2100
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.39 %
    Favored  : 95.61 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.54 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.20), residues: 1940
  helix:  0.42 (0.16), residues: 1027
  sheet:  0.14 (0.47), residues: 122
  loop : -0.08 (0.24), residues: 791

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 109 
 TYR   0.020   0.001   TYR C 237 
 PHE   0.044   0.001   PHE C 505 
 TRP   0.012   0.002   TRP C 194 
 HIS   0.004   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (15382)
  covalent geometry    : angle       0.64007 (20794)
  hydrogen bonds       : bond        0.03190 (  696)
  hydrogen bonds       : angle       4.87657 ( 2026)

*********************** 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
  183 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 161
  time to evaluate  : 0.740 
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: 0.8590 (m-80) cc_final: 0.8247 (m-80)
REVERT: A  200 THR cc_start: 0.8869 (m) cc_final: 0.8582 (p)
REVERT: A  401 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7900 (t80)
REVERT: A  573 GLN cc_start: 0.9404 (tp-100) cc_final: 0.9022 (mm-40)
REVERT: B  294 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.8019 (t80)
REVERT: B  320 ARG cc_start: 0.8822 (mpp80) cc_final: 0.8597 (mtm-85)
REVERT: B  431 MET cc_start: 0.8424 (ttp) cc_final: 0.8097 (ttt)
REVERT: B  432 MET cc_start: 0.8279 (ttm) cc_final: 0.7822 (tpp)
REVERT: C  112 MET cc_start: 0.8888 (mmm) cc_final: 0.8665 (mmm)
REVERT: C  573 GLN cc_start: 0.9170 (mm110) cc_final: 0.8803 (mm110)
REVERT: D  115 MET cc_start: 0.8400 (tpp) cc_final: 0.8185 (tpp)
REVERT: D  340 MET cc_start: 0.8338 (tmm) cc_final: 0.8055 (tmm)
REVERT: D  341 MET cc_start: 0.7079 (mmm) cc_final: 0.6828 (mmm)
REVERT: D  523 LEU cc_start: 0.9443 (tt) cc_final: 0.9115 (mp)
REVERT: D  529 GLU cc_start: 0.8805 (tp30) cc_final: 0.8215 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 178
  average time/residue: 0.1325
  time to fit residues: 35.7068
Evaluate side-chains
  170 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.622 
-------------------------------------------------------------------------------
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  469 CYS
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  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  525 VAL
Chi-restraints excluded: chain D residue  108 LEU
Chi-restraints excluded: chain D residue  216 CYS
Chi-restraints excluded: chain D residue  319 ASP
Chi-restraints excluded: chain D residue  320 ARG
Chi-restraints excluded: chain D residue  433 CYS
Chi-restraints excluded: chain D residue  459 ASN
Chi-restraints excluded: chain D residue  552 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 92 optimal weight:   10.0000
   chunk 115 optimal weight:    0.6980
   chunk 128 optimal weight:    2.9990
   chunk 110 optimal weight:    0.9990
   chunk 91 optimal weight:    6.9990
   chunk 188 optimal weight:    5.9990
   chunk 109 optimal weight:    8.9990
   chunk 6 optimal weight:    1.9990
   chunk 159 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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**
B 388 ASN
** B 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 264 ASN ** 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 = 0.4090 r_free = 0.4090 target = 0.101785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.076273 restraints weight = 98432.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 6.45
r_work: 0.3323 rms_B_bonded: 6.17 restraints_weight: 2.0000
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3324
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3324 r_free = 0.3324    target_work(ls_wunit_k1) = 0.067         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3324
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.4409

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= 0.169
  Angle     :  0.684  11.701  20794  Z= 0.344
  Chirality :  0.042   0.167   2358
  Planarity :  0.004   0.052   2681
  Dihedral  :  4.718  22.838   2100
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.79 %
    Favored  : 84.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.20), residues: 1940
  helix:  0.35 (0.16), residues: 1025
  sheet:  0.15 (0.47), residues: 118
  loop : -0.17 (0.23), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 109 
 TYR   0.021   0.002   TYR C 237 
 PHE   0.043   0.001   PHE C 505 
 TRP   0.007   0.001   TRP C 194 
 HIS   0.005   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (15382)
  covalent geometry    : angle       0.68367 (20794)
  hydrogen bonds       : bond        0.03600 (  696)
  hydrogen bonds       : angle       4.97482 ( 2026)

*********************** 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
  175 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 0.635 
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: 0.8660 (m-80) cc_final: 0.8317 (m-80)
REVERT: A  200 THR cc_start: 0.8900 (m) cc_final: 0.8640 (p)
REVERT: A  573 GLN cc_start: 0.9467 (tp-100) cc_final: 0.9062 (mm-40)
REVERT: B  294 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7918 (t80)
REVERT: C  280 MET cc_start: 0.9074 (pmm) cc_final: 0.8684 (pmm)
REVERT: C  573 GLN cc_start: 0.9212 (mm110) cc_final: 0.8848 (mm110)
REVERT: D  340 MET cc_start: 0.8412 (tmm) cc_final: 0.8095 (tmm)
REVERT: D  523 LEU cc_start: 0.9447 (tt) cc_final: 0.9122 (mp)
REVERT: D  529 GLU cc_start: 0.8827 (tp30) cc_final: 0.8240 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 169
  average time/residue: 0.1312
  time to fit residues: 33.3925
Evaluate side-chains
  166 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 148
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  469 CYS
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  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  525 VAL
Chi-restraints excluded: chain D residue  319 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 146 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 188 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 182 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 127 optimal weight:    0.6980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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**
** 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 = 0.103567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.077956 restraints weight = 103706.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3553 rms_B_bonded: 6.73
r_work: 0.3366 rms_B_bonded: 6.39 restraints_weight: 2.0000
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    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 = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3367
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.4487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  15382  Z= 0.124
  Angle     :  0.669  12.763  20794  Z= 0.334
  Chirality :  0.041   0.200   2358
  Planarity :  0.004   0.055   2681
  Dihedral  :  4.539  23.602   2100
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 14.83 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.19), residues: 1940
  helix:  0.44 (0.16), residues: 1024
  sheet:  0.16 (0.47), residues: 118
  loop : -0.15 (0.23), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 109 
 TYR   0.021   0.001   TYR C 237 
 PHE   0.043   0.001   PHE C 505 
 TRP   0.013   0.002   TRP A 194 
 HIS   0.004   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 (15382)
  covalent geometry    : angle       0.66853 (20794)
  hydrogen bonds       : bond        0.03263 (  696)
  hydrogen bonds       : angle       4.89275 ( 2026)

********************** 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
  168 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 155
  time to evaluate  : 0.614 
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: 0.8601 (m-80) cc_final: 0.8262 (m-80)
REVERT: A  200 THR cc_start: 0.8872 (m) cc_final: 0.8599 (p)
REVERT: A  398 MET cc_start: 0.8370 (mmm) cc_final: 0.7345 (mmm)
REVERT: A  432 MET cc_start: 0.8644 (ttm) cc_final: 0.7865 (mtm)
REVERT: A  573 GLN cc_start: 0.9468 (tp-100) cc_final: 0.9052 (mm-40)
REVERT: B  115 MET cc_start: 0.8340 (mmt) cc_final: 0.7734 (mpp)
REVERT: B  294 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7965 (t80)
REVERT: B  432 MET cc_start: 0.8267 (ttm) cc_final: 0.7765 (tpp)
REVERT: C  112 MET cc_start: 0.8894 (mmm) cc_final: 0.8644 (mmm)
REVERT: C  280 MET cc_start: 0.9059 (pmm) cc_final: 0.8661 (pmm)
REVERT: C  573 GLN cc_start: 0.9198 (mm110) cc_final: 0.8830 (mm110)
REVERT: D  294 TYR cc_start: 0.8075 (OUTLIER) cc_final: 0.6598 (t80)
REVERT: D  340 MET cc_start: 0.8360 (tmm) cc_final: 0.8080 (tmm)
REVERT: D  523 LEU cc_start: 0.9441 (tt) cc_final: 0.9095 (mp)
REVERT: D  529 GLU cc_start: 0.8813 (tp30) cc_final: 0.8215 (tm-30)
REVERT: D  533 GLU cc_start: 0.9445 (pm20) cc_final: 0.9209 (pm20)
  outliers start: 13
  outliers final: 11
  residues processed: 163
  average time/residue: 0.1340
  time to fit residues: 32.6678
Evaluate side-chains
  163 residues out of total 1676 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  366 THR
Chi-restraints excluded: chain A residue  401 PHE
Chi-restraints excluded: chain A residue  469 CYS
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  488 VAL
Chi-restraints excluded: chain B residue  573 GLN
Chi-restraints excluded: chain D residue  294 TYR
Chi-restraints excluded: chain D residue  319 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 188 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 44 optimal weight:    1.9990
   chunk 95 optimal weight:    3.9990
   chunk 70 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 135 optimal weight:    0.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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**
** 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 = 0.4106 r_free = 0.4106 target = 0.102703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.077057 restraints weight = 106217.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3538 rms_B_bonded: 6.75
r_work: 0.3349 rms_B_bonded: 6.25 restraints_weight: 2.0000
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.4537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15382  Z= 0.139
  Angle     :  0.678  12.731  20794  Z= 0.338
  Chirality :  0.041   0.194   2358
  Planarity :  0.004   0.052   2681
  Dihedral  :  4.546  23.132   2100
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.89 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.16 (0.19), residues: 1940
  helix:  0.42 (0.16), residues: 1022
  sheet:  0.33 (0.48), residues: 114
  loop : -0.16 (0.23), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 320 
 TYR   0.027   0.001   TYR A 347 
 PHE   0.045   0.001   PHE C 505 
 TRP   0.010   0.001   TRP A 194 
 HIS   0.004   0.001   HIS D 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15382)
  covalent geometry    : angle       0.67849 (20794)
  hydrogen bonds       : bond        0.03354 (  696)
  hydrogen bonds       : angle       4.89939 ( 2026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6253.67 seconds
wall clock time: 107 minutes 34.10 seconds (6454.10 seconds total)