Starting phenix.real_space_refine
on Wed Nov 19 20:58:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yln_39385/11_2025/8yln_39385.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yln_39385/11_2025/8yln_39385.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yln_39385/11_2025/8yln_39385.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yln_39385/11_2025/8yln_39385.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yln_39385/11_2025/8yln_39385.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yln_39385/11_2025/8yln_39385.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.026
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: 5
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    9074      2.51       5
     N    2252      2.21       5
     O    2672      1.98       5
     H   13732      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 27784
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 11656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 702, 11656
          Classifications: {'peptide': 702}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 692}
    Chain: "B"
      Number of atoms: 11656
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 702, 11656
          Classifications: {'peptide': 702}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 692}
    Chain: "C"
      Number of atoms: 2236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2236
          Classifications: {'peptide': 145}
          Link IDs: {'PTRANS': 5, 'TRANS': 139}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "D"
      Number of atoms: 2236
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2236
          Classifications: {'peptide': 145}
          Link IDs: {'PTRANS': 5, 'TRANS': 139}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 4.85, per 1000 atoms: 0.17
  Number of scatterers: 27784
  At special positions: 0
  Unit cell: (107.52, 105.6, 134.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     O    2672      8.00
     N    2252      7.00
     C    9074      6.00
     H   13732      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 730.1 milliseconds
  

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3232

  Finding SS restraints...
    Secondary structure from input PDB file:
      87 helices and 7 sheets defined
      64.2% alpha, 7.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 304 through 317
      removed outlier: 3.596A  pdb=" N   VAL A 308 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 320
      No H-bonds generated for 'chain 'A' and resid 318 through 320'
    Processing helix  chain 'A' and resid 327 through 334
      removed outlier: 3.813A  pdb=" N   LYS A 331 " --> pdb=" O   ILE A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 366
    Processing helix  chain 'A' and resid 366 through 373
      removed outlier: 3.503A  pdb=" N   ARG A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 392
    Processing helix  chain 'A' and resid 396 through 400
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 431 through 445
    Processing helix  chain 'A' and resid 447 through 466
    Processing helix  chain 'A' and resid 467 through 500
      removed outlier: 5.141A  pdb=" N   LEU A 497 " --> pdb=" O   ASN A 493 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   LEU A 498 " --> pdb=" O   GLY A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 519
    Processing helix  chain 'A' and resid 523 through 525
      No H-bonds generated for 'chain 'A' and resid 523 through 525'
    Processing helix  chain 'A' and resid 526 through 531
      removed outlier: 3.659A  pdb=" N   GLY A 530 " --> pdb=" O   ASP A 526 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   MET A 531 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 526 through 531'
    Processing helix  chain 'A' and resid 532 through 539
    Processing helix  chain 'A' and resid 541 through 546
      removed outlier: 3.809A  pdb=" N   PHE A 544 " --> pdb=" O   ILE A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 572
    Processing helix  chain 'A' and resid 579 through 598
      removed outlier: 3.607A  pdb=" N   VAL A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ASN A 598 " --> pdb=" O   PHE A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 604
      removed outlier: 3.721A  pdb=" N   VAL A 603 " --> pdb=" O   LEU A 600 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   SER A 604 " --> pdb=" O   TRP A 601 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 600 through 604'
    Processing helix  chain 'A' and resid 605 through 629
      removed outlier: 3.564A  pdb=" N   HIS A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 639
    Processing helix  chain 'A' and resid 648 through 659
    Processing helix  chain 'A' and resid 660 through 671
    Processing helix  chain 'A' and resid 672 through 676
    Processing helix  chain 'A' and resid 680 through 701
      removed outlier: 4.131A  pdb=" N   ALA A 701 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 723
      removed outlier: 4.562A  pdb=" N   SER A 714 " --> pdb=" O   THR A 710 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   GLU A 715 " --> pdb=" O   GLN A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 742
    Processing helix  chain 'A' and resid 750 through 765
      removed outlier: 4.201A  pdb=" N   CYS A 764 " --> pdb=" O   ARG A 760 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASN A 765 " --> pdb=" O   LEU A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 786
    Processing helix  chain 'A' and resid 800 through 812
      removed outlier: 3.892A  pdb=" N   TYR A 804 " --> pdb=" O   TYR A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 826
      removed outlier: 3.599A  pdb=" N   SER A 821 " --> pdb=" O   SER A 817 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 831 through 841
    Processing helix  chain 'A' and resid 842 through 845
    Processing helix  chain 'A' and resid 846 through 857
    Processing helix  chain 'A' and resid 861 through 871
    Processing helix  chain 'A' and resid 878 through 900
    Processing helix  chain 'A' and resid 908 through 922
      removed outlier: 3.847A  pdb=" N   TYR A 912 " --> pdb=" O   SER A 908 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 928 through 934
    Processing helix  chain 'A' and resid 937 through 945
    Processing helix  chain 'A' and resid 955 through 961
    Processing helix  chain 'A' and resid 963 through 973
    Processing helix  chain 'A' and resid 973 through 991
      removed outlier: 4.424A  pdb=" N   HIS A 979 " --> pdb=" O   HIS A 975 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 1003
      removed outlier: 3.535A  pdb=" N   TYR A1003 " --> pdb=" O   ILE A 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 305 through 317
    Processing helix  chain 'B' and resid 318 through 321
      removed outlier: 3.574A  pdb=" N   ALA B 321 " --> pdb=" O   PRO B 318 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 318 through 321'
    Processing helix  chain 'B' and resid 327 through 333
    Processing helix  chain 'B' and resid 355 through 366
    Processing helix  chain 'B' and resid 366 through 372
      removed outlier: 3.645A  pdb=" N   ARG B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 374 through 392
    Processing helix  chain 'B' and resid 417 through 427
    Processing helix  chain 'B' and resid 431 through 445
    Processing helix  chain 'B' and resid 447 through 466
      removed outlier: 4.283A  pdb=" N   ASP B 464 " --> pdb=" O   LEU B 460 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 467 through 494
      removed outlier: 3.663A  pdb=" N   GLY B 494 " --> pdb=" O   THR B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 494 through 501
      removed outlier: 4.177A  pdb=" N   LEU B 498 " --> pdb=" O   GLY B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 519
      removed outlier: 3.506A  pdb=" N   MET B 519 " --> pdb=" O   ILE B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 523 through 525
      No H-bonds generated for 'chain 'B' and resid 523 through 525'
    Processing helix  chain 'B' and resid 526 through 531
    Processing helix  chain 'B' and resid 532 through 539
    Processing helix  chain 'B' and resid 542 through 547
      removed outlier: 3.874A  pdb=" N   SER B 546 " --> pdb=" O   LEU B 542 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   ASP B 547 " --> pdb=" O   GLU B 543 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 542 through 547'
    Processing helix  chain 'B' and resid 551 through 572
      removed outlier: 3.568A  pdb=" N   THR B 555 " --> pdb=" O   LEU B 551 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 599
    Processing helix  chain 'B' and resid 600 through 604
      removed outlier: 3.560A  pdb=" N   VAL B 603 " --> pdb=" O   LEU B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 605 through 628
      removed outlier: 3.862A  pdb=" N   HIS B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   THR B 628 " --> pdb=" O   GLU B 624 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 639
      removed outlier: 3.957A  pdb=" N   PHE B 638 " --> pdb=" O   LEU B 634 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   PHE B 639 " --> pdb=" O   GLY B 635 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 634 through 639'
    Processing helix  chain 'B' and resid 648 through 659
    Processing helix  chain 'B' and resid 660 through 671
    Processing helix  chain 'B' and resid 672 through 676
    Processing helix  chain 'B' and resid 680 through 701
      removed outlier: 3.520A  pdb=" N   ILE B 684 " --> pdb=" O   GLU B 680 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA B 701 " --> pdb=" O   LYS B 697 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 705 through 723
      removed outlier: 4.605A  pdb=" N   SER B 714 " --> pdb=" O   THR B 710 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLU B 715 " --> pdb=" O   GLN B 711 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 729 through 744
      removed outlier: 3.666A  pdb=" N   PHE B 744 " --> pdb=" O   LEU B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 762
    Processing helix  chain 'B' and resid 768 through 786
      removed outlier: 3.667A  pdb=" N   ILE B 772 " --> pdb=" O   PRO B 768 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 800 through 812
      removed outlier: 3.733A  pdb=" N   TYR B 804 " --> pdb=" O   TYR B 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 817 through 826
    Processing helix  chain 'B' and resid 831 through 840
      removed outlier: 3.696A  pdb=" N   LYS B 840 " --> pdb=" O   ASP B 836 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 846 through 857
    Processing helix  chain 'B' and resid 861 through 871
    Processing helix  chain 'B' and resid 878 through 901
      removed outlier: 4.018A  pdb=" N   GLU B 901 " --> pdb=" O   ILE B 897 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 908 through 922
      removed outlier: 3.694A  pdb=" N   TYR B 912 " --> pdb=" O   SER B 908 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 928 through 934
      removed outlier: 3.920A  pdb=" N   GLU B 932 " --> pdb=" O   SER B 928 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 939 through 945
    Processing helix  chain 'B' and resid 955 through 960
    Processing helix  chain 'B' and resid 963 through 972
    Processing helix  chain 'B' and resid 973 through 991
      removed outlier: 4.879A  pdb=" N   HIS B 978 " --> pdb=" O   LYS B 974 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   HIS B 979 " --> pdb=" O   HIS B 975 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 993 through 1003
      removed outlier: 3.654A  pdb=" N   LEU B 997 " --> pdb=" O   ASP B 993 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 69 through 76
    Processing helix  chain 'D' and resid 69 through 76
    Processing sheet with id=AA1, first strand: chain 'A' and resid 338 through 340
    Processing sheet with id=AA2, first strand: chain 'A' and resid 573 through 575
      removed outlier: 3.589A  pdb=" N   TYR A 574 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA D  30 " --> pdb=" O   TYR A 574 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   VAL D  22 " --> pdb=" O   PHE D  68 " (cutoff:3.500A)
      removed outlier: 4.601A  pdb=" N   PHE D  68 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   THR D  24 " --> pdb=" O   ALA D  66 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   ALA D  66 " --> pdb=" O   THR D  24 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   THR D  62 " --> pdb=" O   GLN D  28 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   ALA D  30 " --> pdb=" O   ASN D  60 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   ASN D  60 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 4.736A  pdb=" N   PHE D  32 " --> pdb=" O   GLU D  58 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   GLU D  58 " --> pdb=" O   PHE D  32 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   GLN D  34 " --> pdb=" O   GLU D  56 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   GLU D  56 " --> pdb=" O   GLN D  34 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE D 218 " --> pdb=" O   VAL D  63 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 573 through 575
      removed outlier: 3.589A  pdb=" N   TYR A 574 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA D  30 " --> pdb=" O   TYR A 574 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   PHE D  13 " --> pdb=" O   VAL D  22 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   THR D  24 " --> pdb=" O   VAL D  11 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL D  11 " --> pdb=" O   THR D  24 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   TYR D 171 " --> pdb=" O   ASN D 197 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ASN D 197 " --> pdb=" O   TYR D 171 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 339 through 340
    Processing sheet with id=AA5, first strand: chain 'B' and resid 646 through 647
    Processing sheet with id=AA6, first strand: chain 'C' and resid 171 through 173
      removed outlier: 6.651A  pdb=" N   VAL C  11 " --> pdb=" O   THR C  24 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   THR C  24 " --> pdb=" O   VAL C  11 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   PHE C  13 " --> pdb=" O   VAL C  22 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   PHE C  23 " --> pdb=" O   PHE C  68 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   PHE C  68 " --> pdb=" O   PHE C  23 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   ALA C  25 " --> pdb=" O   ALA C  66 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ALA C  66 " --> pdb=" O   ALA C  25 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   ALA C  27 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
      removed outlier: 5.858A  pdb=" N   LYS C  64 " --> pdb=" O   ALA C  27 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 176 through 177
      removed outlier: 3.656A  pdb=" N   VAL C 233 " --> pdb=" O   GLN C 194 " (cutoff:3.500A)

    750 hydrogen bonds defined for protein.
    2160 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 6.50

  Time building geometry restraints manager: 3.40 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 13716
        1.03 -     1.23: 154
        1.23 -     1.43: 6160
        1.43 -     1.62: 7970
        1.62 -     1.82: 92
  Bond restraints: 28092
  Sorted by residual:
  bond pdb=" N   VAL C 198 "
       pdb=" CA  VAL C 198 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.16e+01
  bond pdb=" N   PHE B 639 "
       pdb=" CA  PHE B 639 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.18e-02 7.18e+03 1.06e+01
  bond pdb=" N   VAL C 187 "
       pdb=" CA  VAL C 187 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.14e-02 7.69e+03 1.05e+01
  bond pdb=" N   ARG C  42 "
       pdb=" CA  ARG C  42 "
    ideal  model  delta    sigma   weight residual
    1.455  1.496 -0.041 1.25e-02 6.40e+03 1.05e+01
  bond pdb=" N   ILE B 934 "
       pdb=" CA  ILE B 934 "
    ideal  model  delta    sigma   weight residual
    1.456  1.494 -0.038 1.19e-02 7.06e+03 1.01e+01
  ... (remaining 28087 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.44: 49933
        2.44 -     4.89: 623
        4.89 -     7.33: 23
        7.33 -     9.77: 3
        9.77 -    12.22: 12
  Bond angle restraints: 50594
  Sorted by residual:
  angle pdb=" N   ASP B 590 "
        pdb=" CA  ASP B 590 "
        pdb=" C   ASP B 590 "
      ideal   model   delta    sigma   weight residual
     112.90  106.29    6.61 1.31e+00 5.83e-01 2.54e+01
  angle pdb=" N   THR B 562 "
        pdb=" CA  THR B 562 "
        pdb=" C   THR B 562 "
      ideal   model   delta    sigma   weight residual
     112.45  105.93    6.52 1.39e+00 5.18e-01 2.20e+01
  angle pdb=" CA  LEU A 403 "
        pdb=" C   LEU A 403 "
        pdb=" O   LEU A 403 "
      ideal   model   delta    sigma   weight residual
     121.47  116.34    5.13 1.15e+00 7.56e-01 1.99e+01
  angle pdb=" CA  GLY D 202 "
        pdb=" C   GLY D 202 "
        pdb=" O   GLY D 202 "
      ideal   model   delta    sigma   weight residual
     121.58  117.61    3.97 9.00e-01 1.23e+00 1.95e+01
  angle pdb=" N   SER B 700 "
        pdb=" CA  SER B 700 "
        pdb=" C   SER B 700 "
      ideal   model   delta    sigma   weight residual
     111.82  106.73    5.09 1.16e+00 7.43e-01 1.93e+01
  ... (remaining 50589 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 11603
       17.99 -    35.99: 1198
       35.99 -    53.98: 311
       53.98 -    71.97: 77
       71.97 -    89.96: 21
  Dihedral angle restraints: 13210
    sinusoidal: 6968
      harmonic: 6242
  Sorted by residual:
  dihedral pdb=" CA  ILE A 871 "
           pdb=" C   ILE A 871 "
           pdb=" N   GLY A 872 "
           pdb=" CA  GLY A 872 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.89   24.11     0      5.00e+00 4.00e-02 2.33e+01
  dihedral pdb=" CA  LEU B 551 "
           pdb=" C   LEU B 551 "
           pdb=" N   TYR B 552 "
           pdb=" CA  TYR B 552 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.77   22.23     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  THR B 906 "
           pdb=" C   THR B 906 "
           pdb=" N   PHE B 907 "
           pdb=" CA  PHE B 907 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.17   19.83     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 13207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1512
       0.042 -    0.085: 361
       0.085 -    0.127: 129
       0.127 -    0.170: 36
       0.170 -    0.212: 14
  Chirality restraints: 2052
  Sorted by residual:
  chirality pdb=" CA  MET B 936 "
            pdb=" N   MET B 936 "
            pdb=" C   MET B 936 "
            pdb=" CB  MET B 936 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  VAL C 173 "
            pdb=" N   VAL C 173 "
            pdb=" C   VAL C 173 "
            pdb=" CB  VAL C 173 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.65   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE C 178 "
            pdb=" N   ILE C 178 "
            pdb=" C   ILE C 178 "
            pdb=" CB  ILE C 178 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 2049 not shown)

  Planarity restraints: 4136
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 990 "   -0.181 2.00e-02 2.50e+03   4.18e-01 2.62e+03
        pdb=" CG  ASN B 990 "    0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 990 "    0.180 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 990 "   -0.002 2.00e-02 2.50e+03
        pdb="HD21 ASN B 990 "    0.696 2.00e-02 2.50e+03
        pdb="HD22 ASN B 990 "   -0.707 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 627 "   -0.054 9.50e-02 1.11e+02   3.36e-01 2.53e+03
        pdb=" NE  ARG A 627 "    0.136 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 627 "    0.036 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 627 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 627 "   -0.038 2.00e-02 2.50e+03
        pdb="HH11 ARG A 627 "   -0.702 2.00e-02 2.50e+03
        pdb="HH12 ARG A 627 "    0.695 2.00e-02 2.50e+03
        pdb="HH21 ARG A 627 "   -0.018 2.00e-02 2.50e+03
        pdb="HH22 ARG A 627 "   -0.113 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 629 "   -0.079 9.50e-02 1.11e+02   2.56e-01 1.46e+03
        pdb=" NE  ARG A 629 "    0.045 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 629 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 629 "   -0.052 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 629 "    0.046 2.00e-02 2.50e+03
        pdb="HH11 ARG A 629 "   -0.383 2.00e-02 2.50e+03
        pdb="HH12 ARG A 629 "    0.231 2.00e-02 2.50e+03
        pdb="HH21 ARG A 629 "   -0.379 2.00e-02 2.50e+03
        pdb="HH22 ARG A 629 "    0.485 2.00e-02 2.50e+03
  ... (remaining 4133 not shown)

  Histogram of nonbonded interaction distances:
        1.65 -     2.24: 3263
        2.24 -     2.83: 61973
        2.83 -     3.42: 73775
        3.42 -     4.01: 97691
        4.01 -     4.60: 149174
  Nonbonded interactions: 385876
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 607 "
            pdb="HD21 ASN C 210 "
     model   vdw
     1.654 2.450
  nonbonded pdb=" H   GLY A 935 "
            pdb=" OD1 ASP A 941 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" OE1 GLU B 510 "
            pdb=" H   GLU B 510 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" O   ARG A 587 "
            pdb="HD21 ASN A 591 "
     model   vdw
     1.671 2.450
  nonbonded pdb=" OE1 GLU B 685 "
            pdb=" H   SER B 729 "
     model   vdw
     1.675 2.450
  ... (remaining 385871 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.060
  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:             0.160
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     26.450
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6715
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      :  0.006   0.041  14360  Z= 0.365
  Angle     :  0.812   7.438  19320  Z= 0.543
  Chirality :  0.047   0.212   2052
  Planarity :  0.006   0.116   2476
  Dihedral  : 16.781  89.963   5354
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 19.26 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.30 (0.20), residues: 1682
  helix:  0.85 (0.17), residues: 986
  sheet: -1.82 (0.46), residues: 116
  loop : -1.64 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 987 
 TYR   0.021   0.002   TYR B 589 
 PHE   0.022   0.002   PHE C  23 
 TRP   0.005   0.001   TRP A 958 
 HIS   0.009   0.001   HIS B 786 

Details of bonding type rmsd
  covalent geometry    : bond        0.00565 (14360)
  covalent geometry    : angle       0.81161 (19320)
  hydrogen bonds       : bond        0.14276 (  750)
  hydrogen bonds       : angle       6.18480 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  261 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 244
  time to evaluate  : 0.789 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  519 MET cc_start: 0.5375 (ptm) cc_final: 0.5021 (ptt)
REVERT: B  786 HIS cc_start: 0.6234 (OUTLIER) cc_final: 0.5281 (t70)
  outliers start: 17
  outliers final: 6
  residues processed: 253
  average time/residue: 0.2873
  time to fit residues: 105.9638
Evaluate side-chains
  218 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 211
  time to evaluate  : 0.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  562 THR
Chi-restraints excluded: chain B residue  704 MET
Chi-restraints excluded: chain B residue  707 VAL
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain C residue   20 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.4980
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 598 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.196826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.157832 restraints weight = 53201.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.163273 restraints weight = 30944.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.166779 restraints weight = 21706.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.168863 restraints weight = 17283.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.170305 restraints weight = 14978.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6702
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14360  Z= 0.115
  Angle     :  0.483   6.016  19320  Z= 0.268
  Chirality :  0.036   0.160   2052
  Planarity :  0.004   0.073   2476
  Dihedral  :  4.823  56.832   1873
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 6.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.61 %
    Favored  : 79.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.21), residues: 1682
  helix:  1.32 (0.17), residues: 988
  sheet: -1.74 (0.43), residues: 126
  loop : -1.46 (0.25), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 359 
 TYR   0.013   0.001   TYR A 687 
 PHE   0.017   0.001   PHE B 907 
 TRP   0.004   0.001   TRP B 958 
 HIS   0.004   0.001   HIS A 349 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (14360)
  covalent geometry    : angle       0.48293 (19320)
  hydrogen bonds       : bond        0.04348 (  750)
  hydrogen bonds       : angle       4.68845 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  252 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  647 MET cc_start: 0.6836 (tpp) cc_final: 0.6118 (tpp)
REVERT: B  346 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8488 (p)
REVERT: B  744 PHE cc_start: 0.7845 (OUTLIER) cc_final: 0.7358 (t80)
REVERT: B  786 HIS cc_start: 0.6173 (OUTLIER) cc_final: 0.5316 (t70)
REVERT: B  936 MET cc_start: 0.3461 (tpt) cc_final: 0.3241 (tpt)
REVERT: C  206 MET cc_start: 0.5352 (tpp) cc_final: 0.4826 (tpp)
  outliers start: 29
  outliers final: 21
  residues processed: 239
  average time/residue: 0.2785
  time to fit residues: 97.8849
Evaluate side-chains
  233 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 209
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  808 ILE
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  941 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  704 MET
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  749 LEU
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain C residue   20 LYS
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  191 ILE
Chi-restraints excluded: chain D residue  198 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 33 optimal weight:   10.0000
   chunk 22 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 163 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 2 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 167 optimal weight:    6.9990
   chunk 141 optimal weight:    7.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 349 HIS
A 598 ASN
A 610 GLN
** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.187699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.149411 restraints weight = 54244.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.153884 restraints weight = 31659.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.155450 restraints weight = 21516.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.155966 restraints weight = 18794.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.156148 restraints weight = 18167.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6960
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.067  14360  Z= 0.297
  Angle     :  0.631   7.964  19320  Z= 0.359
  Chirality :  0.041   0.172   2052
  Planarity :  0.005   0.077   2476
  Dihedral  :  5.366  59.156   1871
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.26 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.74 (0.20), residues: 1682
  helix:  0.59 (0.16), residues: 987
  sheet: -1.67 (0.42), residues: 124
  loop : -2.09 (0.23), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 627 
 TYR   0.022   0.002   TYR B 436 
 PHE   0.024   0.002   PHE B 559 
 TRP   0.009   0.002   TRP B 448 
 HIS   0.005   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00694 (14360)
  covalent geometry    : angle       0.63121 (19320)
  hydrogen bonds       : bond        0.06456 (  750)
  hydrogen bonds       : angle       5.29899 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  272 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 226
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 GLU cc_start: 0.6700 (tp30) cc_final: 0.6467 (tp30)
REVERT: A  417 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6622 (mptt)
REVERT: B  346 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8512 (p)
REVERT: B  357 MET cc_start: 0.7634 (mmm) cc_final: 0.6911 (mmm)
REVERT: B  786 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.5741 (t70)
REVERT: B  887 GLU cc_start: 0.8520 (tp30) cc_final: 0.8298 (tm-30)
REVERT: B  929 LYS cc_start: 0.7876 (tptp) cc_final: 0.7661 (tptp)
REVERT: B 1002 ASN cc_start: 0.6186 (OUTLIER) cc_final: 0.5702 (t0)
REVERT: C  231 MET cc_start: 0.7075 (tpp) cc_final: 0.6691 (tpp)
REVERT: D  214 LEU cc_start: 0.4429 (OUTLIER) cc_final: 0.4201 (pp)
  outliers start: 46
  outliers final: 29
  residues processed: 258
  average time/residue: 0.2927
  time to fit residues: 108.6288
Evaluate side-chains
  243 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 209
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  444 CYS
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue 1002 ASN
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  210 ASN
Chi-restraints excluded: chain D residue  214 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 131 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   chunk 101 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A 598 ASN
A 990 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.193207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152902 restraints weight = 53299.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.158452 restraints weight = 30726.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.161938 restraints weight = 21587.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.164169 restraints weight = 17266.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.165315 restraints weight = 14922.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14360  Z= 0.119
  Angle     :  0.485   5.954  19320  Z= 0.269
  Chirality :  0.036   0.172   2052
  Planarity :  0.003   0.073   2476
  Dihedral  :  4.724  56.355   1864
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.58 %
    Favored  : 77.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.20), residues: 1682
  helix:  1.21 (0.17), residues: 986
  sheet: -1.69 (0.40), residues: 136
  loop : -1.84 (0.24), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 566 
 TYR   0.013   0.001   TYR A 436 
 PHE   0.016   0.001   PHE B 907 
 TRP   0.004   0.001   TRP B 958 
 HIS   0.003   0.001   HIS B 786 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (14360)
  covalent geometry    : angle       0.48512 (19320)
  hydrogen bonds       : bond        0.04331 (  750)
  hydrogen bonds       : angle       4.58294 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  269 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 223
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 GLU cc_start: 0.6600 (tp30) cc_final: 0.6348 (tp30)
REVERT: A  417 LYS cc_start: 0.6983 (OUTLIER) cc_final: 0.6430 (mptt)
REVERT: A  519 MET cc_start: 0.7364 (ppp) cc_final: 0.6904 (ppp)
REVERT: B  346 VAL cc_start: 0.8592 (OUTLIER) cc_final: 0.8390 (p)
REVERT: B  744 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7408 (t80)
REVERT: B  786 HIS cc_start: 0.6748 (OUTLIER) cc_final: 0.5597 (t70)
REVERT: B  887 GLU cc_start: 0.8390 (tp30) cc_final: 0.8146 (tm-30)
REVERT: B 1002 ASN cc_start: 0.6063 (OUTLIER) cc_final: 0.5685 (t0)
REVERT: D  214 LEU cc_start: 0.4364 (OUTLIER) cc_final: 0.4125 (pp)
  outliers start: 46
  outliers final: 32
  residues processed: 255
  average time/residue: 0.2663
  time to fit residues: 101.1622
Evaluate side-chains
  252 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 214
  time to evaluate  : 0.939 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  598 ASN
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  882 GLU
Chi-restraints excluded: chain A residue  941 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  966 LEU
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  346 VAL
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  744 PHE
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  811 PHE
Chi-restraints excluded: chain B residue 1002 ASN
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  214 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 155 optimal weight:    5.9990
   chunk 37 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 145 optimal weight:    0.8980
   chunk 92 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 598 ASN
A 990 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.191805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.154495 restraints weight = 54386.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.157451 restraints weight = 31232.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.159165 restraints weight = 23096.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.159894 restraints weight = 20346.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.160201 restraints weight = 18815.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6883
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14360  Z= 0.143
  Angle     :  0.496   5.869  19320  Z= 0.275
  Chirality :  0.036   0.141   2052
  Planarity :  0.004   0.073   2476
  Dihedral  :  4.641  52.396   1864
  Min Nonbonded Distance : 2.267

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 19.78 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.03 (0.20), residues: 1682
  helix:  1.28 (0.17), residues: 990
  sheet: -1.66 (0.39), residues: 136
  loop : -1.87 (0.24), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 566 
 TYR   0.016   0.001   TYR A 687 
 PHE   0.015   0.001   PHE B 907 
 TRP   0.003   0.001   TRP B 448 
 HIS   0.003   0.001   HIS B 786 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (14360)
  covalent geometry    : angle       0.49613 (19320)
  hydrogen bonds       : bond        0.04428 (  750)
  hydrogen bonds       : angle       4.55983 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  252 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 211
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  389 GLU cc_start: 0.6632 (tp30) cc_final: 0.6400 (tp30)
REVERT: A  417 LYS cc_start: 0.7004 (OUTLIER) cc_final: 0.6545 (mptt)
REVERT: B  786 HIS cc_start: 0.6796 (OUTLIER) cc_final: 0.5618 (t70)
REVERT: B  887 GLU cc_start: 0.8588 (tp30) cc_final: 0.8304 (tm-30)
REVERT: D  206 MET cc_start: 0.6255 (tpp) cc_final: 0.4831 (ttp)
REVERT: D  214 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.4265 (pp)
  outliers start: 41
  outliers final: 32
  residues processed: 237
  average time/residue: 0.2751
  time to fit residues: 96.6733
Evaluate side-chains
  244 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 209
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  808 ILE
Chi-restraints excluded: chain A residue  882 GLU
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  941 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain A residue  990 ASN
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  543 GLU
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  811 PHE
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  214 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 165 optimal weight:    5.9990
   chunk 101 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 598 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.188927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.152067 restraints weight = 54435.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.154249 restraints weight = 31438.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.155855 restraints weight = 23614.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.156549 restraints weight = 20635.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.157281 restraints weight = 19480.324|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.2266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14360  Z= 0.206
  Angle     :  0.544   6.107  19320  Z= 0.304
  Chirality :  0.038   0.149   2052
  Planarity :  0.004   0.073   2476
  Dihedral  :  4.790  46.739   1864
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 19.26 %
    Favored  : 77.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.20), residues: 1682
  helix:  1.01 (0.16), residues: 987
  sheet: -1.47 (0.42), residues: 124
  loop : -2.06 (0.24), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 566 
 TYR   0.017   0.002   TYR A 436 
 PHE   0.017   0.002   PHE B 907 
 TRP   0.006   0.001   TRP B 448 
 HIS   0.003   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00476 (14360)
  covalent geometry    : angle       0.54417 (19320)
  hydrogen bonds       : bond        0.05161 (  750)
  hydrogen bonds       : angle       4.77778 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  268 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 213
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6470 (mptt)
REVERT: A  566 ARG cc_start: 0.6946 (mtt-85) cc_final: 0.6716 (mtt-85)
REVERT: A  639 PHE cc_start: 0.5150 (OUTLIER) cc_final: 0.4862 (t80)
REVERT: B  786 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.5702 (t70)
REVERT: B  887 GLU cc_start: 0.8544 (tp30) cc_final: 0.8322 (tm-30)
REVERT: B  929 LYS cc_start: 0.7943 (tptp) cc_final: 0.7649 (tptp)
REVERT: C  206 MET cc_start: 0.5325 (tpp) cc_final: 0.4658 (tpp)
  outliers start: 55
  outliers final: 43
  residues processed: 252
  average time/residue: 0.2872
  time to fit residues: 105.7602
Evaluate side-chains
  257 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 211
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  444 CYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  639 PHE
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  882 GLU
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  941 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  210 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 66 optimal weight:    0.9980
   chunk 164 optimal weight:    2.9990
   chunk 132 optimal weight:   10.0000
   chunk 91 optimal weight:    2.9990
   chunk 60 optimal weight:   10.0000
   chunk 156 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 143 optimal weight:   10.0000
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 598 ASN
** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.188319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.151380 restraints weight = 54634.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.153807 restraints weight = 32452.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155564 restraints weight = 23808.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.156591 restraints weight = 20558.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.156915 restraints weight = 19067.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6947
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14360  Z= 0.193
  Angle     :  0.542   7.597  19320  Z= 0.301
  Chirality :  0.038   0.140   2052
  Planarity :  0.004   0.074   2476
  Dihedral  :  4.794  45.058   1864
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 19.84 %
    Favored  : 76.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.20), residues: 1682
  helix:  0.99 (0.16), residues: 985
  sheet: -1.48 (0.42), residues: 124
  loop : -2.16 (0.23), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 566 
 TYR   0.018   0.002   TYR A 687 
 PHE   0.016   0.002   PHE B 907 
 TRP   0.006   0.001   TRP B 448 
 HIS   0.004   0.001   HIS A 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (14360)
  covalent geometry    : angle       0.54234 (19320)
  hydrogen bonds       : bond        0.05052 (  750)
  hydrogen bonds       : angle       4.75633 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  268 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 212
  time to evaluate  : 0.735 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.6498 (mptt)
REVERT: A  566 ARG cc_start: 0.6950 (mtt-85) cc_final: 0.6735 (mtt-85)
REVERT: A  697 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7134 (tttm)
REVERT: B  765 ASN cc_start: 0.7982 (OUTLIER) cc_final: 0.7716 (m-40)
REVERT: B  786 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.5563 (t70)
REVERT: B  929 LYS cc_start: 0.7966 (tptp) cc_final: 0.7682 (tptp)
REVERT: C  206 MET cc_start: 0.5286 (tpp) cc_final: 0.4588 (tpp)
  outliers start: 56
  outliers final: 48
  residues processed: 250
  average time/residue: 0.2924
  time to fit residues: 106.3030
Evaluate side-chains
  260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 208
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  393 VAL
Chi-restraints excluded: chain A residue  396 MET
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  444 CYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  697 LYS
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  808 ILE
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  882 GLU
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  941 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  750 ASP
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  967 LEU
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  210 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 153 optimal weight:    4.9990
   chunk 158 optimal weight:   10.0000
   chunk 159 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 161 optimal weight:    0.0170
   chunk 47 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   chunk 115 optimal weight:    2.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
** A 963 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.187699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.151987 restraints weight = 53947.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.153687 restraints weight = 32793.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.155510 restraints weight = 24602.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.156168 restraints weight = 21051.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.156641 restraints weight = 19717.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6950
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  14360  Z= 0.196
  Angle     :  0.551   6.257  19320  Z= 0.307
  Chirality :  0.038   0.141   2052
  Planarity :  0.004   0.072   2476
  Dihedral  :  4.818  45.895   1864
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.77 %
    Favored  : 94.23 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 19.26 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.20), residues: 1682
  helix:  0.97 (0.16), residues: 985
  sheet: -1.42 (0.43), residues: 122
  loop : -2.17 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 566 
 TYR   0.018   0.002   TYR A 687 
 PHE   0.025   0.002   PHE B 699 
 TRP   0.006   0.001   TRP B 448 
 HIS   0.004   0.001   HIS A 503 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 (14360)
  covalent geometry    : angle       0.55085 (19320)
  hydrogen bonds       : bond        0.05084 (  750)
  hydrogen bonds       : angle       4.76024 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  267 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 208
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6197 (mmtp)
REVERT: A  592 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8227 (mt)
REVERT: A  697 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7180 (tttm)
REVERT: B  578 MET cc_start: 0.7617 (ttm) cc_final: 0.7394 (ttm)
REVERT: B  647 MET cc_start: 0.7230 (mmt) cc_final: 0.6868 (mmt)
REVERT: B  765 ASN cc_start: 0.7969 (OUTLIER) cc_final: 0.7702 (m-40)
REVERT: B  786 HIS cc_start: 0.6878 (OUTLIER) cc_final: 0.5602 (t70)
REVERT: B  929 LYS cc_start: 0.8139 (tptp) cc_final: 0.7871 (tptp)
REVERT: D  209 GLU cc_start: 0.7455 (pm20) cc_final: 0.7194 (pm20)
  outliers start: 59
  outliers final: 48
  residues processed: 251
  average time/residue: 0.2837
  time to fit residues: 105.0435
Evaluate side-chains
  260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 207
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  444 CYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  697 LYS
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  808 ILE
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  882 GLU
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  750 ASP
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  967 LEU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   70 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue   67 PHE
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  210 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 144 optimal weight:    7.9990
   chunk 21 optimal weight:    2.9990
   chunk 124 optimal weight:    6.9990
   chunk 107 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 963 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.189366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.152235 restraints weight = 54591.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155329 restraints weight = 33051.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.157450 restraints weight = 23180.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.158716 restraints weight = 19021.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.159019 restraints weight = 17581.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6921
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14360  Z= 0.167
  Angle     :  0.530   9.358  19320  Z= 0.294
  Chirality :  0.037   0.142   2052
  Planarity :  0.004   0.075   2476
  Dihedral  :  4.733  45.836   1864
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.97 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.20), residues: 1682
  helix:  1.08 (0.17), residues: 986
  sheet: -1.31 (0.44), residues: 120
  loop : -2.11 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 480 
 TYR   0.017   0.001   TYR A 687 
 PHE   0.016   0.001   PHE B 699 
 TRP   0.004   0.001   TRP B 448 
 HIS   0.003   0.001   HIS B 786 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 (14360)
  covalent geometry    : angle       0.53035 (19320)
  hydrogen bonds       : bond        0.04731 (  750)
  hydrogen bonds       : angle       4.65691 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  265 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 212
  time to evaluate  : 0.715 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6322 (mmtp)
REVERT: A  592 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8209 (mt)
REVERT: A  697 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.7175 (tttm)
REVERT: B  786 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.5618 (t70)
REVERT: B  929 LYS cc_start: 0.8220 (tptp) cc_final: 0.7966 (tptp)
REVERT: C  205 GLU cc_start: 0.6957 (tp30) cc_final: 0.6585 (pt0)
REVERT: D  209 GLU cc_start: 0.7409 (pm20) cc_final: 0.7156 (pm20)
  outliers start: 53
  outliers final: 48
  residues processed: 250
  average time/residue: 0.2824
  time to fit residues: 103.3380
Evaluate side-chains
  260 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 208
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  444 CYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  489 VAL
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  697 LYS
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  808 ILE
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  882 GLU
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  750 ASP
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain B residue  967 LEU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   11 VAL
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue  198 VAL
Chi-restraints excluded: chain D residue  210 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 104 optimal weight:    2.9990
   chunk 148 optimal weight:    9.9990
   chunk 66 optimal weight:    2.9990
   chunk 161 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0980
   chunk 59 optimal weight:    0.9990
   chunk 15 optimal weight:    3.9990
   chunk 125 optimal weight:    7.9990
   overall best weight:    1.4188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.189786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.153943 restraints weight = 53518.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.156435 restraints weight = 30600.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.157736 restraints weight = 23334.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.158683 restraints weight = 20589.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.159025 restraints weight = 19155.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3858
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.2700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14360  Z= 0.146
  Angle     :  0.520   7.968  19320  Z= 0.287
  Chirality :  0.037   0.143   2052
  Planarity :  0.004   0.074   2476
  Dihedral  :  4.658  45.342   1864
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.56 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.20), residues: 1682
  helix:  1.22 (0.17), residues: 986
  sheet: -1.25 (0.44), residues: 120
  loop : -2.10 (0.23), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  42 
 TYR   0.015   0.001   TYR A 687 
 PHE   0.014   0.001   PHE B 699 
 TRP   0.003   0.001   TRP A 601 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (14360)
  covalent geometry    : angle       0.52045 (19320)
  hydrogen bonds       : bond        0.04470 (  750)
  hydrogen bonds       : angle       4.52287 ( 2160)

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

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

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3364 Ramachandran restraints generated.
    1682 Oldfield, 0 Emsley, 1682 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  180 is missing expected H atoms. Skipping.
Residue TYR  180 is missing expected H atoms. Skipping.
Evaluate side-chains
  263 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 214
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  417 LYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6282 (mmtp)
REVERT: A  592 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8172 (mt)
REVERT: A  697 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.7145 (tttm)
REVERT: B  647 MET cc_start: 0.7186 (mmt) cc_final: 0.6825 (mmt)
REVERT: B  786 HIS cc_start: 0.6917 (OUTLIER) cc_final: 0.5732 (t70)
REVERT: B  929 LYS cc_start: 0.8225 (tptp) cc_final: 0.7941 (tptp)
REVERT: C  205 GLU cc_start: 0.6817 (tp30) cc_final: 0.6483 (pt0)
REVERT: C  206 MET cc_start: 0.5261 (tpp) cc_final: 0.4556 (tpp)
REVERT: D  209 GLU cc_start: 0.7396 (pm20) cc_final: 0.7150 (pm20)
  outliers start: 49
  outliers final: 42
  residues processed: 249
  average time/residue: 0.3027
  time to fit residues: 109.7362
Evaluate side-chains
  258 residues out of total 1546 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 212
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  332 HIS
Chi-restraints excluded: chain A residue  354 PHE
Chi-restraints excluded: chain A residue  405 THR
Chi-restraints excluded: chain A residue  417 LYS
Chi-restraints excluded: chain A residue  444 CYS
Chi-restraints excluded: chain A residue  451 SER
Chi-restraints excluded: chain A residue  463 ILE
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  588 LEU
Chi-restraints excluded: chain A residue  592 LEU
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  697 LYS
Chi-restraints excluded: chain A residue  748 ASP
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  786 HIS
Chi-restraints excluded: chain A residue  808 ILE
Chi-restraints excluded: chain A residue  811 PHE
Chi-restraints excluded: chain A residue  938 ASP
Chi-restraints excluded: chain A residue  958 TRP
Chi-restraints excluded: chain A residue  963 ASN
Chi-restraints excluded: chain A residue  980 VAL
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  434 ASP
Chi-restraints excluded: chain B residue  460 LEU
Chi-restraints excluded: chain B residue  484 SER
Chi-restraints excluded: chain B residue  544 PHE
Chi-restraints excluded: chain B residue  579 SER
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  750 ASP
Chi-restraints excluded: chain B residue  756 VAL
Chi-restraints excluded: chain B residue  765 ASN
Chi-restraints excluded: chain B residue  786 HIS
Chi-restraints excluded: chain B residue  967 LEU
Chi-restraints excluded: chain C residue   60 ASN
Chi-restraints excluded: chain C residue   63 VAL
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain D residue   10 ASP
Chi-restraints excluded: chain D residue   22 VAL
Chi-restraints excluded: chain D residue   31 SER
Chi-restraints excluded: chain D residue   57 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 168
   random chunks:
   chunk 60 optimal weight:   10.0000
   chunk 75 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 157 optimal weight:    7.9990
   chunk 55 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 165 optimal weight:    6.9990
   chunk 95 optimal weight:    0.9990
   chunk 149 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 162 optimal weight:    2.9990
   overall best weight:    1.7586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.189003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.152787 restraints weight = 53710.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.157788 restraints weight = 32004.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.159371 restraints weight = 20974.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.159790 restraints weight = 17295.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.160395 restraints weight = 16513.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6902
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14360  Z= 0.166
  Angle     :  0.538   8.587  19320  Z= 0.298
  Chirality :  0.037   0.141   2052
  Planarity :  0.004   0.077   2476
  Dihedral  :  4.686  45.781   1864
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 20.43 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.20), residues: 1682
  helix:  1.19 (0.17), residues: 980
  sheet: -1.40 (0.42), residues: 130
  loop : -2.07 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 359 
 TYR   0.017   0.001   TYR A 687 
 PHE   0.014   0.001   PHE B 907 
 TRP   0.005   0.001   TRP D  72 
 HIS   0.003   0.001   HIS B 786 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (14360)
  covalent geometry    : angle       0.53842 (19320)
  hydrogen bonds       : bond        0.04689 (  750)
  hydrogen bonds       : angle       4.59528 ( 2160)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4388.42 seconds
wall clock time: 75 minutes 40.99 seconds (4540.99 seconds total)