Starting phenix.real_space_refine
on Fri Feb 16 12:11:24 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2024/8gu6_34270.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2024/8gu6_34270.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2024/8gu6_34270.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2024/8gu6_34270.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2024/8gu6_34270.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gu6_34270/02_2024/8gu6_34270.pdb"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.036
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     P      50      5.49       5
     S      51      5.16       5
     C    9590      2.51       5
     N    2670      2.21       5
     O    2896      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "D TYR   76": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  195": "OD1" <-> "OD2"
    Residue "D TYR  259": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR  360": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D ASP  475": "OD1" <-> "OD2"
    Residue "D PHE  703": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  298": "OD1" <-> "OD2"
    Residue "A GLU  412": "OE1" <-> "OE2"
    Residue "A ASP  520": "OD1" <-> "OD2"
    Residue "A ASP  542": "OD1" <-> "OD2"
    Residue "A ASP  771": "OD1" <-> "OD2"
    Residue "A ASP  806": "OD1" <-> "OD2"
    Residue "A PHE 1011": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1022": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1557": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 15261
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 4880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 659, 4880
          Classifications: {'peptide': 659}
          Incomplete info: {'truncation_to_alanine': 125}
          Link IDs: {'PTRANS': 19, 'TRANS': 639}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 479
          Unresolved non-hydrogen angles: 598
          Unresolved non-hydrogen dihedrals: 391
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 15, 'TRP:plan': 1, 'ASP:plan': 22, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 316
    Chain: "A"
      Number of atoms: 9314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1211, 9314
          Classifications: {'peptide': 1211}
          Incomplete info: {'truncation_to_alanine': 133}
          Link IDs: {'PTRANS': 59, 'TRANS': 1151}
          Chain breaks: 13
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 485
          Unresolved non-hydrogen angles: 598
          Unresolved non-hydrogen dihedrals: 385
          Unresolved non-hydrogen chiralities: 15
          Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 26, 'TYR:plan': 2, 'ASN:plan1': 14, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 34, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 337
    Chain: "C"
      Number of atoms: 689
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 689
          Classifications: {'RNA': 33}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 9, 'rna3p_pur': 2, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 18, 'rna3p': 14}
    Chain: "J"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 374
          Classifications: {'RNA': 17}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 12, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 1, 'rna3p': 15}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' ZN': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8188  SG  CYS A 491      42.410  50.382 109.592  1.00 56.88           S
  ATOM   8256  SG  CYS A 501      42.340  50.002 113.239  1.00 43.26           S
  ATOM   8270  SG  CYS A 503      39.054  50.135 111.347  1.00 51.40           S
  ATOM   8292  SG  CYS A 506      41.174  47.041 110.957  1.00 42.41           S
  ATOM   5526  SG  CYS A  88      41.869  29.986 135.607  1.00 52.94           S
  ATOM   5769  SG  CYS A 121      42.592  27.562 138.440  1.00 80.14           S
  ATOM   5800  SG  CYS A 127      41.344  26.344 135.032  1.00 50.36           S
  ATOM   5824  SG  CYS A 130      44.895  27.615 135.412  1.00 49.35           S
  ATOM  10157  SG  CYS A 750      48.196  66.675  85.818  1.00 94.35           S
  ATOM  10170  SG  CYS A 752      45.399  65.843  83.413  1.00 72.34           S
  ATOM  10192  SG  CYS A 755      47.298  62.993  84.983  1.00 66.08           S
  ATOM  12065  SG  CYS A1018      57.375  61.363  49.287  1.00 82.93           S
  ATOM  12218  SG  CYS A1406      57.984  62.296  52.978  1.00 87.64           S
  ATOM  12269  SG  CYS A1414      57.266  64.947  50.377  1.00 79.23           S
  ATOM  12286  SG  CYS A1417      54.544  62.425  51.493  1.00 64.66           S

  Time building chain proxies: 8.50, per 1000 atoms: 0.56
  Number of scatterers: 15261
  At special positions: 0
  Unit cell: (101.65, 95, 158.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      4     29.99
     S      51     16.00
     P      50     15.00
     O    2896      8.00
     N    2670      7.00
     C    9590      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  - 3.50
        Amino acid           : False - 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: 6.40
  Conformation dependent library (CDL) restraints added in 2.4 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1801 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 491 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 503 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 501 "
        pdb="ZN    ZN A1801 " - pdb=" SG  CYS A 506 "
      pdb="  ZN A1802 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 127 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A  88 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 121 "
        pdb="ZN    ZN A1802 " - pdb=" SG  CYS A 130 "
      pdb="  ZN A1803 "
        pdb="ZN    ZN A1803 " - pdb=" ND1 HIS A 747 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 752 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 755 "
        pdb="ZN    ZN A1803 " - pdb=" SG  CYS A 750 "
      pdb="  ZN A1804 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1018 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1417 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1406 "
        pdb="ZN    ZN A1804 " - pdb=" SG  CYS A1414 "
      Number of angles added : 21


  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3464

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 22 sheets defined
      41.7% alpha, 11.9% beta
      11 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 5.54
  Creating SS restraints...
    Processing helix  chain 'D' and resid 15 through 33
    Processing helix  chain 'D' and resid 37 through 59
      removed outlier: 3.938A  pdb=" N   LYS D  43 " --> pdb=" O   VAL D  39 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLU D  58 " --> pdb=" O   GLY D  54 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   LYS D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 64 through 82
      removed outlier: 3.643A  pdb=" N   ILE D  82 " --> pdb=" O   VAL D  78 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 110
      removed outlier: 3.550A  pdb=" N   LYS D  94 " --> pdb=" O   PRO D  90 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ARG D 106 " --> pdb=" O   GLU D 102 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ALA D 107 " --> pdb=" O   PHE D 103 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 114 through 136
    Processing helix  chain 'D' and resid 141 through 156
    Processing helix  chain 'D' and resid 163 through 176
      removed outlier: 3.611A  pdb=" N   ILE D 167 " --> pdb=" O   TYR D 163 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 182
      No H-bonds generated for 'chain 'D' and resid 180 through 182'
    Processing helix  chain 'D' and resid 183 through 190
      removed outlier: 3.942A  pdb=" N   LYS D 189 " --> pdb=" O   ASP D 185 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 205
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 3.703A  pdb=" N   LYS D 218 " --> pdb=" O   GLU D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 230 through 246
      removed outlier: 4.095A  pdb=" N   ASP D 234 " --> pdb=" O   HIS D 230 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 250 through 269
      removed outlier: 3.602A  pdb=" N   PHE D 254 " --> pdb=" O   LEU D 250 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   GLU D 268 " --> pdb=" O   VAL D 264 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   THR D 269 " --> pdb=" O   GLN D 265 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 280 through 297
    Processing helix  chain 'D' and resid 302 through 322
      removed outlier: 3.559A  pdb=" N   LYS D 306 " --> pdb=" O   ASP D 302 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 327 through 332
    Processing helix  chain 'D' and resid 339 through 359
      removed outlier: 3.601A  pdb=" N   GLU D 344 " --> pdb=" O   GLU D 340 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN D 357 " --> pdb=" O   VAL D 353 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLY D 359 " --> pdb=" O   ALA D 355 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 433 through 448
    Processing helix  chain 'D' and resid 451 through 453
      No H-bonds generated for 'chain 'D' and resid 451 through 453'
    Processing helix  chain 'D' and resid 454 through 469
    Processing helix  chain 'D' and resid 470 through 473
      removed outlier: 3.501A  pdb=" N   PHE D 473 " --> pdb=" O   PRO D 470 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 470 through 473'
    Processing helix  chain 'D' and resid 496 through 500
    Processing helix  chain 'D' and resid 509 through 514
      removed outlier: 4.261A  pdb=" N   ASN D 513 " --> pdb=" O   LEU D 509 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   HIS D 514 " --> pdb=" O   PHE D 510 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 509 through 514'
    Processing helix  chain 'D' and resid 521 through 525
    Processing helix  chain 'D' and resid 566 through 572
    Processing helix  chain 'D' and resid 592 through 595
    Processing helix  chain 'D' and resid 607 through 613
    Processing helix  chain 'D' and resid 628 through 632
      removed outlier: 3.550A  pdb=" N   VAL D 632 " --> pdb=" O   THR D 629 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 644 through 653
      removed outlier: 3.684A  pdb=" N   ALA D 648 " --> pdb=" O   SER D 644 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 665 through 675
      removed outlier: 3.851A  pdb=" N   THR D 669 " --> pdb=" O   ARG D 665 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 685 through 691
      removed outlier: 4.165A  pdb=" N   LYS D 689 " --> pdb=" O   ASN D 685 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 699 through 708
      removed outlier: 3.999A  pdb=" N   ALA D 708 " --> pdb=" O   TYR D 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 30
      removed outlier: 4.404A  pdb=" N   LYS A  30 " --> pdb=" O   TRP A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
    Processing helix  chain 'A' and resid 59 through 78
    Processing helix  chain 'A' and resid 127 through 134
    Processing helix  chain 'A' and resid 168 through 173
      removed outlier: 3.563A  pdb=" N   ILE A 172 " --> pdb=" O   ARG A 168 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 215
      No H-bonds generated for 'chain 'A' and resid 213 through 215'
    Processing helix  chain 'A' and resid 216 through 227
      removed outlier: 3.548A  pdb=" N   LEU A 220 " --> pdb=" O   ALA A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 287
    Processing helix  chain 'A' and resid 292 through 303
    Processing helix  chain 'A' and resid 308 through 313
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 471 through 488
    Processing helix  chain 'A' and resid 503 through 510
      removed outlier: 3.582A  pdb=" N   GLU A 508 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 580
    Processing helix  chain 'A' and resid 594 through 598
    Processing helix  chain 'A' and resid 617 through 624
      removed outlier: 3.631A  pdb=" N   TYR A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 625 through 628
    Processing helix  chain 'A' and resid 630 through 637
      removed outlier: 3.579A  pdb=" N   LEU A 634 " --> pdb=" O   LYS A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 657
    Processing helix  chain 'A' and resid 658 through 665
    Processing helix  chain 'A' and resid 687 through 693
      removed outlier: 3.546A  pdb=" N   LEU A 691 " --> pdb=" O   THR A 687 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   THR A 692 " --> pdb=" O   ILE A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 740
    Processing helix  chain 'A' and resid 752 through 759
    Processing helix  chain 'A' and resid 831 through 848
    Processing helix  chain 'A' and resid 873 through 881
      removed outlier: 3.670A  pdb=" N   MET A 879 " --> pdb=" O   ASP A 875 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 880 " --> pdb=" O   PHE A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.889A  pdb=" N   ASP A 914 " --> pdb=" O   SER A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1015
      removed outlier: 3.745A  pdb=" N   LEU A1003 " --> pdb=" O   PRO A 999 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1395 through 1399
      removed outlier: 3.574A  pdb=" N   LYS A1398 " --> pdb=" O   LEU A1395 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU A1399 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1395 through 1399'
    Processing helix  chain 'A' and resid 1408 through 1412
      removed outlier: 3.625A  pdb=" N   ASP A1411 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1414 through 1421
    Processing helix  chain 'A' and resid 1463 through 1468
      removed outlier: 4.064A  pdb=" N   SER A1467 " --> pdb=" O   ARG A1463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1486 through 1493
      removed outlier: 3.791A  pdb=" N   ILE A1490 " --> pdb=" O   GLY A1486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1493 through 1499
    Processing helix  chain 'A' and resid 1528 through 1540
      removed outlier: 3.779A  pdb=" N   GLY A1533 " --> pdb=" O   GLU A1529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1552 through 1556
    Processing helix  chain 'A' and resid 1583 through 1588
    Processing helix  chain 'A' and resid 1590 through 1601
      removed outlier: 3.541A  pdb=" N   GLU A1600 " --> pdb=" O   GLN A1596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1615 through 1618
    Processing helix  chain 'A' and resid 1619 through 1629
    Processing helix  chain 'A' and resid 1675 through 1681
    Processing sheet with id=AA1, first strand: chain 'D' and resid 425 through 431
      removed outlier: 3.765A  pdb=" N   ASP D 420 " --> pdb=" O   SER D 425 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   CYS D 516 " --> pdb=" O   PHE D 709 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   SER D 711 " --> pdb=" O   CYS D 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 562 through 563
      removed outlier: 6.583A  pdb=" N   VAL D 537 " --> pdb=" O   THR D 581 " (cutoff:3.500A)
      removed outlier: 7.925A  pdb=" N   LEU D 583 " --> pdb=" O   VAL D 537 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   LEU D 539 " --> pdb=" O   LEU D 583 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 597 through 598
    Processing sheet with id=AA4, first strand: chain 'A' and resid 20 through 22
      removed outlier: 6.507A  pdb=" N   VAL A  21 " --> pdb=" O   TRP A  44 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   SER A  56 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 20 through 22
      removed outlier: 6.507A  pdb=" N   VAL A  21 " --> pdb=" O   TRP A  44 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   SER A  56 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA7, first strand: chain 'A' and resid 110 through 111
      removed outlier: 6.008A  pdb=" N   THR A 110 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 176 through 181
      removed outlier: 3.701A  pdb=" N   PHE A 192 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ASP A 190 " --> pdb=" O   ARG A 180 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 229 through 230
    Processing sheet with id=AB1, first strand: chain 'A' and resid 512 through 514
      removed outlier: 3.515A  pdb=" N   PHE A 557 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   ILE A 417 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   ILE A 609 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   VAL A 419 " --> pdb=" O   ILE A 607 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ILE A 607 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 431 through 432
      removed outlier: 4.258A  pdb=" N   ASN A 459 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 469 through 470
      removed outlier: 3.587A  pdb=" N   SER A 517 " --> pdb=" O   ILE A 470 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 526 through 530
    Processing sheet with id=AB5, first strand: chain 'A' and resid 721 through 722
      removed outlier: 3.872A  pdb=" N   GLU A 773 " --> pdb=" O   LYS A 821 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 721 through 722
      removed outlier: 3.872A  pdb=" N   GLU A 773 " --> pdb=" O   LYS A 821 " (cutoff:3.500A)
      removed outlier: 7.906A  pdb=" N   GLN A 673 " --> pdb=" O   ILE A 868 " (cutoff:3.500A)
      removed outlier: 5.290A  pdb=" N   ILE A 868 " --> pdb=" O   GLN A 673 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   THR A 675 " --> pdb=" O   ILE A 866 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   ILE A 866 " --> pdb=" O   THR A 675 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   GLU A 677 " --> pdb=" O   ALA A 864 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 699 through 700
      removed outlier: 7.161A  pdb=" N   ALA A 699 " --> pdb=" O   TYR A 808 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 920 through 921
      removed outlier: 3.672A  pdb=" N   TYR A 921 " --> pdb=" O   ASP A1642 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'A' and resid 924 through 927
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1519 through 1522
      removed outlier: 6.819A  pdb=" N   ASN A 955 " --> pdb=" O   ASP A1565 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 985 through 987
      removed outlier: 3.917A  pdb=" N   GLU A1510 " --> pdb=" O   TYR A 987 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   THR A1509 " --> pdb=" O   LEU A1454 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 991 through 992
    Processing sheet with id=AC4, first strand: chain 'A' and resid 1647 through 1648
      removed outlier: 6.753A  pdb=" N   VAL A1647 " --> pdb=" O   TYR A1663 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4

    589 hydrogen bonds defined for protein.
    1647 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      29 hydrogen bonds
      58 hydrogen bond angles
      0 basepair planarities
      11 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 6.51

  Time building geometry restraints manager: 6.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 4328
        1.33 -     1.45: 2854
        1.45 -     1.57: 8353
        1.57 -     1.69: 98
        1.69 -     1.81: 69
  Bond restraints: 15702
  Sorted by residual:
  bond pdb=" C   SER A 910 "
       pdb=" N   PRO A 911 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 9.80e-03 1.04e+04 1.96e+00
  bond pdb=" CB  GLU D 398 "
       pdb=" CG  GLU D 398 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.16e-01
  bond pdb=" C   PRO D 700 "
       pdb=" N   PRO D 701 "
    ideal  model  delta    sigma   weight residual
    1.336  1.345 -0.010 1.23e-02 6.61e+03 6.44e-01
  bond pdb=" CG1 ILE D  45 "
       pdb=" CD1 ILE D  45 "
    ideal  model  delta    sigma   weight residual
    1.513  1.483  0.030 3.90e-02 6.57e+02 5.92e-01
  bond pdb=" CB  GLU D  23 "
       pdb=" CG  GLU D  23 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.85e-01
  ... (remaining 15697 not shown)

  Histogram of bond angle deviations from ideal:
       99.51 -   106.48: 672
      106.48 -   113.44: 8573
      113.44 -   120.41: 5791
      120.41 -   127.38: 6202
      127.38 -   134.34: 268
  Bond angle restraints: 21506
  Sorted by residual:
  angle pdb=" O4'   G C  11 "
        pdb=" C1'   G C  11 "
        pdb=" N9    G C  11 "
      ideal   model   delta    sigma   weight residual
     108.20  115.61   -7.41 1.50e+00 4.44e-01 2.44e+01
  angle pdb=" CA  LEU A 366 "
        pdb=" CB  LEU A 366 "
        pdb=" CG  LEU A 366 "
      ideal   model   delta    sigma   weight residual
     116.30  131.40  -15.10 3.50e+00 8.16e-02 1.86e+01
  angle pdb=" O4'   A C  -2 "
        pdb=" C1'   A C  -2 "
        pdb=" N9    A C  -2 "
      ideal   model   delta    sigma   weight residual
     108.20  112.52   -4.32 1.50e+00 4.44e-01 8.29e+00
  angle pdb=" N   GLU A1441 "
        pdb=" CA  GLU A1441 "
        pdb=" C   GLU A1441 "
      ideal   model   delta    sigma   weight residual
     110.97  114.10   -3.13 1.09e+00 8.42e-01 8.23e+00
  angle pdb=" N   LEU A 366 "
        pdb=" CA  LEU A 366 "
        pdb=" CB  LEU A 366 "
      ideal   model   delta    sigma   weight residual
     110.28  114.68   -4.40 1.55e+00 4.16e-01 8.07e+00
  ... (remaining 21501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.68: 8925
       35.68 -    71.36: 417
       71.36 -   107.04: 21
      107.04 -   142.72: 2
      142.72 -   178.40: 2
  Dihedral angle restraints: 9367
    sinusoidal: 3991
      harmonic: 5376
  Sorted by residual:
  dihedral pdb=" O4'   U C  -9 "
           pdb=" C1'   U C  -9 "
           pdb=" N1    U C  -9 "
           pdb=" C2    U C  -9 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   53.60  178.40     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U C  10 "
           pdb=" C1'   U C  10 "
           pdb=" N1    U C  10 "
           pdb=" C2    U C  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   44.11 -172.11     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" O4'   U C -15 "
           pdb=" C1'   U C -15 "
           pdb=" N1    U C -15 "
           pdb=" C2    U C -15 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00  -91.17  -68.83     1      1.50e+01 4.44e-03 2.73e+01
  ... (remaining 9364 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 2239
       0.073 -    0.146: 186
       0.146 -    0.218: 6
       0.218 -    0.291: 0
       0.291 -    0.364: 1
  Chirality restraints: 2432
  Sorted by residual:
  chirality pdb=" C1'   G C  11 "
            pdb=" O4'   G C  11 "
            pdb=" C2'   G C  11 "
            pdb=" N9    G C  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.07    0.36 2.00e-01 2.50e+01 3.31e+00
  chirality pdb=" C1'   A C  -2 "
            pdb=" O4'   A C  -2 "
            pdb=" C2'   A C  -2 "
            pdb=" N9    A C  -2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.18 2.00e-01 2.50e+01 8.42e-01
  chirality pdb=" CB  ILE D  80 "
            pdb=" CA  ILE D  80 "
            pdb=" CG1 ILE D  80 "
            pdb=" CG2 ILE D  80 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 7.88e-01
  ... (remaining 2429 not shown)

  Planarity restraints: 2558
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G C  11 "   -0.047 2.00e-02 2.50e+03   2.16e-02 1.40e+01
        pdb=" N9    G C  11 "    0.056 2.00e-02 2.50e+03
        pdb=" C8    G C  11 "    0.004 2.00e-02 2.50e+03
        pdb=" N7    G C  11 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G C  11 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6    G C  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" O6    G C  11 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    G C  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2    G C  11 "   -0.003 2.00e-02 2.50e+03
        pdb=" N2    G C  11 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    G C  11 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    G C  11 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A1475 "   -0.051 5.00e-02 4.00e+02   7.76e-02 9.63e+00
        pdb=" N   PRO A1476 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A1476 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A1476 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A C   3 "   -0.031 2.00e-02 2.50e+03   1.45e-02 5.78e+00
        pdb=" N9    A C   3 "    0.036 2.00e-02 2.50e+03
        pdb=" C8    A C   3 "    0.000 2.00e-02 2.50e+03
        pdb=" N7    A C   3 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A C   3 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    A C   3 "   -0.004 2.00e-02 2.50e+03
        pdb=" N6    A C   3 "   -0.006 2.00e-02 2.50e+03
        pdb=" N1    A C   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2    A C   3 "    0.003 2.00e-02 2.50e+03
        pdb=" N3    A C   3 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    A C   3 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2555 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 295
        2.65 -     3.21: 14000
        3.21 -     3.78: 25283
        3.78 -     4.34: 34607
        4.34 -     4.90: 56189
  Nonbonded interactions: 130374
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 186 "
            pdb=" O2'   C C  -1 "
     model   vdw
     2.091 2.440
  nonbonded pdb=" O   LYS D 321 "
            pdb=" OH  TYR D 643 "
     model   vdw
     2.136 2.440
  nonbonded pdb=" O   ALA A 685 "
            pdb=" O2'   U C   5 "
     model   vdw
     2.163 2.440
  nonbonded pdb=" O   ASN A 179 "
            pdb=" O2'   G C  -4 "
     model   vdw
     2.189 2.440
  nonbonded pdb=" N   THR D 629 "
            pdb=" O   THR D 660 "
     model   vdw
     2.194 2.520
  ... (remaining 130369 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          6.460
  Check model and map are aligned:         0.220
  Set scattering table:                    0.140
  Process input model:                     50.090
  Find NCS groups from input model:        0.410
  Set up NCS constraints:                  0.060
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
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      :  0.002   0.033  15702  Z= 0.157
  Angle     :  0.534  15.101  21506  Z= 0.283
  Chirality :  0.040   0.364   2432
  Planarity :  0.004   0.078   2558
  Dihedral  : 18.657 178.395   5903
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 13.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 28.99 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.19), residues: 1832
  helix:  1.28 (0.21), residues: 647
  sheet: -0.79 (0.35), residues: 221
  loop : -1.15 (0.19), residues: 964

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D 165 
 HIS   0.012   0.001   HIS A1621 
 PHE   0.019   0.001   PHE A1011 
 TYR   0.022   0.001   TYR D 259 
 ARG   0.007   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 167
  time to evaluate  : 1.856 
Fit side-chains
REVERT: D  420 ASP cc_start: 0.7551 (p0) cc_final: 0.7033 (p0)
REVERT: D  630 ASP cc_start: 0.7911 (p0) cc_final: 0.7527 (p0)
REVERT: D  666 SER cc_start: 0.7254 (m) cc_final: 0.6776 (p)
REVERT: A  308 GLU cc_start: 0.6421 (pm20) cc_final: 0.5741 (pt0)
REVERT: A  762 HIS cc_start: 0.7015 (m170) cc_final: 0.6804 (m-70)
REVERT: A  771 ASP cc_start: 0.8249 (m-30) cc_final: 0.7603 (m-30)
REVERT: A  995 GLU cc_start: 0.7704 (pt0) cc_final: 0.7268 (pt0)
  outliers start: 2
  outliers final: 2
  residues processed: 169
  average time/residue: 0.3292
  time to fit residues: 80.2164
Evaluate side-chains
  155 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 1.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  195 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    4.9990
   chunk 144 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 148 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 90 optimal weight:    0.9990
   chunk 110 optimal weight:    0.0270
   chunk 172 optimal weight:    3.9990
   overall best weight:    1.6046

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 448 ASN
A 306 HIS
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 924 HIS
A1494 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.0942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  15702  Z= 0.308
  Angle     :  0.571   8.789  21506  Z= 0.297
  Chirality :  0.043   0.382   2432
  Planarity :  0.004   0.060   2558
  Dihedral  : 15.083 172.407   2777
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 26.39 %
    Favored  : 69.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.44 (0.19), residues: 1832
  helix:  1.18 (0.20), residues: 663
  sheet: -1.00 (0.34), residues: 229
  loop : -1.20 (0.19), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 330 
 HIS   0.011   0.001   HIS A1621 
 PHE   0.016   0.002   PHE A 358 
 TYR   0.018   0.001   TYR D 607 
 ARG   0.005   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 151
  time to evaluate  : 1.649 
Fit side-chains
   revert: symmetry clash
REVERT: D  542 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.6610 (m-80)
REVERT: A  107 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.7951 (ptmt)
REVERT: A  762 HIS cc_start: 0.7048 (m170) cc_final: 0.6825 (m-70)
REVERT: A  877 LYS cc_start: 0.7199 (tptm) cc_final: 0.6837 (mtpp)
REVERT: A  927 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.7140 (tt)
REVERT: A 1487 TRP cc_start: 0.7679 (p-90) cc_final: 0.7389 (p-90)
  outliers start: 56
  outliers final: 27
  residues processed: 193
  average time/residue: 0.3016
  time to fit residues: 84.5662
Evaluate side-chains
  171 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 30
    poor density    : 141
  time to evaluate  : 1.603 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  195 ASP
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  468 THR
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 143 optimal weight:    1.9990
   chunk 117 optimal weight:    0.6980
   chunk 47 optimal weight:    0.1980
   chunk 172 optimal weight:    0.9990
   chunk 186 optimal weight:    4.9990
   chunk 153 optimal weight:   10.0000
   chunk 171 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 138 optimal weight:    3.9990
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1494 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15702  Z= 0.190
  Angle     :  0.506   9.667  21506  Z= 0.265
  Chirality :  0.041   0.377   2432
  Planarity :  0.004   0.052   2558
  Dihedral  : 14.963 175.739   2774
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 25.38 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.19), residues: 1832
  helix:  1.36 (0.20), residues: 664
  sheet: -0.91 (0.35), residues: 221
  loop : -1.14 (0.19), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP A 330 
 HIS   0.008   0.001   HIS A1621 
 PHE   0.014   0.001   PHE D 491 
 TYR   0.016   0.001   TYR D 607 
 ARG   0.006   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 155
  time to evaluate  : 1.629 
Fit side-chains
   revert: symmetry clash
REVERT: D  542 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6467 (m-80)
REVERT: D  585 HIS cc_start: 0.6356 (OUTLIER) cc_final: 0.6035 (p-80)
REVERT: A  389 TYR cc_start: 0.8062 (t80) cc_final: 0.7756 (t80)
REVERT: A  529 TYR cc_start: 0.8514 (m-80) cc_final: 0.8079 (m-80)
REVERT: A  605 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7808 (ptpt)
REVERT: A  771 ASP cc_start: 0.8184 (m-30) cc_final: 0.7515 (m-30)
REVERT: A  877 LYS cc_start: 0.7241 (tptm) cc_final: 0.6834 (mtpp)
REVERT: A  927 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7188 (tt)
REVERT: A 1487 TRP cc_start: 0.7776 (p-90) cc_final: 0.7550 (p-90)
  outliers start: 68
  outliers final: 29
  residues processed: 203
  average time/residue: 0.2832
  time to fit residues: 85.4476
Evaluate side-chains
  179 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 146
  time to evaluate  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain D residue  594 PHE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1511 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 170 optimal weight:    5.9990
   chunk 129 optimal weight:    4.9990
   chunk 89 optimal weight:    0.8980
   chunk 19 optimal weight:    0.6980
   chunk 82 optimal weight:    4.9990
   chunk 116 optimal weight:    4.9990
   chunk 173 optimal weight:    3.9990
   chunk 183 optimal weight:   20.0000
   chunk 90 optimal weight:    0.9980
   chunk 164 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0020
   overall best weight:    1.1190

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15702  Z= 0.240
  Angle     :  0.530  10.150  21506  Z= 0.274
  Chirality :  0.042   0.373   2432
  Planarity :  0.004   0.046   2558
  Dihedral  : 14.924 173.274   2772
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  5.86 %
    Allowed  : 24.87 %
    Favored  : 69.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.31 (0.19), residues: 1832
  helix:  1.33 (0.20), residues: 667
  sheet: -0.98 (0.34), residues: 221
  loop : -1.16 (0.19), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 330 
 HIS   0.010   0.001   HIS A1484 
 PHE   0.014   0.001   PHE D 491 
 TYR   0.016   0.001   TYR D 607 
 ARG   0.006   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 81
    poor density    : 155
  time to evaluate  : 1.910 
Fit side-chains
REVERT: D  260 ARG cc_start: 0.6880 (mtt90) cc_final: 0.6670 (mtt90)
REVERT: D  280 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7233 (tpp-160)
REVERT: D  398 GLU cc_start: 0.8461 (tp30) cc_final: 0.8009 (tt0)
REVERT: D  542 PHE cc_start: 0.7709 (OUTLIER) cc_final: 0.6506 (m-80)
REVERT: D  585 HIS cc_start: 0.6304 (OUTLIER) cc_final: 0.5897 (p-80)
REVERT: A  107 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8073 (pttt)
REVERT: A  141 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7891 (mttp)
REVERT: A  389 TYR cc_start: 0.8038 (t80) cc_final: 0.7792 (t80)
REVERT: A  605 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.7855 (ptpt)
REVERT: A  877 LYS cc_start: 0.7254 (tptm) cc_final: 0.6701 (mtpp)
REVERT: A  927 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7276 (tt)
REVERT: A  984 HIS cc_start: 0.7411 (t70) cc_final: 0.7204 (t-170)
  outliers start: 81
  outliers final: 46
  residues processed: 219
  average time/residue: 0.2905
  time to fit residues: 93.0400
Evaluate side-chains
  203 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 53
    poor density    : 150
  time to evaluate  : 1.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  280 ARG
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  468 THR
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  542 ASP
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1529 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 152 optimal weight:    0.2980
   chunk 104 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 136 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 156 optimal weight:    2.9990
   chunk 126 optimal weight:    3.9990
   chunk 0 optimal weight:   40.0000
   chunk 93 optimal weight:    4.9990
   chunk 164 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN
A1494 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7703
moved from start:          0.1262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15702  Z= 0.246
  Angle     :  0.531  10.567  21506  Z= 0.275
  Chirality :  0.041   0.372   2432
  Planarity :  0.004   0.046   2558
  Dihedral  : 14.920 173.799   2772
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 25.52 %
    Favored  : 68.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.19), residues: 1832
  helix:  1.36 (0.20), residues: 667
  sheet: -1.03 (0.34), residues: 223
  loop : -1.18 (0.19), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 330 
 HIS   0.007   0.001   HIS A1484 
 PHE   0.014   0.001   PHE D 491 
 TYR   0.015   0.001   TYR D 607 
 ARG   0.006   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 84
    poor density    : 153
  time to evaluate  : 1.797 
Fit side-chains
REVERT: D  260 ARG cc_start: 0.6870 (mtt90) cc_final: 0.6647 (mtt90)
REVERT: D  280 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7354 (tpp-160)
REVERT: D  542 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6610 (m-80)
REVERT: D  585 HIS cc_start: 0.6312 (OUTLIER) cc_final: 0.5903 (p-80)
REVERT: A  107 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8078 (pttt)
REVERT: A  141 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7897 (mttp)
REVERT: A  389 TYR cc_start: 0.8045 (t80) cc_final: 0.7812 (t80)
REVERT: A  605 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7864 (ptpt)
REVERT: A  877 LYS cc_start: 0.7265 (tptm) cc_final: 0.6676 (mtpp)
REVERT: A  927 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7271 (tt)
  outliers start: 84
  outliers final: 51
  residues processed: 219
  average time/residue: 0.2891
  time to fit residues: 93.2187
Evaluate side-chains
  208 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 58
    poor density    : 150
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  280 ARG
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  468 THR
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain A residue   22 GLU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  542 ASP
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1497 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1582 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 165 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 45 optimal weight:    0.6980
   chunk 183 optimal weight:    9.9990
   chunk 152 optimal weight:    0.9990
   chunk 85 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 96 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN
A1494 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7681
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15702  Z= 0.200
  Angle     :  0.518  11.775  21506  Z= 0.267
  Chirality :  0.041   0.367   2432
  Planarity :  0.004   0.044   2558
  Dihedral  : 14.872 174.895   2772
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 25.81 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.19), residues: 1832
  helix:  1.45 (0.20), residues: 667
  sheet: -1.05 (0.34), residues: 225
  loop : -1.16 (0.19), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 330 
 HIS   0.007   0.001   HIS A1484 
 PHE   0.014   0.001   PHE D 491 
 TYR   0.015   0.001   TYR D 607 
 ARG   0.007   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 157
  time to evaluate  : 1.602 
Fit side-chains
REVERT: D  260 ARG cc_start: 0.6847 (mtt90) cc_final: 0.6618 (mtt90)
REVERT: D  398 GLU cc_start: 0.8460 (tp30) cc_final: 0.8013 (tt0)
REVERT: D  542 PHE cc_start: 0.7713 (OUTLIER) cc_final: 0.6450 (m-80)
REVERT: D  585 HIS cc_start: 0.6279 (OUTLIER) cc_final: 0.5883 (p-80)
REVERT: A  107 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7982 (pttt)
REVERT: A  141 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7882 (mttp)
REVERT: A  605 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7989 (ptpt)
REVERT: A  877 LYS cc_start: 0.7190 (tptm) cc_final: 0.6679 (mtpp)
REVERT: A  927 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7361 (tt)
  outliers start: 77
  outliers final: 55
  residues processed: 217
  average time/residue: 0.2807
  time to fit residues: 89.8180
Evaluate side-chains
  212 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 61
    poor density    : 151
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  195 ASP
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain D residue  594 PHE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1497 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1510 GLU
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1601 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 177 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 104 optimal weight:    0.9980
   chunk 134 optimal weight:    3.9990
   chunk 154 optimal weight:    6.9990
   chunk 102 optimal weight:    0.8980
   chunk 183 optimal weight:    8.9990
   chunk 114 optimal weight:    0.8980
   chunk 111 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN
A1494 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15702  Z= 0.198
  Angle     :  0.519  11.747  21506  Z= 0.266
  Chirality :  0.041   0.365   2432
  Planarity :  0.004   0.043   2558
  Dihedral  : 14.841 174.704   2772
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 12.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 26.03 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.19), residues: 1832
  helix:  1.47 (0.20), residues: 667
  sheet: -1.02 (0.34), residues: 225
  loop : -1.18 (0.19), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 330 
 HIS   0.006   0.001   HIS A1484 
 PHE   0.019   0.001   PHE D 289 
 TYR   0.014   0.001   TYR D 607 
 ARG   0.007   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 72
    poor density    : 152
  time to evaluate  : 1.700 
Fit side-chains
REVERT: D  174 CYS cc_start: 0.7250 (t) cc_final: 0.6929 (t)
REVERT: D  260 ARG cc_start: 0.6782 (mtt90) cc_final: 0.6550 (mtt90)
REVERT: D  542 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6496 (m-80)
REVERT: D  585 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.5838 (p-80)
REVERT: A  107 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.7991 (pttt)
REVERT: A  141 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7881 (mttp)
REVERT: A  389 TYR cc_start: 0.8049 (t80) cc_final: 0.7780 (t80)
REVERT: A  605 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8061 (ptpt)
REVERT: A  877 LYS cc_start: 0.7228 (tptm) cc_final: 0.6746 (mtpp)
REVERT: A  927 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7335 (tt)
  outliers start: 72
  outliers final: 54
  residues processed: 207
  average time/residue: 0.3091
  time to fit residues: 93.3038
Evaluate side-chains
  209 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 60
    poor density    : 149
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  195 ASP
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  927 LEU
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1497 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1601 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 116 optimal weight:    0.0870
   chunk 124 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 17 optimal weight:   10.0000
   chunk 143 optimal weight:    3.9990
   chunk 166 optimal weight:    8.9990
   chunk 175 optimal weight:    5.9990
   overall best weight:    1.0162

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1494 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15702  Z= 0.222
  Angle     :  0.531  12.691  21506  Z= 0.272
  Chirality :  0.041   0.362   2432
  Planarity :  0.004   0.043   2558
  Dihedral  : 14.837 174.047   2772
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 25.96 %
    Favored  : 68.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.19), residues: 1832
  helix:  1.44 (0.20), residues: 669
  sheet: -1.02 (0.33), residues: 225
  loop : -1.20 (0.19), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 330 
 HIS   0.005   0.001   HIS A1621 
 PHE   0.017   0.001   PHE D 289 
 TYR   0.015   0.001   TYR D 607 
 ARG   0.007   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 77
    poor density    : 151
  time to evaluate  : 1.617 
Fit side-chains
REVERT: D  260 ARG cc_start: 0.6777 (mtt90) cc_final: 0.6543 (mtt90)
REVERT: D  398 GLU cc_start: 0.8430 (tp30) cc_final: 0.7991 (tt0)
REVERT: D  542 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.6498 (m-80)
REVERT: D  585 HIS cc_start: 0.6285 (OUTLIER) cc_final: 0.5846 (p-80)
REVERT: A  107 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8045 (pttt)
REVERT: A  141 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7899 (mttp)
REVERT: A  342 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6982 (ptpp)
REVERT: A  389 TYR cc_start: 0.8046 (t80) cc_final: 0.7779 (t80)
REVERT: A  605 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8082 (ptpt)
REVERT: A  877 LYS cc_start: 0.7282 (tptm) cc_final: 0.6778 (mtpp)
  outliers start: 77
  outliers final: 59
  residues processed: 212
  average time/residue: 0.2867
  time to fit residues: 90.1474
Evaluate side-chains
  212 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 65
    poor density    : 147
  time to evaluate  : 1.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  195 ASP
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  342 LYS
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  586 ASN
Chi-restraints excluded: chain A residue  605 LYS
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1497 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1601 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 160 optimal weight:    2.9990
   chunk 170 optimal weight:    5.9990
   chunk 175 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 134 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 154 optimal weight:    4.9990
   chunk 161 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9990
   chunk 180 optimal weight:    3.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 586 ASN
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1494 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15702  Z= 0.210
  Angle     :  0.530  12.891  21506  Z= 0.271
  Chirality :  0.041   0.361   2432
  Planarity :  0.004   0.043   2558
  Dihedral  : 14.822 174.391   2772
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 26.17 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.19), residues: 1832
  helix:  1.47 (0.20), residues: 669
  sheet: -1.00 (0.34), residues: 225
  loop : -1.19 (0.19), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1487 
 HIS   0.005   0.001   HIS A1621 
 PHE   0.016   0.001   PHE D 289 
 TYR   0.016   0.001   TYR D 607 
 ARG   0.007   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 73
    poor density    : 148
  time to evaluate  : 1.513 
Fit side-chains
REVERT: D  260 ARG cc_start: 0.6773 (mtt90) cc_final: 0.6539 (mtt90)
REVERT: D  398 GLU cc_start: 0.8447 (tp30) cc_final: 0.8025 (tt0)
REVERT: D  542 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.6477 (m-80)
REVERT: D  585 HIS cc_start: 0.6272 (OUTLIER) cc_final: 0.5783 (p-80)
REVERT: A  107 LYS cc_start: 0.8453 (OUTLIER) cc_final: 0.8026 (pttt)
REVERT: A  141 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7896 (mttp)
REVERT: A  342 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6981 (ptpp)
REVERT: A  389 TYR cc_start: 0.8061 (t80) cc_final: 0.7789 (t80)
REVERT: A  877 LYS cc_start: 0.7252 (tptm) cc_final: 0.6776 (mtpp)
  outliers start: 73
  outliers final: 57
  residues processed: 205
  average time/residue: 0.2921
  time to fit residues: 88.2710
Evaluate side-chains
  207 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 145
  time to evaluate  : 1.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  195 ASP
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain D residue  594 PHE
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  342 LYS
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1006 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1497 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1601 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 85 optimal weight:    3.9990
   chunk 125 optimal weight:    0.8980
   chunk 189 optimal weight:   10.0000
   chunk 174 optimal weight:    0.7980
   chunk 150 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 116 optimal weight:    2.9990
   chunk 92 optimal weight:    0.8980
   chunk 119 optimal weight:    3.9990
   chunk 160 optimal weight:    2.9990
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.1554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15702  Z= 0.256
  Angle     :  0.557  12.395  21506  Z= 0.283
  Chirality :  0.042   0.361   2432
  Planarity :  0.004   0.043   2558
  Dihedral  : 14.853 173.111   2772
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 26.39 %
    Favored  : 68.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.19), residues: 1832
  helix:  1.34 (0.20), residues: 673
  sheet: -1.11 (0.33), residues: 233
  loop : -1.25 (0.19), residues: 926

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1487 
 HIS   0.005   0.001   HIS A1484 
 PHE   0.016   0.002   PHE D 289 
 TYR   0.017   0.001   TYR D 607 
 ARG   0.007   0.000   ARG A1581 

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

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

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3664 Ramachandran restraints generated.
    1832 Oldfield, 0 Emsley, 1832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 68
    poor density    : 147
  time to evaluate  : 1.670 
Fit side-chains
REVERT: D  260 ARG cc_start: 0.6770 (mtt90) cc_final: 0.6532 (mtt90)
REVERT: D  398 GLU cc_start: 0.8435 (tp30) cc_final: 0.8059 (tt0)
REVERT: D  542 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.6455 (m-80)
REVERT: D  585 HIS cc_start: 0.6332 (OUTLIER) cc_final: 0.5790 (p-80)
REVERT: A  107 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7911 (ptmt)
REVERT: A  141 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7917 (mttp)
REVERT: A  342 LYS cc_start: 0.7171 (OUTLIER) cc_final: 0.6954 (ptpp)
REVERT: A  491 CYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8023 (p)
REVERT: A  877 LYS cc_start: 0.7217 (tptm) cc_final: 0.6679 (mtpp)
  outliers start: 68
  outliers final: 56
  residues processed: 202
  average time/residue: 0.2989
  time to fit residues: 89.5837
Evaluate side-chains
  206 residues out of total 1641 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 62
    poor density    : 144
  time to evaluate  : 1.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   58 GLU
Chi-restraints excluded: chain D residue   89 ILE
Chi-restraints excluded: chain D residue  190 SER
Chi-restraints excluded: chain D residue  195 ASP
Chi-restraints excluded: chain D residue  246 ASP
Chi-restraints excluded: chain D residue  328 LEU
Chi-restraints excluded: chain D residue  329 SER
Chi-restraints excluded: chain D residue  353 VAL
Chi-restraints excluded: chain D residue  401 VAL
Chi-restraints excluded: chain D residue  485 LEU
Chi-restraints excluded: chain D residue  491 PHE
Chi-restraints excluded: chain D residue  542 PHE
Chi-restraints excluded: chain D residue  585 HIS
Chi-restraints excluded: chain D residue  617 LEU
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  131 ILE
Chi-restraints excluded: chain A residue  141 LYS
Chi-restraints excluded: chain A residue  150 ASP
Chi-restraints excluded: chain A residue  201 THR
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  237 ILE
Chi-restraints excluded: chain A residue  279 VAL
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  314 ASP
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  342 LYS
Chi-restraints excluded: chain A residue  413 THR
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  419 VAL
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  494 SER
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  513 THR
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  609 ILE
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  750 CYS
Chi-restraints excluded: chain A residue  806 ASP
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  852 LEU
Chi-restraints excluded: chain A residue  858 VAL
Chi-restraints excluded: chain A residue  867 SER
Chi-restraints excluded: chain A residue  899 ILE
Chi-restraints excluded: chain A residue  936 GLU
Chi-restraints excluded: chain A residue  950 LEU
Chi-restraints excluded: chain A residue  970 SER
Chi-restraints excluded: chain A residue  995 GLU
Chi-restraints excluded: chain A residue  997 MET
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1441 GLU
Chi-restraints excluded: chain A residue 1468 ILE
Chi-restraints excluded: chain A residue 1497 ILE
Chi-restraints excluded: chain A residue 1507 VAL
Chi-restraints excluded: chain A residue 1509 THR
Chi-restraints excluded: chain A residue 1534 LEU
Chi-restraints excluded: chain A residue 1582 VAL
Chi-restraints excluded: chain A residue 1601 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 46 optimal weight:    0.0170
   chunk 138 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 150 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 155 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0470
   chunk 27 optimal weight:    3.9990
   chunk 132 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** D 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 433 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1494 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.177022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.131411 restraints weight = 16941.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3521 rms_B_bonded: 1.92
r_work: 0.3393 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7656
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15702  Z= 0.167
  Angle     :  0.513  13.681  21506  Z= 0.261
  Chirality :  0.040   0.358   2432
  Planarity :  0.004   0.042   2558
  Dihedral  : 14.746 176.691   2772
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 27.11 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.20), residues: 1832
  helix:  1.57 (0.20), residues: 667
  sheet: -0.89 (0.34), residues: 217
  loop : -1.17 (0.19), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D 278 
 HIS   0.005   0.001   HIS A1621 
 PHE   0.016   0.001   PHE A1011 
 TYR   0.016   0.001   TYR D 607 
 ARG   0.007   0.000   ARG A1581 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3455.08 seconds
wall clock time: 63 minutes 34.89 seconds (3814.89 seconds total)