Starting phenix.real_space_refine
on Fri Sep 27 22:17:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/09_2024/5va1_8650.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/09_2024/5va1_8650.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/09_2024/5va1_8650.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/09_2024/5va1_8650.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/09_2024/5va1_8650.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5va1_8650/09_2024/5va1_8650.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S     108      5.16       5
     C   11484      2.51       5
     N    3008      2.21       5
     O    3028      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 17628
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 560, 4407
          Classifications: {'peptide': 560}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 22, 'TRANS': 537}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 92
          Unresolved non-hydrogen dihedrals: 63
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 5, 'TRP:plan': 1, 'ASP:plan': 3}
          Unresolved non-hydrogen planarities: 63
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 10.26, per 1000 atoms: 0.58
  Number of scatterers: 17628
  At special positions: 0
  Unit cell: (146.87, 146.77, 121.283, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     108     16.00
     O    3028      8.00
     N    3008      7.00
     C   11484      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.39
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4200

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 12 sheets defined
      61.1% alpha, 10.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 26
    Processing helix  chain 'A' and resid 45 through 53
      removed outlier: 3.532A  pdb=" N   CYS A  49 " --> pdb=" O   ASN A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 60
    Processing helix  chain 'A' and resid 75 through 89
      removed outlier: 3.567A  pdb=" N   GLN A  81 " --> pdb=" O   ARG A  77 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE A  82 " --> pdb=" O   ALA A  78 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA A  83 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU A  86 " --> pdb=" O   ILE A  82 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU A  87 " --> pdb=" O   ALA A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 431
      removed outlier: 3.763A  pdb=" N   TRP A 412 " --> pdb=" O   ALA A 408 " (cutoff:3.500A)
      Proline residue:  A 426  - end of helix
    Processing helix  chain 'A' and resid 450 through 473
      removed outlier: 3.564A  pdb=" N   VAL A 455 " --> pdb=" O   PRO A 451 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE A 471 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG A 472 " --> pdb=" O   LEU A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 494
      removed outlier: 3.566A  pdb=" N   ILE A 489 " --> pdb=" O   HIS A 485 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA A 490 " --> pdb=" O   PRO A 486 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   VAL A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS A 492 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 505
      removed outlier: 3.765A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 504 " --> pdb=" O   ILE A 500 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA A 505 " --> pdb=" O   ASP A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 531
      removed outlier: 3.534A  pdb=" N   ALA A 527 " --> pdb=" O   LEU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 3.851A  pdb=" N   ALA A 536 " --> pdb=" O   LEU A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 543
      removed outlier: 3.894A  pdb=" N   TYR A 542 " --> pdb=" O   LYS A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 575
      removed outlier: 3.605A  pdb=" N   VAL A 549 " --> pdb=" O   TYR A 545 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU A 550 " --> pdb=" O   GLY A 546 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY A 572 " --> pdb=" O   TRP A 568 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU A 575 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 593
      removed outlier: 3.624A  pdb=" N   ASN A 588 " --> pdb=" O   GLY A 584 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 623
      removed outlier: 3.549A  pdb=" N   ALA A 614 " --> pdb=" O   LYS A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 667
      removed outlier: 3.870A  pdb=" N   PHE A 656 " --> pdb=" O   TYR A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 688
      removed outlier: 3.583A  pdb=" N   HIS A 674 " --> pdb=" O   THR A 670 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR A 675 " --> pdb=" O   ALA A 671 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL A 680 " --> pdb=" O   GLN A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 709
      removed outlier: 4.037A  pdb=" N   ARG A 696 " --> pdb=" O   PRO A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 718
      removed outlier: 3.714A  pdb=" N   VAL A 716 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 733 through 740
      removed outlier: 3.924A  pdb=" N   HIS A 739 " --> pdb=" O   SER A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 747 through 758
      removed outlier: 3.871A  pdb=" N   LYS A 757 " --> pdb=" O   ALA A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 813
      removed outlier: 4.658A  pdb=" N   TYR A 812 " --> pdb=" O   PRO A 808 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 808 through 813'
    Processing helix  chain 'A' and resid 834 through 845
      removed outlier: 3.743A  pdb=" N   GLU A 840 " --> pdb=" O   ASP A 836 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL A 841 " --> pdb=" O   ASP A 837 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET A 844 " --> pdb=" O   GLU A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 856
      removed outlier: 3.823A  pdb=" N   ASP A 850 " --> pdb=" O   PRO A 846 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   HIS A 851 " --> pdb=" O   GLU A 847 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER A 854 " --> pdb=" O   ASP A 850 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 26
    Processing helix  chain 'B' and resid 45 through 53
      removed outlier: 3.532A  pdb=" N   CYS B  49 " --> pdb=" O   ASN B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 60
    Processing helix  chain 'B' and resid 75 through 89
      removed outlier: 3.567A  pdb=" N   GLN B  81 " --> pdb=" O   ARG B  77 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA B  83 " --> pdb=" O   ALA B  79 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU B  86 " --> pdb=" O   ILE B  82 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 431
      removed outlier: 3.763A  pdb=" N   TRP B 412 " --> pdb=" O   ALA B 408 " (cutoff:3.500A)
      Proline residue:  B 426  - end of helix
    Processing helix  chain 'B' and resid 450 through 473
      removed outlier: 3.564A  pdb=" N   VAL B 455 " --> pdb=" O   PRO B 451 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG B 472 " --> pdb=" O   LEU B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 494
      removed outlier: 3.566A  pdb=" N   ILE B 489 " --> pdb=" O   HIS B 485 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA B 490 " --> pdb=" O   PRO B 486 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   VAL B 491 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS B 492 " --> pdb=" O   ARG B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 505
      removed outlier: 3.765A  pdb=" N   VAL B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B 504 " --> pdb=" O   ILE B 500 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA B 505 " --> pdb=" O   ASP B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 531
      removed outlier: 3.534A  pdb=" N   ALA B 527 " --> pdb=" O   LEU B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 3.851A  pdb=" N   ALA B 536 " --> pdb=" O   LEU B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 543
      removed outlier: 3.894A  pdb=" N   TYR B 542 " --> pdb=" O   LYS B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 575
      removed outlier: 3.605A  pdb=" N   VAL B 549 " --> pdb=" O   TYR B 545 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU B 550 " --> pdb=" O   GLY B 546 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE B 557 " --> pdb=" O   LEU B 553 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY B 572 " --> pdb=" O   TRP B 568 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU B 575 " --> pdb=" O   ILE B 571 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 584 through 593
      removed outlier: 3.624A  pdb=" N   ASN B 588 " --> pdb=" O   GLY B 584 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 606 through 623
      removed outlier: 3.549A  pdb=" N   ALA B 614 " --> pdb=" O   LYS B 610 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 634 through 667
      removed outlier: 3.870A  pdb=" N   PHE B 656 " --> pdb=" O   TYR B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 688
      removed outlier: 3.583A  pdb=" N   HIS B 674 " --> pdb=" O   THR B 670 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR B 675 " --> pdb=" O   ALA B 671 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL B 680 " --> pdb=" O   GLN B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 709
      removed outlier: 4.037A  pdb=" N   ARG B 696 " --> pdb=" O   PRO B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 718
      removed outlier: 3.714A  pdb=" N   VAL B 716 " --> pdb=" O   ASP B 712 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU B 717 " --> pdb=" O   MET B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 721 through 733
    Processing helix  chain 'B' and resid 733 through 740
      removed outlier: 3.924A  pdb=" N   HIS B 739 " --> pdb=" O   SER B 735 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 758
      removed outlier: 3.871A  pdb=" N   LYS B 757 " --> pdb=" O   ALA B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 808 through 813
      removed outlier: 4.658A  pdb=" N   TYR B 812 " --> pdb=" O   PRO B 808 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA B 813 " --> pdb=" O   LEU B 809 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 808 through 813'
    Processing helix  chain 'B' and resid 834 through 845
      removed outlier: 3.743A  pdb=" N   GLU B 840 " --> pdb=" O   ASP B 836 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL B 841 " --> pdb=" O   ASP B 837 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET B 844 " --> pdb=" O   GLU B 840 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 845 through 856
      removed outlier: 3.823A  pdb=" N   ASP B 850 " --> pdb=" O   PRO B 846 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   HIS B 851 " --> pdb=" O   GLU B 847 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER B 854 " --> pdb=" O   ASP B 850 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 26
    Processing helix  chain 'C' and resid 45 through 53
      removed outlier: 3.532A  pdb=" N   CYS C  49 " --> pdb=" O   ASN C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 60
    Processing helix  chain 'C' and resid 75 through 89
      removed outlier: 3.567A  pdb=" N   GLN C  81 " --> pdb=" O   ARG C  77 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE C  82 " --> pdb=" O   ALA C  78 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA C  83 " --> pdb=" O   ALA C  79 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU C  86 " --> pdb=" O   ILE C  82 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU C  87 " --> pdb=" O   ALA C  83 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 431
      removed outlier: 3.763A  pdb=" N   TRP C 412 " --> pdb=" O   ALA C 408 " (cutoff:3.500A)
      Proline residue:  C 426  - end of helix
    Processing helix  chain 'C' and resid 450 through 473
      removed outlier: 3.564A  pdb=" N   VAL C 455 " --> pdb=" O   PRO C 451 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE C 471 " --> pdb=" O   ILE C 467 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG C 472 " --> pdb=" O   LEU C 468 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 485 through 494
      removed outlier: 3.566A  pdb=" N   ILE C 489 " --> pdb=" O   HIS C 485 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA C 490 " --> pdb=" O   PRO C 486 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   VAL C 491 " --> pdb=" O   GLY C 487 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS C 492 " --> pdb=" O   ARG C 488 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 497 through 505
      removed outlier: 3.765A  pdb=" N   VAL C 503 " --> pdb=" O   LEU C 499 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA C 504 " --> pdb=" O   ILE C 500 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA C 505 " --> pdb=" O   ASP C 501 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 522 through 531
      removed outlier: 3.534A  pdb=" N   ALA C 527 " --> pdb=" O   LEU C 524 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 532 through 538
      removed outlier: 3.851A  pdb=" N   ALA C 536 " --> pdb=" O   LEU C 532 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 543
      removed outlier: 3.894A  pdb=" N   TYR C 542 " --> pdb=" O   LYS C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 545 through 575
      removed outlier: 3.605A  pdb=" N   VAL C 549 " --> pdb=" O   TYR C 545 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU C 550 " --> pdb=" O   GLY C 546 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE C 557 " --> pdb=" O   LEU C 553 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY C 572 " --> pdb=" O   TRP C 568 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU C 575 " --> pdb=" O   ILE C 571 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 584 through 593
      removed outlier: 3.624A  pdb=" N   ASN C 588 " --> pdb=" O   GLY C 584 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP C 591 " --> pdb=" O   HIS C 587 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 606 through 623
      removed outlier: 3.549A  pdb=" N   ALA C 614 " --> pdb=" O   LYS C 610 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 634 through 667
      removed outlier: 3.870A  pdb=" N   PHE C 656 " --> pdb=" O   TYR C 652 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 668 through 688
      removed outlier: 3.583A  pdb=" N   HIS C 674 " --> pdb=" O   THR C 670 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR C 675 " --> pdb=" O   ALA C 671 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL C 680 " --> pdb=" O   GLN C 676 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 690 through 709
      removed outlier: 4.037A  pdb=" N   ARG C 696 " --> pdb=" O   PRO C 692 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 712 through 718
      removed outlier: 3.714A  pdb=" N   VAL C 716 " --> pdb=" O   ASP C 712 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU C 717 " --> pdb=" O   MET C 713 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 721 through 733
    Processing helix  chain 'C' and resid 733 through 740
      removed outlier: 3.924A  pdb=" N   HIS C 739 " --> pdb=" O   SER C 735 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 747 through 758
      removed outlier: 3.871A  pdb=" N   LYS C 757 " --> pdb=" O   ALA C 753 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 808 through 813
      removed outlier: 4.658A  pdb=" N   TYR C 812 " --> pdb=" O   PRO C 808 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA C 813 " --> pdb=" O   LEU C 809 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 808 through 813'
    Processing helix  chain 'C' and resid 834 through 845
      removed outlier: 3.743A  pdb=" N   GLU C 840 " --> pdb=" O   ASP C 836 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL C 841 " --> pdb=" O   ASP C 837 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET C 844 " --> pdb=" O   GLU C 840 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 845 through 856
      removed outlier: 3.823A  pdb=" N   ASP C 850 " --> pdb=" O   PRO C 846 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   HIS C 851 " --> pdb=" O   GLU C 847 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER C 854 " --> pdb=" O   ASP C 850 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 13 through 26
    Processing helix  chain 'D' and resid 45 through 53
      removed outlier: 3.532A  pdb=" N   CYS D  49 " --> pdb=" O   ASN D  45 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 60
    Processing helix  chain 'D' and resid 75 through 89
      removed outlier: 3.567A  pdb=" N   GLN D  81 " --> pdb=" O   ARG D  77 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE D  82 " --> pdb=" O   ALA D  78 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ALA D  83 " --> pdb=" O   ALA D  79 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LEU D  86 " --> pdb=" O   ILE D  82 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   LEU D  87 " --> pdb=" O   ALA D  83 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 404 through 431
      removed outlier: 3.763A  pdb=" N   TRP D 412 " --> pdb=" O   ALA D 408 " (cutoff:3.500A)
      Proline residue:  D 426  - end of helix
    Processing helix  chain 'D' and resid 450 through 473
      removed outlier: 3.564A  pdb=" N   VAL D 455 " --> pdb=" O   PRO D 451 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   PHE D 471 " --> pdb=" O   ILE D 467 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   ARG D 472 " --> pdb=" O   LEU D 468 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 485 through 494
      removed outlier: 3.566A  pdb=" N   ILE D 489 " --> pdb=" O   HIS D 485 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA D 490 " --> pdb=" O   PRO D 486 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   VAL D 491 " --> pdb=" O   GLY D 487 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   HIS D 492 " --> pdb=" O   ARG D 488 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 497 through 505
      removed outlier: 3.765A  pdb=" N   VAL D 503 " --> pdb=" O   LEU D 499 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA D 504 " --> pdb=" O   ILE D 500 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA D 505 " --> pdb=" O   ASP D 501 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 522 through 531
      removed outlier: 3.534A  pdb=" N   ALA D 527 " --> pdb=" O   LEU D 524 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 532 through 538
      removed outlier: 3.851A  pdb=" N   ALA D 536 " --> pdb=" O   LEU D 532 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 538 through 543
      removed outlier: 3.894A  pdb=" N   TYR D 542 " --> pdb=" O   LYS D 538 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 545 through 575
      removed outlier: 3.605A  pdb=" N   VAL D 549 " --> pdb=" O   TYR D 545 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU D 550 " --> pdb=" O   GLY D 546 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   PHE D 557 " --> pdb=" O   LEU D 553 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   GLY D 572 " --> pdb=" O   TRP D 568 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   GLU D 575 " --> pdb=" O   ILE D 571 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 584 through 593
      removed outlier: 3.624A  pdb=" N   ASN D 588 " --> pdb=" O   GLY D 584 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASP D 591 " --> pdb=" O   HIS D 587 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 606 through 623
      removed outlier: 3.549A  pdb=" N   ALA D 614 " --> pdb=" O   LYS D 610 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 634 through 667
      removed outlier: 3.870A  pdb=" N   PHE D 656 " --> pdb=" O   TYR D 652 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 668 through 688
      removed outlier: 3.583A  pdb=" N   HIS D 674 " --> pdb=" O   THR D 670 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   THR D 675 " --> pdb=" O   ALA D 671 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL D 680 " --> pdb=" O   GLN D 676 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 690 through 709
      removed outlier: 4.037A  pdb=" N   ARG D 696 " --> pdb=" O   PRO D 692 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 712 through 718
      removed outlier: 3.714A  pdb=" N   VAL D 716 " --> pdb=" O   ASP D 712 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU D 717 " --> pdb=" O   MET D 713 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 721 through 733
    Processing helix  chain 'D' and resid 733 through 740
      removed outlier: 3.924A  pdb=" N   HIS D 739 " --> pdb=" O   SER D 735 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 747 through 758
      removed outlier: 3.871A  pdb=" N   LYS D 757 " --> pdb=" O   ALA D 753 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 808 through 813
      removed outlier: 4.658A  pdb=" N   TYR D 812 " --> pdb=" O   PRO D 808 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA D 813 " --> pdb=" O   LEU D 809 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 808 through 813'
    Processing helix  chain 'D' and resid 834 through 845
      removed outlier: 3.743A  pdb=" N   GLU D 840 " --> pdb=" O   ASP D 836 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   VAL D 841 " --> pdb=" O   ASP D 837 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   MET D 844 " --> pdb=" O   GLU D 840 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 845 through 856
      removed outlier: 3.823A  pdb=" N   ASP D 850 " --> pdb=" O   PRO D 846 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   HIS D 851 " --> pdb=" O   GLU D 847 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   SER D 854 " --> pdb=" O   ASP D 850 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 41 through 44
      removed outlier: 6.274A  pdb=" N   ILE A  31 " --> pdb=" O   ILE A  42 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   CYS A  44 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   PHE A  29 " --> pdb=" O   CYS A  44 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS A  28 " --> pdb=" O   PHE A 129 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A  30 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   MET A 124 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 130 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL A 112 " --> pdb=" O   ARG A  92 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ARG A  92 " --> pdb=" O   VAL A 112 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 759 through 763
      removed outlier: 3.908A  pdb=" N   LEU A 830 " --> pdb=" O   THR A 761 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP A 803 " --> pdb=" O   ILE A 782 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   PHE A 860 " --> pdb=" O   ILE A 804 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY A 806 " --> pdb=" O   PHE A 860 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'A' and resid 768 through 770
      removed outlier: 7.088A  pdb=" N   VAL A 822 " --> pdb=" O   LEU A 769 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'B' and resid 41 through 44
      removed outlier: 6.274A  pdb=" N   ILE B  31 " --> pdb=" O   ILE B  42 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   CYS B  44 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   PHE B  29 " --> pdb=" O   CYS B  44 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS B  28 " --> pdb=" O   PHE B 129 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE B  30 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   MET B 124 " --> pdb=" O   VAL B 115 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU B 130 " --> pdb=" O   LEU B 109 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL B 112 " --> pdb=" O   ARG B  92 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ARG B  92 " --> pdb=" O   VAL B 112 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'B' and resid 759 through 763
      removed outlier: 3.908A  pdb=" N   LEU B 830 " --> pdb=" O   THR B 761 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP B 803 " --> pdb=" O   ILE B 782 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   PHE B 860 " --> pdb=" O   ILE B 804 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY B 806 " --> pdb=" O   PHE B 860 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'B' and resid 768 through 770
      removed outlier: 7.088A  pdb=" N   VAL B 822 " --> pdb=" O   LEU B 769 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'C' and resid 41 through 44
      removed outlier: 6.274A  pdb=" N   ILE C  31 " --> pdb=" O   ILE C  42 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   CYS C  44 " --> pdb=" O   PHE C  29 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   PHE C  29 " --> pdb=" O   CYS C  44 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS C  28 " --> pdb=" O   PHE C 129 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE C  30 " --> pdb=" O   LEU C 127 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   MET C 124 " --> pdb=" O   VAL C 115 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU C 130 " --> pdb=" O   LEU C 109 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL C 112 " --> pdb=" O   ARG C  92 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ARG C  92 " --> pdb=" O   VAL C 112 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'C' and resid 759 through 763
      removed outlier: 3.908A  pdb=" N   LEU C 830 " --> pdb=" O   THR C 761 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP C 803 " --> pdb=" O   ILE C 782 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   PHE C 860 " --> pdb=" O   ILE C 804 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY C 806 " --> pdb=" O   PHE C 860 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'C' and resid 768 through 770
      removed outlier: 7.088A  pdb=" N   VAL C 822 " --> pdb=" O   LEU C 769 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'D' and resid 41 through 44
      removed outlier: 6.274A  pdb=" N   ILE D  31 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   CYS D  44 " --> pdb=" O   PHE D  29 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   PHE D  29 " --> pdb=" O   CYS D  44 " (cutoff:3.500A)
      removed outlier: 4.549A  pdb=" N   LYS D  28 " --> pdb=" O   PHE D 129 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE D  30 " --> pdb=" O   LEU D 127 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   MET D 124 " --> pdb=" O   VAL D 115 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU D 130 " --> pdb=" O   LEU D 109 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   VAL D 112 " --> pdb=" O   ARG D  92 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ARG D  92 " --> pdb=" O   VAL D 112 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'D' and resid 759 through 763
      removed outlier: 3.908A  pdb=" N   LEU D 830 " --> pdb=" O   THR D 761 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ASP D 803 " --> pdb=" O   ILE D 782 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   PHE D 860 " --> pdb=" O   ILE D 804 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLY D 806 " --> pdb=" O   PHE D 860 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'D' and resid 768 through 770
      removed outlier: 7.088A  pdb=" N   VAL D 822 " --> pdb=" O   LEU D 769 " (cutoff:3.500A)

    940 hydrogen bonds defined for protein.
    2688 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: 5.20

  Time building geometry restraints manager: 5.16 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 5512
        1.34 -     1.46: 2352
        1.46 -     1.58: 10040
        1.58 -     1.69: 0
        1.69 -     1.81: 152
  Bond restraints: 18056
  Sorted by residual:
  bond pdb=" N   GLY B 603 "
       pdb=" CA  GLY B 603 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 1.60e-02 3.91e+03 6.68e+00
  bond pdb=" N   GLY A 603 "
       pdb=" CA  GLY A 603 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 1.60e-02 3.91e+03 6.68e+00
  bond pdb=" N   GLY D 603 "
       pdb=" CA  GLY D 603 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 1.60e-02 3.91e+03 6.68e+00
  bond pdb=" N   GLY C 603 "
       pdb=" CA  GLY C 603 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 1.60e-02 3.91e+03 6.68e+00
  bond pdb=" CA  PRO B 764 "
       pdb=" C   PRO B 764 "
    ideal  model  delta    sigma   weight residual
    1.517  1.540 -0.023 9.30e-03 1.16e+04 6.32e+00
  ... (remaining 18051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 19660
        1.22 -     2.44: 4172
        2.44 -     3.66: 600
        3.66 -     4.88: 48
        4.88 -     6.10: 32
  Bond angle restraints: 24512
  Sorted by residual:
  angle pdb=" N   ASN D 691 "
        pdb=" CA  ASN D 691 "
        pdb=" C   ASN D 691 "
      ideal   model   delta    sigma   weight residual
     112.75  118.20   -5.45 1.36e+00 5.41e-01 1.60e+01
  angle pdb=" N   ASN B 691 "
        pdb=" CA  ASN B 691 "
        pdb=" C   ASN B 691 "
      ideal   model   delta    sigma   weight residual
     112.75  118.20   -5.45 1.36e+00 5.41e-01 1.60e+01
  angle pdb=" N   ASN A 691 "
        pdb=" CA  ASN A 691 "
        pdb=" C   ASN A 691 "
      ideal   model   delta    sigma   weight residual
     112.75  118.20   -5.45 1.36e+00 5.41e-01 1.60e+01
  angle pdb=" N   ASN C 691 "
        pdb=" CA  ASN C 691 "
        pdb=" C   ASN C 691 "
      ideal   model   delta    sigma   weight residual
     112.75  118.20   -5.45 1.36e+00 5.41e-01 1.60e+01
  angle pdb=" N   ASN B 629 "
        pdb=" CA  ASN B 629 "
        pdb=" C   ASN B 629 "
      ideal   model   delta    sigma   weight residual
     111.14  107.14    4.00 1.08e+00 8.57e-01 1.37e+01
  ... (remaining 24507 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.03: 9312
       12.03 -    24.06: 860
       24.06 -    36.09: 288
       36.09 -    48.12: 96
       48.12 -    60.16: 24
  Dihedral angle restraints: 10580
    sinusoidal: 4072
      harmonic: 6508
  Sorted by residual:
  dihedral pdb=" CA  GLY C 628 "
           pdb=" C   GLY C 628 "
           pdb=" N   ASN C 629 "
           pdb=" CA  ASN C 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  GLY D 628 "
           pdb=" C   GLY D 628 "
           pdb=" N   ASN D 629 "
           pdb=" CA  ASN D 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  dihedral pdb=" CA  GLY B 628 "
           pdb=" C   GLY B 628 "
           pdb=" N   ASN B 629 "
           pdb=" CA  ASN B 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.61   19.39     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 10577 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1712
       0.046 -    0.091: 720
       0.091 -    0.137: 216
       0.137 -    0.182: 104
       0.182 -    0.228: 40
  Chirality restraints: 2792
  Sorted by residual:
  chirality pdb=" CA  ILE A 804 "
            pdb=" N   ILE A 804 "
            pdb=" C   ILE A 804 "
            pdb=" CB  ILE A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  ILE D 804 "
            pdb=" N   ILE D 804 "
            pdb=" C   ILE D 804 "
            pdb=" CB  ILE D 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.30e+00
  chirality pdb=" CA  ILE B 804 "
            pdb=" N   ILE B 804 "
            pdb=" C   ILE B 804 "
            pdb=" CB  ILE B 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.23 2.00e-01 2.50e+01 1.30e+00
  ... (remaining 2789 not shown)

  Planarity restraints: 3080
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B 450 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO B 451 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 450 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO C 451 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO C 451 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C 451 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 450 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 451 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 3077 not shown)

  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 16
        2.35 -     2.99: 7492
        2.99 -     3.63: 24892
        3.63 -     4.26: 36240
        4.26 -     4.90: 63270
  Nonbonded interactions: 131910
  Sorted by model distance:
  nonbonded pdb=" CG2 ILE C  42 "
            pdb=" O   VAL D 796 "
     model   vdw
     1.715 3.460
  nonbonded pdb=" CG2 ILE A  42 "
            pdb=" O   VAL B 796 "
     model   vdw
     1.715 3.460
  nonbonded pdb=" CG2 ILE B  42 "
            pdb=" O   VAL C 796 "
     model   vdw
     1.715 3.460
  nonbonded pdb=" O   VAL A 796 "
            pdb=" CG2 ILE D  42 "
     model   vdw
     1.715 3.460
  nonbonded pdb=" NH1 ARG C 752 "
            pdb=" NE2 HIS D 771 "
     model   vdw
     1.963 3.200
  ... (remaining 131905 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'
  selection = 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:             2.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          3.950
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     38.100
  Find NCS groups from input model:        0.480
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   47.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
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      :  0.008   0.046  18056  Z= 0.498
  Angle     :  1.020   6.103  24512  Z= 0.703
  Chirality :  0.063   0.228   2792
  Planarity :  0.004   0.032   3080
  Dihedral  : 11.845  60.156   6380
  Min Nonbonded Distance : 1.715

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  5.83 %
    Favored  : 92.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.52 (0.14), residues: 2192
  helix: -2.21 (0.11), residues: 1124
  sheet: -2.62 (0.37), residues: 132
  loop : -2.27 (0.18), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 585 
 HIS   0.004   0.001   HIS A 674 
 PHE   0.011   0.001   PHE D  68 
 TYR   0.011   0.001   TYR D 652 
 ARG   0.002   0.000   ARG A 863 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  743 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 719
  time to evaluate  : 1.815 
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: A    4 ARG cc_start: 0.9090 (ttp-170) cc_final: 0.8504 (ttt180)
REVERT: A  130 GLU cc_start: 0.9714 (tp30) cc_final: 0.9514 (pm20)
REVERT: A  407 LYS cc_start: 0.9550 (tptm) cc_final: 0.9159 (tptp)
REVERT: A  466 ASP cc_start: 0.9632 (t0) cc_final: 0.9354 (t0)
REVERT: A  541 ARG cc_start: 0.9271 (ttm170) cc_final: 0.8417 (ttp80)
REVERT: A  542 TYR cc_start: 0.9264 (m-80) cc_final: 0.8022 (m-80)
REVERT: A  576 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7897 (tp40)
REVERT: A  640 PHE cc_start: 0.9684 (t80) cc_final: 0.9364 (t80)
REVERT: A  668 SER cc_start: 0.9591 (t) cc_final: 0.9341 (m)
REVERT: A  677 MET cc_start: 0.9883 (tpp) cc_final: 0.9645 (tpp)
REVERT: A  679 ARG cc_start: 0.9798 (mtt180) cc_final: 0.9588 (mtt180)
REVERT: A  681 ARG cc_start: 0.9736 (mtt180) cc_final: 0.9390 (ptp-110)
REVERT: A  682 GLU cc_start: 0.9686 (mt-10) cc_final: 0.9442 (pt0)
REVERT: A  695 GLN cc_start: 0.9667 (mt0) cc_final: 0.9352 (mp10)
REVERT: A  698 GLU cc_start: 0.9691 (mt-10) cc_final: 0.9479 (pt0)
REVERT: A  702 GLN cc_start: 0.9699 (mt0) cc_final: 0.9485 (mm-40)
REVERT: A  714 ASN cc_start: 0.9774 (m-40) cc_final: 0.9442 (p0)
REVERT: A  723 CYS cc_start: 0.9433 (m) cc_final: 0.8706 (p)
REVERT: A  729 CYS cc_start: 0.9529 (m) cc_final: 0.8719 (p)
REVERT: A  734 ARG cc_start: 0.9735 (ptt180) cc_final: 0.9476 (mtm110)
REVERT: A  739 HIS cc_start: 0.9843 (m-70) cc_final: 0.9634 (m90)
REVERT: A  748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9568 (tttm)
REVERT: A  756 MET cc_start: 0.9134 (mmm) cc_final: 0.8833 (mmm)
REVERT: A  782 ILE cc_start: 0.9756 (mt) cc_final: 0.9452 (tp)
REVERT: A  821 ASP cc_start: 0.9309 (m-30) cc_final: 0.9026 (p0)
REVERT: A  854 SER cc_start: 0.9799 (t) cc_final: 0.9590 (p)
REVERT: A  857 GLU cc_start: 0.9416 (mt-10) cc_final: 0.9123 (mm-30)
REVERT: B    4 ARG cc_start: 0.9067 (ttp-170) cc_final: 0.8457 (ttt180)
REVERT: B   31 ILE cc_start: 0.9799 (mt) cc_final: 0.9578 (pt)
REVERT: B  126 ILE cc_start: 0.9785 (mt) cc_final: 0.9584 (tt)
REVERT: B  130 GLU cc_start: 0.9723 (tp30) cc_final: 0.9488 (pm20)
REVERT: B  407 LYS cc_start: 0.9573 (tptm) cc_final: 0.9205 (tptp)
REVERT: B  415 LEU cc_start: 0.9955 (tt) cc_final: 0.9715 (tt)
REVERT: B  466 ASP cc_start: 0.9687 (t0) cc_final: 0.9311 (t0)
REVERT: B  541 ARG cc_start: 0.9287 (ttm170) cc_final: 0.8508 (ttp80)
REVERT: B  542 TYR cc_start: 0.9262 (m-80) cc_final: 0.8157 (m-80)
REVERT: B  576 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8156 (tp40)
REVERT: B  588 ASN cc_start: 0.9739 (t0) cc_final: 0.9423 (t0)
REVERT: B  592 GLN cc_start: 0.9142 (mt0) cc_final: 0.8894 (mt0)
REVERT: B  620 SER cc_start: 0.9693 (p) cc_final: 0.9459 (t)
REVERT: B  677 MET cc_start: 0.9871 (tpp) cc_final: 0.9630 (tpp)
REVERT: B  681 ARG cc_start: 0.9728 (mtt180) cc_final: 0.9373 (ptp-110)
REVERT: B  682 GLU cc_start: 0.9707 (mt-10) cc_final: 0.9479 (pt0)
REVERT: B  695 GLN cc_start: 0.9625 (mt0) cc_final: 0.9308 (mp10)
REVERT: B  698 GLU cc_start: 0.9656 (mt-10) cc_final: 0.9419 (pt0)
REVERT: B  702 GLN cc_start: 0.9685 (mt0) cc_final: 0.9442 (mm-40)
REVERT: B  705 TRP cc_start: 0.9450 (t60) cc_final: 0.9223 (t60)
REVERT: B  714 ASN cc_start: 0.9793 (m-40) cc_final: 0.9508 (p0)
REVERT: B  723 CYS cc_start: 0.9405 (m) cc_final: 0.8611 (p)
REVERT: B  729 CYS cc_start: 0.9526 (m) cc_final: 0.8746 (p)
REVERT: B  734 ARG cc_start: 0.9746 (ptt180) cc_final: 0.9484 (mtm110)
REVERT: B  739 HIS cc_start: 0.9837 (m-70) cc_final: 0.9636 (m90)
REVERT: B  748 LYS cc_start: 0.9894 (mttt) cc_final: 0.9614 (tttm)
REVERT: B  756 MET cc_start: 0.9073 (mmm) cc_final: 0.8771 (mmm)
REVERT: B  782 ILE cc_start: 0.9754 (mt) cc_final: 0.9447 (tp)
REVERT: B  821 ASP cc_start: 0.9306 (m-30) cc_final: 0.9061 (p0)
REVERT: B  854 SER cc_start: 0.9771 (t) cc_final: 0.9541 (p)
REVERT: B  857 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9061 (mm-30)
REVERT: C    4 ARG cc_start: 0.9049 (ttp-170) cc_final: 0.8496 (ttt180)
REVERT: C  130 GLU cc_start: 0.9721 (tp30) cc_final: 0.9509 (pm20)
REVERT: C  407 LYS cc_start: 0.9562 (tptm) cc_final: 0.9189 (tptp)
REVERT: C  466 ASP cc_start: 0.9655 (t0) cc_final: 0.9405 (t0)
REVERT: C  501 ASP cc_start: 0.9460 (m-30) cc_final: 0.9050 (p0)
REVERT: C  541 ARG cc_start: 0.9241 (ttm170) cc_final: 0.8504 (ttp80)
REVERT: C  542 TYR cc_start: 0.9323 (m-80) cc_final: 0.8065 (m-80)
REVERT: C  576 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8003 (tp40)
REVERT: C  588 ASN cc_start: 0.9710 (t0) cc_final: 0.9390 (t0)
REVERT: C  592 GLN cc_start: 0.9238 (mt0) cc_final: 0.8936 (mt0)
REVERT: C  620 SER cc_start: 0.9642 (p) cc_final: 0.9430 (t)
REVERT: C  677 MET cc_start: 0.9864 (tpp) cc_final: 0.9536 (tpp)
REVERT: C  681 ARG cc_start: 0.9724 (mtt180) cc_final: 0.9366 (ptp-110)
REVERT: C  682 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9463 (pt0)
REVERT: C  695 GLN cc_start: 0.9631 (mt0) cc_final: 0.9356 (mp10)
REVERT: C  697 LEU cc_start: 0.9936 (mt) cc_final: 0.9634 (pp)
REVERT: C  698 GLU cc_start: 0.9643 (mt-10) cc_final: 0.9437 (pt0)
REVERT: C  699 GLU cc_start: 0.9703 (pt0) cc_final: 0.9498 (pt0)
REVERT: C  702 GLN cc_start: 0.9677 (mt0) cc_final: 0.9420 (mm-40)
REVERT: C  705 TRP cc_start: 0.9469 (t60) cc_final: 0.9227 (t60)
REVERT: C  714 ASN cc_start: 0.9800 (m-40) cc_final: 0.9488 (p0)
REVERT: C  723 CYS cc_start: 0.9364 (m) cc_final: 0.8700 (p)
REVERT: C  729 CYS cc_start: 0.9544 (m) cc_final: 0.8783 (p)
REVERT: C  748 LYS cc_start: 0.9900 (mttt) cc_final: 0.9632 (tttm)
REVERT: C  756 MET cc_start: 0.9115 (mmm) cc_final: 0.8835 (mmm)
REVERT: C  782 ILE cc_start: 0.9704 (mt) cc_final: 0.9358 (tp)
REVERT: C  821 ASP cc_start: 0.9254 (m-30) cc_final: 0.9041 (p0)
REVERT: C  854 SER cc_start: 0.9801 (t) cc_final: 0.9560 (p)
REVERT: C  857 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9067 (mm-30)
REVERT: D    4 ARG cc_start: 0.9089 (ttp-170) cc_final: 0.8535 (ttt180)
REVERT: D   31 ILE cc_start: 0.9806 (mt) cc_final: 0.9538 (tp)
REVERT: D  124 MET cc_start: 0.9335 (mmt) cc_final: 0.9086 (mmm)
REVERT: D  407 LYS cc_start: 0.9529 (tptm) cc_final: 0.9134 (tptp)
REVERT: D  415 LEU cc_start: 0.9945 (tt) cc_final: 0.9683 (tt)
REVERT: D  466 ASP cc_start: 0.9603 (t0) cc_final: 0.9338 (t0)
REVERT: D  501 ASP cc_start: 0.9415 (m-30) cc_final: 0.9078 (p0)
REVERT: D  541 ARG cc_start: 0.9214 (ttm170) cc_final: 0.8411 (ttp80)
REVERT: D  542 TYR cc_start: 0.9328 (m-80) cc_final: 0.8195 (m-80)
REVERT: D  576 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7764 (tp40)
REVERT: D  655 ILE cc_start: 0.9616 (tt) cc_final: 0.9415 (tp)
REVERT: D  677 MET cc_start: 0.9876 (tpp) cc_final: 0.9558 (tpp)
REVERT: D  679 ARG cc_start: 0.9807 (mtt180) cc_final: 0.9597 (mtt180)
REVERT: D  681 ARG cc_start: 0.9731 (mtt180) cc_final: 0.9395 (ptp-110)
REVERT: D  682 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9448 (pt0)
REVERT: D  695 GLN cc_start: 0.9674 (mt0) cc_final: 0.9376 (mp10)
REVERT: D  698 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9417 (pt0)
REVERT: D  702 GLN cc_start: 0.9683 (mt0) cc_final: 0.9453 (mm-40)
REVERT: D  714 ASN cc_start: 0.9779 (m-40) cc_final: 0.9392 (p0)
REVERT: D  723 CYS cc_start: 0.9371 (m) cc_final: 0.8786 (p)
REVERT: D  729 CYS cc_start: 0.9538 (m) cc_final: 0.8752 (p)
REVERT: D  748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9582 (tttm)
REVERT: D  756 MET cc_start: 0.9156 (mmm) cc_final: 0.8869 (mmm)
REVERT: D  782 ILE cc_start: 0.9711 (mt) cc_final: 0.9356 (tp)
REVERT: D  821 ASP cc_start: 0.9255 (m-30) cc_final: 0.9012 (p0)
REVERT: D  837 ASP cc_start: 0.9537 (m-30) cc_final: 0.9322 (m-30)
REVERT: D  857 GLU cc_start: 0.9410 (mt-10) cc_final: 0.9122 (mm-30)
  outliers start: 24
  outliers final: 0
  residues processed: 735
  average time/residue: 0.3046
  time to fit residues: 327.5516
Evaluate side-chains
  542 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 538
  time to evaluate  : 1.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 GLN
Chi-restraints excluded: chain B residue  576 GLN
Chi-restraints excluded: chain C residue  576 GLN
Chi-restraints excluded: chain D residue  576 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 189 optimal weight:   30.0000
   chunk 169 optimal weight:    8.9990
   chunk 94 optimal weight:   30.0000
   chunk 57 optimal weight:    5.9990
   chunk 114 optimal weight:   30.0000
   chunk 90 optimal weight:    6.9990
   chunk 175 optimal weight:   50.0000
   chunk 67 optimal weight:   50.0000
   chunk 106 optimal weight:   20.0000
   chunk 130 optimal weight:    8.9990
   chunk 203 optimal weight:    8.9990
   overall best weight:    7.9990

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
A  70 HIS
A 576 GLN
A 802 ASN
B  61 GLN
B  70 HIS
B 576 GLN
B 592 GLN
B 802 ASN
C  61 GLN
C  70 HIS
C 576 GLN
C 592 GLN
C 802 ASN
D  70 HIS
D 576 GLN
D 802 ASN

Total number of N/Q/H flips: 17

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  18056  Z= 0.236
  Angle     :  0.720  10.602  24512  Z= 0.354
  Chirality :  0.045   0.180   2792
  Planarity :  0.005   0.042   3080
  Dihedral  :  4.793  29.897   2440
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.85 %
    Favored  : 83.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.17), residues: 2192
  helix: -0.15 (0.14), residues: 1216
  sheet: -1.64 (0.35), residues: 168
  loop : -1.59 (0.20), residues: 808

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 497 
 HIS   0.007   0.001   HIS C 831 
 PHE   0.023   0.002   PHE A 557 
 TYR   0.018   0.001   TYR B 545 
 ARG   0.006   0.001   ARG C 734 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  561 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 524
  time to evaluate  : 1.951 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    4 ARG cc_start: 0.9261 (ttp-170) cc_final: 0.8673 (ttt90)
REVERT: A  124 MET cc_start: 0.9745 (mmm) cc_final: 0.8989 (tpp)
REVERT: A  466 ASP cc_start: 0.9676 (t0) cc_final: 0.9405 (t0)
REVERT: A  470 ASN cc_start: 0.9329 (m-40) cc_final: 0.8903 (m-40)
REVERT: A  542 TYR cc_start: 0.8804 (m-80) cc_final: 0.8387 (m-80)
REVERT: A  651 MET cc_start: 0.9691 (mmp) cc_final: 0.9480 (mmp)
REVERT: A  677 MET cc_start: 0.9887 (tpp) cc_final: 0.9610 (tpp)
REVERT: A  681 ARG cc_start: 0.9653 (mtt180) cc_final: 0.9433 (ptp-110)
REVERT: A  691 ASN cc_start: 0.9841 (m-40) cc_final: 0.9639 (p0)
REVERT: A  723 CYS cc_start: 0.9143 (m) cc_final: 0.8921 (p)
REVERT: A  729 CYS cc_start: 0.9250 (m) cc_final: 0.8795 (m)
REVERT: A  748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9606 (ttpp)
REVERT: A  756 MET cc_start: 0.9207 (mmm) cc_final: 0.8828 (mmm)
REVERT: A  836 ASP cc_start: 0.9278 (OUTLIER) cc_final: 0.9023 (p0)
REVERT: A  837 ASP cc_start: 0.9530 (m-30) cc_final: 0.9293 (m-30)
REVERT: B    4 ARG cc_start: 0.9239 (ttp-170) cc_final: 0.8666 (ttt90)
REVERT: B  466 ASP cc_start: 0.9709 (t0) cc_final: 0.9489 (t0)
REVERT: B  542 TYR cc_start: 0.8808 (m-80) cc_final: 0.8386 (m-80)
REVERT: B  677 MET cc_start: 0.9879 (tpp) cc_final: 0.9479 (tpp)
REVERT: B  681 ARG cc_start: 0.9642 (mtt180) cc_final: 0.9405 (ptp-110)
REVERT: B  682 GLU cc_start: 0.9765 (mt-10) cc_final: 0.9550 (pt0)
REVERT: B  691 ASN cc_start: 0.9816 (m-40) cc_final: 0.9594 (p0)
REVERT: B  723 CYS cc_start: 0.9069 (m) cc_final: 0.8813 (p)
REVERT: B  729 CYS cc_start: 0.9413 (m) cc_final: 0.8959 (m)
REVERT: B  748 LYS cc_start: 0.9878 (mttt) cc_final: 0.9634 (ttpp)
REVERT: B  756 MET cc_start: 0.9186 (mmm) cc_final: 0.8802 (mmm)
REVERT: C    4 ARG cc_start: 0.9260 (ttp-170) cc_final: 0.8771 (ttm-80)
REVERT: C   31 ILE cc_start: 0.9728 (pt) cc_final: 0.9492 (tp)
REVERT: C  466 ASP cc_start: 0.9688 (t0) cc_final: 0.9341 (t0)
REVERT: C  470 ASN cc_start: 0.9330 (m-40) cc_final: 0.8852 (m110)
REVERT: C  500 ILE cc_start: 0.8918 (mm) cc_final: 0.8668 (pt)
REVERT: C  542 TYR cc_start: 0.8864 (m-80) cc_final: 0.8460 (m-80)
REVERT: C  677 MET cc_start: 0.9878 (tpp) cc_final: 0.9444 (tpp)
REVERT: C  681 ARG cc_start: 0.9644 (mtt180) cc_final: 0.9401 (ptp-110)
REVERT: C  682 GLU cc_start: 0.9758 (mt-10) cc_final: 0.9530 (pt0)
REVERT: C  691 ASN cc_start: 0.9824 (m-40) cc_final: 0.9605 (p0)
REVERT: C  697 LEU cc_start: 0.9916 (mt) cc_final: 0.9672 (pp)
REVERT: C  729 CYS cc_start: 0.9425 (m) cc_final: 0.8949 (m)
REVERT: C  748 LYS cc_start: 0.9873 (mttt) cc_final: 0.9631 (ttpp)
REVERT: C  756 MET cc_start: 0.9233 (mmm) cc_final: 0.8875 (mmm)
REVERT: C  844 MET cc_start: 0.9467 (mmm) cc_final: 0.9198 (mmm)
REVERT: D    4 ARG cc_start: 0.9273 (ttp-170) cc_final: 0.8662 (ttt90)
REVERT: D  466 ASP cc_start: 0.9649 (t0) cc_final: 0.9333 (t0)
REVERT: D  470 ASN cc_start: 0.9332 (m-40) cc_final: 0.8864 (m110)
REVERT: D  500 ILE cc_start: 0.8857 (mm) cc_final: 0.8617 (pt)
REVERT: D  542 TYR cc_start: 0.8894 (m-80) cc_final: 0.8465 (m-80)
REVERT: D  677 MET cc_start: 0.9870 (tpp) cc_final: 0.9507 (tpp)
REVERT: D  681 ARG cc_start: 0.9645 (mtt180) cc_final: 0.9406 (ptp-110)
REVERT: D  691 ASN cc_start: 0.9841 (m-40) cc_final: 0.9525 (t0)
REVERT: D  729 CYS cc_start: 0.9344 (m) cc_final: 0.8849 (m)
REVERT: D  748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9623 (tttm)
REVERT: D  756 MET cc_start: 0.9272 (mmm) cc_final: 0.8905 (mmm)
REVERT: D  836 ASP cc_start: 0.9286 (p0) cc_final: 0.9036 (p0)
  outliers start: 37
  outliers final: 22
  residues processed: 535
  average time/residue: 0.2783
  time to fit residues: 224.4490
Evaluate side-chains
  457 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 434
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  630 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  836 ASP
Chi-restraints excluded: chain B residue  479 ASN
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  549 VAL
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  630 VAL
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  549 VAL
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  779 LEU
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  630 VAL
Chi-restraints excluded: chain D residue  779 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 63 optimal weight:   50.0000
   chunk 169 optimal weight:    4.9990
   chunk 138 optimal weight:   30.0000
   chunk 56 optimal weight:   60.0000
   chunk 203 optimal weight:    5.9990
   chunk 220 optimal weight:   30.0000
   chunk 181 optimal weight:   20.0000
   chunk 202 optimal weight:    7.9990
   chunk 69 optimal weight:    7.9990
   chunk 163 optimal weight:    6.9990
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 592 GLN
C  33 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8236
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  18056  Z= 0.200
  Angle     :  0.684  12.756  24512  Z= 0.335
  Chirality :  0.044   0.165   2792
  Planarity :  0.004   0.038   3080
  Dihedral  :  4.328  20.621   2428
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 16.79 %
    Favored  : 80.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.83 (0.17), residues: 2192
  helix:  0.24 (0.14), residues: 1256
  sheet: -1.39 (0.34), residues: 184
  loop : -1.55 (0.20), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 705 
 HIS   0.005   0.001   HIS D 771 
 PHE   0.025   0.002   PHE A 640 
 TYR   0.015   0.001   TYR D 616 
 ARG   0.006   0.001   ARG D 679 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  514 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 45
    poor density    : 469
  time to evaluate  : 1.991 
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: symmetry clash
   revert: symmetry clash
REVERT: A    4 ARG cc_start: 0.9217 (ttp-170) cc_final: 0.8697 (ttm-80)
REVERT: A  462 MET cc_start: 0.9833 (mmm) cc_final: 0.9626 (mmm)
REVERT: A  466 ASP cc_start: 0.9690 (t0) cc_final: 0.9311 (t0)
REVERT: A  470 ASN cc_start: 0.9311 (m-40) cc_final: 0.8819 (m-40)
REVERT: A  542 TYR cc_start: 0.8861 (m-80) cc_final: 0.8327 (m-80)
REVERT: A  677 MET cc_start: 0.9874 (tpp) cc_final: 0.9515 (tpp)
REVERT: A  681 ARG cc_start: 0.9652 (mtt180) cc_final: 0.9383 (mmm160)
REVERT: A  691 ASN cc_start: 0.9832 (m-40) cc_final: 0.9526 (t0)
REVERT: A  729 CYS cc_start: 0.9117 (m) cc_final: 0.8569 (m)
REVERT: A  748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9605 (ttpp)
REVERT: A  756 MET cc_start: 0.9053 (mmm) cc_final: 0.8650 (mmm)
REVERT: A  857 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8986 (mm-30)
REVERT: B    4 ARG cc_start: 0.9210 (ttp-170) cc_final: 0.8701 (ttm-80)
REVERT: B  542 TYR cc_start: 0.8816 (m-80) cc_final: 0.8371 (m-80)
REVERT: B  677 MET cc_start: 0.9810 (tpp) cc_final: 0.9536 (tpp)
REVERT: B  691 ASN cc_start: 0.9810 (m-40) cc_final: 0.9593 (p0)
REVERT: B  748 LYS cc_start: 0.9876 (mttt) cc_final: 0.9631 (ttpp)
REVERT: B  756 MET cc_start: 0.9016 (mmm) cc_final: 0.8796 (mmm)
REVERT: B  857 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8928 (mm-30)
REVERT: C    4 ARG cc_start: 0.9242 (ttp-170) cc_final: 0.8642 (ttt90)
REVERT: C   31 ILE cc_start: 0.9722 (pt) cc_final: 0.9516 (tp)
REVERT: C   42 ILE cc_start: 0.9831 (pt) cc_final: 0.9585 (mt)
REVERT: C  542 TYR cc_start: 0.8886 (m-80) cc_final: 0.8417 (m-80)
REVERT: C  677 MET cc_start: 0.9713 (tpp) cc_final: 0.9490 (tpp)
REVERT: C  680 VAL cc_start: 0.9937 (t) cc_final: 0.9683 (m)
REVERT: C  681 ARG cc_start: 0.9549 (mtt180) cc_final: 0.9288 (mmm160)
REVERT: C  691 ASN cc_start: 0.9811 (m-40) cc_final: 0.9484 (t0)
REVERT: C  748 LYS cc_start: 0.9858 (mttt) cc_final: 0.9620 (ttpp)
REVERT: C  756 MET cc_start: 0.9042 (mmm) cc_final: 0.8819 (mmm)
REVERT: C  857 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8857 (mm-30)
REVERT: D    4 ARG cc_start: 0.9302 (ttp-170) cc_final: 0.8715 (ttt90)
REVERT: D  542 TYR cc_start: 0.8920 (m-80) cc_final: 0.8445 (m-80)
REVERT: D  677 MET cc_start: 0.9685 (tpp) cc_final: 0.9421 (tpp)
REVERT: D  680 VAL cc_start: 0.9922 (t) cc_final: 0.9680 (m)
REVERT: D  681 ARG cc_start: 0.9543 (mtt180) cc_final: 0.9339 (mmm160)
REVERT: D  691 ASN cc_start: 0.9832 (m-40) cc_final: 0.9530 (t0)
REVERT: D  729 CYS cc_start: 0.9157 (m) cc_final: 0.8672 (m)
REVERT: D  748 LYS cc_start: 0.9864 (mttt) cc_final: 0.9617 (ttpp)
REVERT: D  756 MET cc_start: 0.9085 (mmm) cc_final: 0.8715 (mmm)
  outliers start: 45
  outliers final: 27
  residues processed: 492
  average time/residue: 0.2556
  time to fit residues: 195.2900
Evaluate side-chains
  448 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 421
  time to evaluate  : 1.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  822 VAL
Chi-restraints excluded: chain C residue  549 VAL
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  622 LEU
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  716 VAL
Chi-restraints excluded: chain C residue  779 LEU
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  630 VAL
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  822 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 201 optimal weight:    6.9990
   chunk 153 optimal weight:   10.0000
   chunk 105 optimal weight:   40.0000
   chunk 22 optimal weight:   30.0000
   chunk 97 optimal weight:   40.0000
   chunk 136 optimal weight:   30.0000
   chunk 204 optimal weight:   20.0000
   chunk 216 optimal weight:   30.0000
   chunk 106 optimal weight:   30.0000
   chunk 193 optimal weight:    9.9990
   chunk 58 optimal weight:   50.0000
   overall best weight:   15.3996

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

Flipped N/Q/H residues before XYZ refinement:
A  33 ASN
B  33 ASN
B 470 ASN
C 470 ASN
D  33 ASN
D  61 GLN
D 470 ASN
D 592 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.5851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  18056  Z= 0.326
  Angle     :  0.720  11.397  24512  Z= 0.373
  Chirality :  0.045   0.151   2792
  Planarity :  0.004   0.047   3080
  Dihedral  :  4.580  20.943   2428
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 18.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 17.55 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.17), residues: 2192
  helix:  0.36 (0.14), residues: 1220
  sheet: -1.03 (0.36), residues: 168
  loop : -1.01 (0.21), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 705 
 HIS   0.009   0.002   HIS B 831 
 PHE   0.021   0.002   PHE A 557 
 TYR   0.018   0.002   TYR D 493 
 ARG   0.005   0.001   ARG A 696 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  511 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 79
    poor density    : 432
  time to evaluate  : 2.032 
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    4 ARG cc_start: 0.9223 (ttp-170) cc_final: 0.8638 (ttm-80)
REVERT: A  124 MET cc_start: 0.9820 (mmm) cc_final: 0.9117 (tpp)
REVERT: A  538 LYS cc_start: 0.9671 (mmtt) cc_final: 0.9192 (mppt)
REVERT: A  542 TYR cc_start: 0.9002 (m-80) cc_final: 0.8396 (m-80)
REVERT: A  677 MET cc_start: 0.9852 (tpp) cc_final: 0.9515 (tpp)
REVERT: A  681 ARG cc_start: 0.9669 (mtt180) cc_final: 0.9353 (ttm110)
REVERT: A  695 GLN cc_start: 0.9851 (mt0) cc_final: 0.9604 (tm-30)
REVERT: A  729 CYS cc_start: 0.9213 (m) cc_final: 0.8771 (m)
REVERT: A  748 LYS cc_start: 0.9870 (mttt) cc_final: 0.9635 (ttpp)
REVERT: A  756 MET cc_start: 0.9038 (mmm) cc_final: 0.8640 (mmm)
REVERT: B    4 ARG cc_start: 0.9244 (ttp-170) cc_final: 0.8641 (ttm-80)
REVERT: B  542 TYR cc_start: 0.8958 (m-80) cc_final: 0.8566 (m-80)
REVERT: B  699 GLU cc_start: 0.9741 (pt0) cc_final: 0.9490 (pp20)
REVERT: B  729 CYS cc_start: 0.9218 (m) cc_final: 0.8731 (m)
REVERT: B  748 LYS cc_start: 0.9874 (mttt) cc_final: 0.9651 (ttpp)
REVERT: B  756 MET cc_start: 0.8970 (mmm) cc_final: 0.8573 (mmm)
REVERT: C    4 ARG cc_start: 0.9276 (ttp-170) cc_final: 0.8743 (ttm-80)
REVERT: C   60 MET cc_start: 0.9309 (mmp) cc_final: 0.9091 (mmm)
REVERT: C  124 MET cc_start: 0.9796 (mmm) cc_final: 0.9152 (tpp)
REVERT: C  542 TYR cc_start: 0.9000 (m-80) cc_final: 0.8613 (m-80)
REVERT: C  638 LYS cc_start: 0.9801 (mttt) cc_final: 0.9423 (mttm)
REVERT: C  677 MET cc_start: 0.9754 (tpp) cc_final: 0.9482 (tpp)
REVERT: C  681 ARG cc_start: 0.9601 (mtt180) cc_final: 0.9306 (mmm160)
REVERT: C  691 ASN cc_start: 0.9819 (m-40) cc_final: 0.9518 (t0)
REVERT: C  697 LEU cc_start: 0.9876 (mt) cc_final: 0.9657 (pp)
REVERT: C  748 LYS cc_start: 0.9861 (mttt) cc_final: 0.9636 (ttpp)
REVERT: C  756 MET cc_start: 0.9038 (mmm) cc_final: 0.8820 (mmm)
REVERT: D    4 ARG cc_start: 0.9290 (ttp-170) cc_final: 0.8699 (ttt180)
REVERT: D  410 TRP cc_start: 0.9594 (OUTLIER) cc_final: 0.9307 (t60)
REVERT: D  542 TYR cc_start: 0.8991 (m-80) cc_final: 0.8606 (m-80)
REVERT: D  638 LYS cc_start: 0.9804 (mttt) cc_final: 0.9437 (mttm)
REVERT: D  691 ASN cc_start: 0.9839 (m-40) cc_final: 0.9560 (t0)
REVERT: D  695 GLN cc_start: 0.9845 (mt0) cc_final: 0.9616 (mm-40)
REVERT: D  729 CYS cc_start: 0.9154 (m) cc_final: 0.8615 (m)
REVERT: D  748 LYS cc_start: 0.9865 (mttt) cc_final: 0.9636 (ttpp)
REVERT: D  756 MET cc_start: 0.9013 (mmm) cc_final: 0.8629 (mmm)
  outliers start: 79
  outliers final: 55
  residues processed: 467
  average time/residue: 0.2708
  time to fit residues: 193.6992
Evaluate side-chains
  441 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 56
    poor density    : 385
  time to evaluate  : 2.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  549 VAL
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  758 PHE
Chi-restraints excluded: chain A residue  779 LEU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  500 ILE
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  591 ASP
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  716 VAL
Chi-restraints excluded: chain B residue  758 PHE
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  822 VAL
Chi-restraints excluded: chain B residue  842 LEU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  500 ILE
Chi-restraints excluded: chain C residue  535 VAL
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  591 ASP
Chi-restraints excluded: chain C residue  630 VAL
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  716 VAL
Chi-restraints excluded: chain C residue  758 PHE
Chi-restraints excluded: chain C residue  779 LEU
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain C residue  840 GLU
Chi-restraints excluded: chain D residue  410 TRP
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  500 ILE
Chi-restraints excluded: chain D residue  524 LEU
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain D residue  549 VAL
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  758 PHE
Chi-restraints excluded: chain D residue  779 LEU
Chi-restraints excluded: chain D residue  822 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 180 optimal weight:   40.0000
   chunk 122 optimal weight:   40.0000
   chunk 3 optimal weight:    9.9990
   chunk 161 optimal weight:   40.0000
   chunk 89 optimal weight:    7.9990
   chunk 184 optimal weight:    5.9990
   chunk 149 optimal weight:    1.9990
   chunk 0 optimal weight:   60.0000
   chunk 110 optimal weight:    7.9990
   chunk 194 optimal weight:    8.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  33 ASN
B 470 ASN
B 691 ASN
C 470 ASN
C 592 GLN
D  33 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.6035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  18056  Z= 0.201
  Angle     :  0.706  11.023  24512  Z= 0.347
  Chirality :  0.045   0.297   2792
  Planarity :  0.004   0.051   3080
  Dihedral  :  4.354  20.348   2428
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 14.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 20.63 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.18), residues: 2192
  helix:  0.47 (0.15), residues: 1212
  sheet: -0.75 (0.37), residues: 168
  loop : -0.79 (0.22), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 585 
 HIS   0.005   0.001   HIS B 831 
 PHE   0.030   0.001   PHE C 640 
 TYR   0.015   0.001   TYR D 616 
 ARG   0.006   0.001   ARG D 823 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  485 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 51
    poor density    : 434
  time to evaluate  : 2.129 
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    4 ARG cc_start: 0.9234 (ttp-170) cc_final: 0.8633 (ttm-80)
REVERT: A  124 MET cc_start: 0.9809 (mmm) cc_final: 0.9138 (tpp)
REVERT: A  538 LYS cc_start: 0.9669 (mmtt) cc_final: 0.9207 (mppt)
REVERT: A  542 TYR cc_start: 0.8928 (m-80) cc_final: 0.8414 (m-80)
REVERT: A  574 MET cc_start: 0.7313 (mmt) cc_final: 0.6963 (ppp)
REVERT: A  677 MET cc_start: 0.9840 (tpp) cc_final: 0.9569 (tpp)
REVERT: A  681 ARG cc_start: 0.9652 (mtt180) cc_final: 0.9447 (ttm110)
REVERT: A  729 CYS cc_start: 0.9101 (m) cc_final: 0.8581 (m)
REVERT: A  741 LYS cc_start: 0.9373 (pttp) cc_final: 0.8715 (pttm)
REVERT: A  748 LYS cc_start: 0.9871 (mttt) cc_final: 0.9625 (ttpp)
REVERT: A  756 MET cc_start: 0.8977 (mmm) cc_final: 0.8578 (mmm)
REVERT: B    4 ARG cc_start: 0.9284 (ttp-170) cc_final: 0.8596 (ttm-80)
REVERT: B  410 TRP cc_start: 0.9572 (OUTLIER) cc_final: 0.9324 (t60)
REVERT: B  462 MET cc_start: 0.9726 (mmp) cc_final: 0.9470 (tpt)
REVERT: B  538 LYS cc_start: 0.9662 (mmtt) cc_final: 0.9208 (mppt)
REVERT: B  542 TYR cc_start: 0.8939 (m-80) cc_final: 0.8473 (m-80)
REVERT: B  638 LYS cc_start: 0.9744 (mttt) cc_final: 0.9270 (mmtm)
REVERT: B  677 MET cc_start: 0.9795 (tpp) cc_final: 0.9483 (mmm)
REVERT: B  729 CYS cc_start: 0.9177 (m) cc_final: 0.8670 (m)
REVERT: B  741 LYS cc_start: 0.9369 (pttp) cc_final: 0.8703 (pttm)
REVERT: B  748 LYS cc_start: 0.9877 (mttt) cc_final: 0.9642 (ttpp)
REVERT: B  756 MET cc_start: 0.8972 (mmm) cc_final: 0.8587 (mmm)
REVERT: B  857 GLU cc_start: 0.9093 (mm-30) cc_final: 0.8883 (mp0)
REVERT: C    4 ARG cc_start: 0.9299 (ttp-170) cc_final: 0.8652 (ttm-80)
REVERT: C   60 MET cc_start: 0.9263 (mmp) cc_final: 0.9014 (mmm)
REVERT: C  124 MET cc_start: 0.9803 (mmm) cc_final: 0.9154 (tpp)
REVERT: C  462 MET cc_start: 0.9647 (mmp) cc_final: 0.9416 (tpt)
REVERT: C  542 TYR cc_start: 0.9002 (m-80) cc_final: 0.8615 (m-80)
REVERT: C  574 MET cc_start: 0.7307 (mmt) cc_final: 0.7005 (ppp)
REVERT: C  638 LYS cc_start: 0.9735 (mttt) cc_final: 0.9253 (mmtm)
REVERT: C  677 MET cc_start: 0.9721 (tpp) cc_final: 0.9503 (tpp)
REVERT: C  680 VAL cc_start: 0.9905 (t) cc_final: 0.9527 (t)
REVERT: C  681 ARG cc_start: 0.9580 (mtt180) cc_final: 0.9299 (mmm160)
REVERT: C  691 ASN cc_start: 0.9817 (m-40) cc_final: 0.9506 (t0)
REVERT: C  697 LEU cc_start: 0.9882 (mt) cc_final: 0.9642 (pp)
REVERT: C  741 LYS cc_start: 0.9402 (pttp) cc_final: 0.8753 (pttm)
REVERT: C  748 LYS cc_start: 0.9864 (mttt) cc_final: 0.9632 (ttpp)
REVERT: C  756 MET cc_start: 0.8994 (mmm) cc_final: 0.8776 (mmm)
REVERT: C  857 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8852 (mp0)
REVERT: D    4 ARG cc_start: 0.9294 (ttp-170) cc_final: 0.8701 (ttt180)
REVERT: D  542 TYR cc_start: 0.8968 (m-80) cc_final: 0.8724 (m-80)
REVERT: D  574 MET cc_start: 0.7394 (mmt) cc_final: 0.7063 (ppp)
REVERT: D  638 LYS cc_start: 0.9746 (mttt) cc_final: 0.9278 (mmtm)
REVERT: D  691 ASN cc_start: 0.9844 (m-40) cc_final: 0.9582 (t0)
REVERT: D  729 CYS cc_start: 0.9064 (m) cc_final: 0.8392 (m)
REVERT: D  748 LYS cc_start: 0.9868 (mttt) cc_final: 0.9626 (ttpp)
REVERT: D  756 MET cc_start: 0.8940 (mmm) cc_final: 0.8562 (mmm)
REVERT: D  857 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8927 (mp0)
  outliers start: 51
  outliers final: 36
  residues processed: 464
  average time/residue: 0.2650
  time to fit residues: 188.4275
Evaluate side-chains
  443 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 406
  time to evaluate  : 1.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  691 ASN
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  758 PHE
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain B residue  410 TRP
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  676 GLN
Chi-restraints excluded: chain B residue  758 PHE
Chi-restraints excluded: chain B residue  779 LEU
Chi-restraints excluded: chain B residue  822 VAL
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  500 ILE
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  716 VAL
Chi-restraints excluded: chain C residue  758 PHE
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  500 ILE
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  622 LEU
Chi-restraints excluded: chain D residue  822 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 72 optimal weight:   40.0000
   chunk 194 optimal weight:    5.9990
   chunk 42 optimal weight:   40.0000
   chunk 127 optimal weight:    0.0980
   chunk 53 optimal weight:   20.0000
   chunk 216 optimal weight:   40.0000
   chunk 179 optimal weight:   50.0000
   chunk 100 optimal weight:    7.9990
   chunk 18 optimal weight:   20.0000
   chunk 71 optimal weight:   10.0000
   chunk 113 optimal weight:   30.0000
   overall best weight:    8.8192

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

Flipped N/Q/H residues before XYZ refinement:
B 702 GLN
D 470 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.6293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  18056  Z= 0.231
  Angle     :  0.708  11.428  24512  Z= 0.352
  Chirality :  0.045   0.182   2792
  Planarity :  0.004   0.055   3080
  Dihedral  :  4.325  19.621   2428
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.28 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 21.33 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.18), residues: 2192
  helix:  0.47 (0.15), residues: 1212
  sheet:  0.17 (0.37), residues: 204
  loop : -0.87 (0.22), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 705 
 HIS   0.006   0.001   HIS B 831 
 PHE   0.021   0.002   PHE A 551 
 TYR   0.020   0.001   TYR C 707 
 ARG   0.012   0.001   ARG D 681 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  479 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 57
    poor density    : 422
  time to evaluate  : 1.910 
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: A    4 ARG cc_start: 0.9242 (ttp-170) cc_final: 0.8800 (ptm160)
REVERT: A  462 MET cc_start: 0.9658 (tpp) cc_final: 0.9436 (tpt)
REVERT: A  538 LYS cc_start: 0.9665 (mmtt) cc_final: 0.9204 (mppt)
REVERT: A  542 TYR cc_start: 0.8955 (m-80) cc_final: 0.8460 (m-80)
REVERT: A  574 MET cc_start: 0.7380 (mmt) cc_final: 0.7066 (ppp)
REVERT: A  677 MET cc_start: 0.9838 (tpp) cc_final: 0.9450 (tpp)
REVERT: A  681 ARG cc_start: 0.9652 (mtt180) cc_final: 0.9345 (ttm110)
REVERT: A  729 CYS cc_start: 0.8999 (m) cc_final: 0.8650 (m)
REVERT: A  748 LYS cc_start: 0.9871 (mttt) cc_final: 0.9633 (ttpp)
REVERT: B    4 ARG cc_start: 0.9291 (ttp-170) cc_final: 0.8586 (ttm-80)
REVERT: B  462 MET cc_start: 0.9731 (mmp) cc_final: 0.9515 (tpt)
REVERT: B  538 LYS cc_start: 0.9661 (mmtt) cc_final: 0.9197 (mppt)
REVERT: B  542 TYR cc_start: 0.8968 (m-80) cc_final: 0.8473 (m-80)
REVERT: B  638 LYS cc_start: 0.9748 (mttt) cc_final: 0.9314 (mmtm)
REVERT: B  677 MET cc_start: 0.9803 (tpp) cc_final: 0.9381 (mmm)
REVERT: B  691 ASN cc_start: 0.9756 (p0) cc_final: 0.9530 (t0)
REVERT: B  729 CYS cc_start: 0.9204 (m) cc_final: 0.8715 (m)
REVERT: B  748 LYS cc_start: 0.9874 (mttt) cc_final: 0.9642 (ttpp)
REVERT: B  756 MET cc_start: 0.8973 (mmm) cc_final: 0.8575 (mmm)
REVERT: B  857 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8867 (mm-30)
REVERT: C    4 ARG cc_start: 0.9309 (ttp-170) cc_final: 0.8709 (ttm-80)
REVERT: C   60 MET cc_start: 0.9208 (mmp) cc_final: 0.8958 (mmm)
REVERT: C  538 LYS cc_start: 0.9644 (mmtt) cc_final: 0.9165 (mppt)
REVERT: C  542 TYR cc_start: 0.9075 (m-80) cc_final: 0.8640 (m-80)
REVERT: C  574 MET cc_start: 0.7394 (mmt) cc_final: 0.7142 (ppp)
REVERT: C  677 MET cc_start: 0.9710 (tpp) cc_final: 0.9486 (tpp)
REVERT: C  680 VAL cc_start: 0.9899 (t) cc_final: 0.9566 (t)
REVERT: C  681 ARG cc_start: 0.9585 (mtt180) cc_final: 0.9300 (mmm160)
REVERT: C  691 ASN cc_start: 0.9820 (m-40) cc_final: 0.9509 (t0)
REVERT: C  748 LYS cc_start: 0.9863 (mttt) cc_final: 0.9632 (ttpp)
REVERT: C  756 MET cc_start: 0.9000 (mmm) cc_final: 0.8776 (mmm)
REVERT: C  857 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8919 (mp0)
REVERT: D    4 ARG cc_start: 0.9294 (ttp-170) cc_final: 0.8695 (ttt180)
REVERT: D  538 LYS cc_start: 0.9658 (mmtt) cc_final: 0.9233 (mppt)
REVERT: D  542 TYR cc_start: 0.8996 (m-80) cc_final: 0.8658 (m-80)
REVERT: D  574 MET cc_start: 0.7452 (mmt) cc_final: 0.7152 (ppp)
REVERT: D  638 LYS cc_start: 0.9756 (mttt) cc_final: 0.9321 (mmtm)
REVERT: D  677 MET cc_start: 0.9696 (tpp) cc_final: 0.9381 (tpp)
REVERT: D  680 VAL cc_start: 0.9750 (p) cc_final: 0.9529 (m)
REVERT: D  691 ASN cc_start: 0.9840 (m-40) cc_final: 0.9577 (t0)
REVERT: D  729 CYS cc_start: 0.9075 (m) cc_final: 0.8423 (m)
REVERT: D  748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9629 (ttpp)
REVERT: D  756 MET cc_start: 0.8949 (mmm) cc_final: 0.8567 (mmm)
REVERT: D  857 GLU cc_start: 0.9201 (mm-30) cc_final: 0.8960 (mp0)
  outliers start: 57
  outliers final: 43
  residues processed: 444
  average time/residue: 0.2655
  time to fit residues: 180.7485
Evaluate side-chains
  442 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 43
    poor density    : 399
  time to evaluate  : 2.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  691 ASN
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  758 PHE
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  622 LEU
Chi-restraints excluded: chain B residue  676 GLN
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain B residue  758 PHE
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  500 ILE
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  676 GLN
Chi-restraints excluded: chain C residue  722 GLU
Chi-restraints excluded: chain C residue  758 PHE
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain C residue  827 TYR
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 ILE
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  722 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 208 optimal weight:    0.0670
   chunk 24 optimal weight:   10.0000
   chunk 123 optimal weight:    9.9990
   chunk 158 optimal weight:   50.0000
   chunk 122 optimal weight:   10.0000
   chunk 182 optimal weight:   20.0000
   chunk 121 optimal weight:    9.9990
   chunk 215 optimal weight:   30.0000
   chunk 135 optimal weight:   30.0000
   chunk 131 optimal weight:   30.0000
   chunk 99 optimal weight:    7.9990
   overall best weight:    7.6128

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

Flipped N/Q/H residues before XYZ refinement:
B 592 GLN
D 592 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.6448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18056  Z= 0.217
  Angle     :  0.739  11.620  24512  Z= 0.361
  Chirality :  0.046   0.333   2792
  Planarity :  0.004   0.030   3080
  Dihedral  :  4.287  18.954   2428
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 15.81
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  2.33 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 23.16 %
    Favored  : 74.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.18), residues: 2192
  helix:  0.53 (0.15), residues: 1212
  sheet:  0.17 (0.34), residues: 244
  loop : -0.76 (0.23), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 705 
 HIS   0.005   0.001   HIS B 831 
 PHE   0.018   0.001   PHE D 557 
 TYR   0.019   0.001   TYR C 707 
 ARG   0.008   0.000   ARG B 681 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  468 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 50
    poor density    : 418
  time to evaluate  : 2.001 
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: A    4 ARG cc_start: 0.9233 (ttp-170) cc_final: 0.8438 (ttt180)
REVERT: A  124 MET cc_start: 0.9836 (mmm) cc_final: 0.9159 (tpp)
REVERT: A  462 MET cc_start: 0.9707 (tpp) cc_final: 0.9457 (tpt)
REVERT: A  538 LYS cc_start: 0.9664 (mmtt) cc_final: 0.9204 (mppt)
REVERT: A  541 ARG cc_start: 0.9266 (tpp80) cc_final: 0.8739 (ttp80)
REVERT: A  542 TYR cc_start: 0.9004 (m-80) cc_final: 0.8450 (m-80)
REVERT: A  574 MET cc_start: 0.7369 (mmt) cc_final: 0.7081 (ppp)
REVERT: A  638 LYS cc_start: 0.9773 (mttt) cc_final: 0.9345 (mmtm)
REVERT: A  677 MET cc_start: 0.9838 (tpp) cc_final: 0.9455 (tpp)
REVERT: A  681 ARG cc_start: 0.9648 (mtt180) cc_final: 0.9370 (mmm160)
REVERT: A  729 CYS cc_start: 0.9180 (m) cc_final: 0.8719 (m)
REVERT: A  748 LYS cc_start: 0.9872 (mttt) cc_final: 0.9633 (ttpp)
REVERT: A  756 MET cc_start: 0.9507 (tpp) cc_final: 0.9112 (mmm)
REVERT: A  768 THR cc_start: 0.8706 (p) cc_final: 0.8264 (t)
REVERT: B    4 ARG cc_start: 0.9284 (ttp-170) cc_final: 0.8559 (ttm-80)
REVERT: B  538 LYS cc_start: 0.9656 (mmtt) cc_final: 0.9192 (mppt)
REVERT: B  542 TYR cc_start: 0.8993 (m-80) cc_final: 0.8510 (m-80)
REVERT: B  574 MET cc_start: 0.7334 (mmt) cc_final: 0.7039 (ppp)
REVERT: B  638 LYS cc_start: 0.9747 (mttt) cc_final: 0.9320 (mmtm)
REVERT: B  677 MET cc_start: 0.9731 (tpp) cc_final: 0.9382 (mmm)
REVERT: B  691 ASN cc_start: 0.9743 (p0) cc_final: 0.9539 (t0)
REVERT: B  729 CYS cc_start: 0.9194 (m) cc_final: 0.8695 (m)
REVERT: B  748 LYS cc_start: 0.9874 (mttt) cc_final: 0.9637 (ttpp)
REVERT: B  756 MET cc_start: 0.8959 (mmm) cc_final: 0.8564 (mmm)
REVERT: C    4 ARG cc_start: 0.9297 (ttp-170) cc_final: 0.8688 (ttm-80)
REVERT: C  124 MET cc_start: 0.9834 (mmm) cc_final: 0.9155 (tpp)
REVERT: C  462 MET cc_start: 0.9594 (tpt) cc_final: 0.9377 (tpt)
REVERT: C  538 LYS cc_start: 0.9641 (mmtt) cc_final: 0.9170 (mppt)
REVERT: C  542 TYR cc_start: 0.9067 (m-80) cc_final: 0.8643 (m-80)
REVERT: C  574 MET cc_start: 0.7422 (mmt) cc_final: 0.7185 (ppp)
REVERT: C  638 LYS cc_start: 0.9767 (mttt) cc_final: 0.9356 (mmtm)
REVERT: C  677 MET cc_start: 0.9705 (tpp) cc_final: 0.9500 (tpp)
REVERT: C  680 VAL cc_start: 0.9894 (t) cc_final: 0.9534 (t)
REVERT: C  681 ARG cc_start: 0.9578 (mtt180) cc_final: 0.9292 (mmm160)
REVERT: C  691 ASN cc_start: 0.9816 (m-40) cc_final: 0.9504 (t0)
REVERT: C  748 LYS cc_start: 0.9865 (mttt) cc_final: 0.9638 (ttpp)
REVERT: C  756 MET cc_start: 0.9007 (mmm) cc_final: 0.8788 (mmm)
REVERT: C  857 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8841 (mm-30)
REVERT: D    4 ARG cc_start: 0.9299 (ttp-170) cc_final: 0.8692 (ttt180)
REVERT: D  538 LYS cc_start: 0.9656 (mmtt) cc_final: 0.9231 (mppt)
REVERT: D  542 TYR cc_start: 0.8985 (m-80) cc_final: 0.8648 (m-80)
REVERT: D  574 MET cc_start: 0.7458 (mmt) cc_final: 0.7184 (ppp)
REVERT: D  638 LYS cc_start: 0.9758 (mttt) cc_final: 0.9315 (mmtm)
REVERT: D  680 VAL cc_start: 0.9753 (p) cc_final: 0.9488 (m)
REVERT: D  691 ASN cc_start: 0.9837 (m-40) cc_final: 0.9564 (t0)
REVERT: D  729 CYS cc_start: 0.9053 (m) cc_final: 0.8391 (m)
REVERT: D  748 LYS cc_start: 0.9867 (mttt) cc_final: 0.9626 (ttpp)
REVERT: D  756 MET cc_start: 0.8942 (mmm) cc_final: 0.8557 (mmm)
REVERT: D  857 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8935 (mp0)
  outliers start: 50
  outliers final: 36
  residues processed: 441
  average time/residue: 0.2784
  time to fit residues: 186.8735
Evaluate side-chains
  422 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 36
    poor density    : 386
  time to evaluate  : 1.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  535 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  698 GLU
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  722 GLU
Chi-restraints excluded: chain C residue  758 PHE
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  500 ILE
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  722 GLU
Chi-restraints excluded: chain D residue  758 PHE
Chi-restraints excluded: chain D residue  822 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 133 optimal weight:    9.9990
   chunk 86 optimal weight:    0.5980
   chunk 128 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 42 optimal weight:   30.0000
   chunk 41 optimal weight:    4.9990
   chunk 137 optimal weight:    9.9990
   chunk 147 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   chunk 20 optimal weight:    5.9990
   chunk 169 optimal weight:    8.9990
   overall best weight:    4.9188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.6573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  18056  Z= 0.189
  Angle     :  0.765  10.905  24512  Z= 0.369
  Chirality :  0.047   0.414   2792
  Planarity :  0.004   0.055   3080
  Dihedral  :  4.264  19.869   2428
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 24.46 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.18), residues: 2192
  helix:  0.56 (0.15), residues: 1216
  sheet:  0.29 (0.35), residues: 244
  loop : -0.71 (0.23), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP C 705 
 HIS   0.005   0.001   HIS C 762 
 PHE   0.026   0.001   PHE A 551 
 TYR   0.020   0.001   TYR D 707 
 ARG   0.015   0.001   ARG D 681 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 38
    poor density    : 415
  time to evaluate  : 2.009 
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: A    4 ARG cc_start: 0.9220 (ttp-170) cc_final: 0.8458 (ttm-80)
REVERT: A  124 MET cc_start: 0.9828 (mmm) cc_final: 0.9152 (tpp)
REVERT: A  462 MET cc_start: 0.9719 (tpp) cc_final: 0.9477 (tpt)
REVERT: A  538 LYS cc_start: 0.9662 (mmtt) cc_final: 0.9200 (mppt)
REVERT: A  541 ARG cc_start: 0.9281 (tpp80) cc_final: 0.8744 (ttp80)
REVERT: A  542 TYR cc_start: 0.9021 (m-80) cc_final: 0.8455 (m-80)
REVERT: A  574 MET cc_start: 0.7361 (mmt) cc_final: 0.7100 (ppp)
REVERT: A  638 LYS cc_start: 0.9764 (mttt) cc_final: 0.9380 (mmtm)
REVERT: A  677 MET cc_start: 0.9840 (tpp) cc_final: 0.9448 (tpp)
REVERT: A  681 ARG cc_start: 0.9648 (mtt180) cc_final: 0.9347 (ttm110)
REVERT: A  729 CYS cc_start: 0.9193 (m) cc_final: 0.8751 (m)
REVERT: A  748 LYS cc_start: 0.9869 (mttt) cc_final: 0.9618 (ttpp)
REVERT: A  756 MET cc_start: 0.9528 (tpp) cc_final: 0.9137 (mmm)
REVERT: B    4 ARG cc_start: 0.9295 (ttp-170) cc_final: 0.8660 (ttm-80)
REVERT: B  538 LYS cc_start: 0.9657 (mmtt) cc_final: 0.9203 (mppt)
REVERT: B  541 ARG cc_start: 0.9266 (tpp80) cc_final: 0.8730 (ttp80)
REVERT: B  542 TYR cc_start: 0.8980 (m-80) cc_final: 0.8456 (m-80)
REVERT: B  574 MET cc_start: 0.7316 (mmt) cc_final: 0.7042 (ppp)
REVERT: B  638 LYS cc_start: 0.9740 (mttt) cc_final: 0.9362 (mmtm)
REVERT: B  677 MET cc_start: 0.9748 (tpp) cc_final: 0.9411 (mmm)
REVERT: B  691 ASN cc_start: 0.9732 (p0) cc_final: 0.9527 (t0)
REVERT: B  729 CYS cc_start: 0.9181 (m) cc_final: 0.8676 (m)
REVERT: B  748 LYS cc_start: 0.9875 (mttt) cc_final: 0.9634 (ttpp)
REVERT: B  756 MET cc_start: 0.8950 (mmm) cc_final: 0.8565 (mmm)
REVERT: C    4 ARG cc_start: 0.9281 (ttp-170) cc_final: 0.8532 (ttm-80)
REVERT: C  124 MET cc_start: 0.9831 (mmm) cc_final: 0.9140 (tpp)
REVERT: C  462 MET cc_start: 0.9609 (tpt) cc_final: 0.9368 (tpt)
REVERT: C  538 LYS cc_start: 0.9642 (mmtt) cc_final: 0.9190 (mppt)
REVERT: C  542 TYR cc_start: 0.9056 (m-80) cc_final: 0.8694 (m-80)
REVERT: C  574 MET cc_start: 0.7401 (mmt) cc_final: 0.7198 (ppp)
REVERT: C  638 LYS cc_start: 0.9764 (mttt) cc_final: 0.9380 (mmtm)
REVERT: C  677 MET cc_start: 0.9682 (tpp) cc_final: 0.9446 (tpp)
REVERT: C  680 VAL cc_start: 0.9896 (t) cc_final: 0.9679 (t)
REVERT: C  681 ARG cc_start: 0.9561 (mtt180) cc_final: 0.9255 (mmm160)
REVERT: C  691 ASN cc_start: 0.9816 (m-40) cc_final: 0.9505 (t0)
REVERT: C  748 LYS cc_start: 0.9864 (mttt) cc_final: 0.9630 (ttpp)
REVERT: C  756 MET cc_start: 0.9000 (mmm) cc_final: 0.8787 (mmm)
REVERT: C  768 THR cc_start: 0.8628 (p) cc_final: 0.8412 (p)
REVERT: D    4 ARG cc_start: 0.9293 (ttp-170) cc_final: 0.8688 (ttt180)
REVERT: D  538 LYS cc_start: 0.9651 (mmtt) cc_final: 0.9209 (mppt)
REVERT: D  541 ARG cc_start: 0.9232 (tpp80) cc_final: 0.8655 (ttp80)
REVERT: D  542 TYR cc_start: 0.8971 (m-80) cc_final: 0.8523 (m-80)
REVERT: D  574 MET cc_start: 0.7441 (mmt) cc_final: 0.7211 (ppp)
REVERT: D  638 LYS cc_start: 0.9753 (mttt) cc_final: 0.9378 (mmtm)
REVERT: D  691 ASN cc_start: 0.9834 (m-40) cc_final: 0.9558 (t0)
REVERT: D  729 CYS cc_start: 0.9035 (m) cc_final: 0.8454 (m)
REVERT: D  748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9598 (ttpp)
REVERT: D  756 MET cc_start: 0.8934 (mmm) cc_final: 0.8526 (mmm)
  outliers start: 38
  outliers final: 31
  residues processed: 431
  average time/residue: 0.2794
  time to fit residues: 183.0928
Evaluate side-chains
  420 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 31
    poor density    : 389
  time to evaluate  : 2.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  698 GLU
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain B residue  822 VAL
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  722 GLU
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  550 LEU
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  758 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 196 optimal weight:    0.0030
   chunk 206 optimal weight:   10.0000
   chunk 188 optimal weight:   50.0000
   chunk 201 optimal weight:    8.9990
   chunk 121 optimal weight:   30.0000
   chunk 87 optimal weight:    4.9990
   chunk 157 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 181 optimal weight:    6.9990
   chunk 190 optimal weight:   20.0000
   chunk 200 optimal weight:    0.6980
   overall best weight:    4.3396

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

Flipped N/Q/H residues before XYZ refinement:
A 592 GLN
D 702 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.6707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18056  Z= 0.189
  Angle     :  0.785  12.057  24512  Z= 0.374
  Chirality :  0.047   0.443   2792
  Planarity :  0.004   0.055   3080
  Dihedral  :  4.262  21.303   2428
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 25.16 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.18), residues: 2192
  helix:  0.54 (0.15), residues: 1216
  sheet:  0.06 (0.37), residues: 208
  loop : -0.62 (0.22), residues: 768

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 705 
 HIS   0.004   0.001   HIS B 831 
 PHE   0.020   0.001   PHE B 640 
 TYR   0.017   0.001   TYR D 707 
 ARG   0.013   0.001   ARG D 681 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  451 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 418
  time to evaluate  : 2.087 
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    4 ARG cc_start: 0.9218 (ttp-170) cc_final: 0.8394 (ttt180)
REVERT: A  124 MET cc_start: 0.9824 (mmm) cc_final: 0.9142 (tpp)
REVERT: A  462 MET cc_start: 0.9727 (tpp) cc_final: 0.9496 (tpt)
REVERT: A  541 ARG cc_start: 0.9290 (tpp80) cc_final: 0.8746 (ttp80)
REVERT: A  542 TYR cc_start: 0.9039 (m-80) cc_final: 0.8535 (m-80)
REVERT: A  574 MET cc_start: 0.7353 (mmt) cc_final: 0.7120 (ppp)
REVERT: A  638 LYS cc_start: 0.9750 (mttt) cc_final: 0.9411 (mmtm)
REVERT: A  677 MET cc_start: 0.9840 (tpp) cc_final: 0.9444 (tpp)
REVERT: A  681 ARG cc_start: 0.9652 (mtt180) cc_final: 0.9358 (ttm110)
REVERT: A  729 CYS cc_start: 0.9188 (m) cc_final: 0.8700 (m)
REVERT: A  733 ASN cc_start: 0.9003 (m-40) cc_final: 0.8599 (t0)
REVERT: A  748 LYS cc_start: 0.9872 (mttt) cc_final: 0.9618 (ttpp)
REVERT: A  756 MET cc_start: 0.9571 (tpp) cc_final: 0.9153 (mmm)
REVERT: A  768 THR cc_start: 0.8636 (p) cc_final: 0.8429 (p)
REVERT: A  784 ARG cc_start: 0.9087 (ttp80) cc_final: 0.8875 (tmt-80)
REVERT: B    4 ARG cc_start: 0.9262 (ttp-170) cc_final: 0.8595 (ttm-80)
REVERT: B  538 LYS cc_start: 0.9659 (mmtt) cc_final: 0.9214 (mppt)
REVERT: B  541 ARG cc_start: 0.9285 (tpp80) cc_final: 0.8749 (ttp80)
REVERT: B  542 TYR cc_start: 0.8981 (m-80) cc_final: 0.8440 (m-80)
REVERT: B  574 MET cc_start: 0.7348 (mmt) cc_final: 0.7106 (ppp)
REVERT: B  638 LYS cc_start: 0.9731 (mttt) cc_final: 0.9414 (mmtm)
REVERT: B  677 MET cc_start: 0.9734 (tpp) cc_final: 0.9404 (mmm)
REVERT: B  691 ASN cc_start: 0.9724 (p0) cc_final: 0.9523 (t0)
REVERT: B  729 CYS cc_start: 0.9199 (m) cc_final: 0.8709 (m)
REVERT: B  748 LYS cc_start: 0.9873 (mttt) cc_final: 0.9624 (ttpp)
REVERT: B  756 MET cc_start: 0.8984 (mmm) cc_final: 0.8613 (mmm)
REVERT: B  768 THR cc_start: 0.8631 (p) cc_final: 0.8405 (p)
REVERT: C    4 ARG cc_start: 0.9244 (ttp-170) cc_final: 0.8428 (ttt90)
REVERT: C  124 MET cc_start: 0.9827 (mmm) cc_final: 0.9129 (tpp)
REVERT: C  462 MET cc_start: 0.9615 (tpt) cc_final: 0.9375 (tpt)
REVERT: C  538 LYS cc_start: 0.9642 (mmtt) cc_final: 0.9196 (mppt)
REVERT: C  542 TYR cc_start: 0.9052 (m-80) cc_final: 0.8694 (m-80)
REVERT: C  638 LYS cc_start: 0.9736 (mttt) cc_final: 0.9374 (mmtm)
REVERT: C  677 MET cc_start: 0.9688 (tpp) cc_final: 0.9320 (tpp)
REVERT: C  680 VAL cc_start: 0.9904 (t) cc_final: 0.9648 (m)
REVERT: C  681 ARG cc_start: 0.9564 (mtt180) cc_final: 0.9227 (mmm160)
REVERT: C  691 ASN cc_start: 0.9811 (m-40) cc_final: 0.9497 (t0)
REVERT: C  748 LYS cc_start: 0.9863 (mttt) cc_final: 0.9606 (ttpp)
REVERT: C  756 MET cc_start: 0.8988 (mmm) cc_final: 0.8780 (mmm)
REVERT: C  768 THR cc_start: 0.8580 (p) cc_final: 0.8358 (p)
REVERT: D    4 ARG cc_start: 0.9294 (ttp-170) cc_final: 0.8665 (ttt90)
REVERT: D  538 LYS cc_start: 0.9649 (mmtt) cc_final: 0.9205 (mppt)
REVERT: D  541 ARG cc_start: 0.9240 (tpp80) cc_final: 0.8659 (ttp80)
REVERT: D  542 TYR cc_start: 0.8956 (m-80) cc_final: 0.8507 (m-80)
REVERT: D  574 MET cc_start: 0.7448 (mmt) cc_final: 0.7228 (ppp)
REVERT: D  638 LYS cc_start: 0.9747 (mttt) cc_final: 0.9417 (mmtm)
REVERT: D  691 ASN cc_start: 0.9834 (m-40) cc_final: 0.9539 (t0)
REVERT: D  695 GLN cc_start: 0.9846 (mt0) cc_final: 0.9563 (mm-40)
REVERT: D  729 CYS cc_start: 0.9083 (m) cc_final: 0.8460 (m)
REVERT: D  733 ASN cc_start: 0.9013 (m-40) cc_final: 0.8618 (t0)
REVERT: D  748 LYS cc_start: 0.9864 (mttt) cc_final: 0.9584 (ttpp)
REVERT: D  756 MET cc_start: 0.8924 (mmm) cc_final: 0.8542 (mmm)
  outliers start: 33
  outliers final: 28
  residues processed: 432
  average time/residue: 0.2692
  time to fit residues: 176.9026
Evaluate side-chains
  431 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 403
  time to evaluate  : 2.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  500 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  698 GLU
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  722 GLU
Chi-restraints excluded: chain D residue  758 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 132 optimal weight:   50.0000
   chunk 212 optimal weight:   20.0000
   chunk 129 optimal weight:    9.9990
   chunk 100 optimal weight:    7.9990
   chunk 147 optimal weight:    5.9990
   chunk 223 optimal weight:   40.0000
   chunk 205 optimal weight:    8.9990
   chunk 177 optimal weight:    9.9990
   chunk 18 optimal weight:    5.9990
   chunk 137 optimal weight:   10.0000
   chunk 108 optimal weight:   50.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 592 GLN
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 573 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.6833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  18056  Z= 0.228
  Angle     :  0.815  12.739  24512  Z= 0.396
  Chirality :  0.048   0.402   2792
  Planarity :  0.004   0.049   3080
  Dihedral  :  4.406  21.780   2428
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.28 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 25.38 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.18), residues: 2192
  helix:  0.49 (0.15), residues: 1220
  sheet:  0.46 (0.35), residues: 244
  loop : -0.56 (0.23), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 705 
 HIS   0.005   0.001   HIS B 831 
 PHE   0.021   0.001   PHE C 551 
 TYR   0.017   0.001   TYR D 707 
 ARG   0.005   0.000   ARG B 679 

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

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

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4384 Ramachandran restraints generated.
    2192 Oldfield, 0 Emsley, 2192 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  440 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 401
  time to evaluate  : 1.944 
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: A    4 ARG cc_start: 0.9227 (ttp-170) cc_final: 0.8480 (ttm-80)
REVERT: A  124 MET cc_start: 0.9828 (mmm) cc_final: 0.9146 (tpp)
REVERT: A  462 MET cc_start: 0.9732 (tpp) cc_final: 0.9500 (tpt)
REVERT: A  541 ARG cc_start: 0.9298 (tpp80) cc_final: 0.8769 (ttp80)
REVERT: A  542 TYR cc_start: 0.9057 (m-80) cc_final: 0.8555 (m-80)
REVERT: A  574 MET cc_start: 0.7384 (mmt) cc_final: 0.7148 (ppp)
REVERT: A  638 LYS cc_start: 0.9753 (mttt) cc_final: 0.9418 (mmtm)
REVERT: A  677 MET cc_start: 0.9840 (tpp) cc_final: 0.9457 (tpp)
REVERT: A  681 ARG cc_start: 0.9656 (mtt180) cc_final: 0.9383 (mmm160)
REVERT: A  729 CYS cc_start: 0.9213 (m) cc_final: 0.8728 (m)
REVERT: A  733 ASN cc_start: 0.9026 (m-40) cc_final: 0.8606 (t0)
REVERT: A  748 LYS cc_start: 0.9873 (mttt) cc_final: 0.9611 (ttpp)
REVERT: A  756 MET cc_start: 0.9577 (tpp) cc_final: 0.9158 (mmm)
REVERT: A  784 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8851 (tmt-80)
REVERT: B    4 ARG cc_start: 0.9251 (ttp-170) cc_final: 0.8726 (ptm160)
REVERT: B  538 LYS cc_start: 0.9652 (mmtt) cc_final: 0.9200 (mppt)
REVERT: B  541 ARG cc_start: 0.9283 (tpp80) cc_final: 0.8754 (ttp80)
REVERT: B  542 TYR cc_start: 0.9003 (m-80) cc_final: 0.8471 (m-80)
REVERT: B  574 MET cc_start: 0.7362 (mmt) cc_final: 0.7121 (ppp)
REVERT: B  638 LYS cc_start: 0.9746 (mttt) cc_final: 0.9411 (mmtm)
REVERT: B  677 MET cc_start: 0.9797 (tpp) cc_final: 0.9356 (mmm)
REVERT: B  691 ASN cc_start: 0.9726 (p0) cc_final: 0.9525 (t0)
REVERT: B  729 CYS cc_start: 0.9213 (m) cc_final: 0.8734 (m)
REVERT: B  748 LYS cc_start: 0.9874 (mttt) cc_final: 0.9634 (ttpp)
REVERT: B  756 MET cc_start: 0.9034 (mmm) cc_final: 0.8674 (mmm)
REVERT: B  768 THR cc_start: 0.8711 (p) cc_final: 0.8496 (p)
REVERT: C    4 ARG cc_start: 0.9238 (ttp-170) cc_final: 0.8739 (ptm160)
REVERT: C  124 MET cc_start: 0.9827 (mmm) cc_final: 0.9127 (tpp)
REVERT: C  462 MET cc_start: 0.9624 (tpt) cc_final: 0.9379 (tpt)
REVERT: C  538 LYS cc_start: 0.9637 (mmtt) cc_final: 0.9168 (mppt)
REVERT: C  542 TYR cc_start: 0.9075 (m-80) cc_final: 0.8662 (m-80)
REVERT: C  574 MET cc_start: 0.8990 (ppp) cc_final: 0.8723 (mmt)
REVERT: C  638 LYS cc_start: 0.9742 (mttt) cc_final: 0.9401 (mmtm)
REVERT: C  677 MET cc_start: 0.9690 (tpp) cc_final: 0.9406 (tpp)
REVERT: C  680 VAL cc_start: 0.9903 (t) cc_final: 0.9674 (t)
REVERT: C  681 ARG cc_start: 0.9571 (mtt180) cc_final: 0.9259 (mmm160)
REVERT: C  691 ASN cc_start: 0.9811 (m-40) cc_final: 0.9496 (t0)
REVERT: C  748 LYS cc_start: 0.9854 (mttt) cc_final: 0.9598 (ttpp)
REVERT: C  756 MET cc_start: 0.9011 (mmm) cc_final: 0.8792 (mmm)
REVERT: C  768 THR cc_start: 0.8629 (p) cc_final: 0.8417 (p)
REVERT: D    4 ARG cc_start: 0.9289 (ttp-170) cc_final: 0.8685 (ttt180)
REVERT: D  538 LYS cc_start: 0.9643 (mmtt) cc_final: 0.9174 (mppt)
REVERT: D  541 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8979 (tpp80)
REVERT: D  542 TYR cc_start: 0.8960 (m-80) cc_final: 0.8494 (m-80)
REVERT: D  574 MET cc_start: 0.7464 (mmt) cc_final: 0.7237 (ppp)
REVERT: D  638 LYS cc_start: 0.9759 (mttt) cc_final: 0.9412 (mmtm)
REVERT: D  677 MET cc_start: 0.9797 (tpp) cc_final: 0.9424 (mmm)
REVERT: D  691 ASN cc_start: 0.9834 (m-40) cc_final: 0.9543 (t0)
REVERT: D  695 GLN cc_start: 0.9851 (mt0) cc_final: 0.9573 (mm-40)
REVERT: D  729 CYS cc_start: 0.9139 (m) cc_final: 0.8542 (m)
REVERT: D  733 ASN cc_start: 0.9024 (m-40) cc_final: 0.8631 (t0)
REVERT: D  748 LYS cc_start: 0.9866 (mttt) cc_final: 0.9603 (ttpp)
REVERT: D  756 MET cc_start: 0.8975 (mmm) cc_final: 0.8591 (mmm)
  outliers start: 39
  outliers final: 33
  residues processed: 415
  average time/residue: 0.2759
  time to fit residues: 174.2657
Evaluate side-chains
  426 residues out of total 1916 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 393
  time to evaluate  : 2.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  559 LEU
Chi-restraints excluded: chain A residue  676 GLN
Chi-restraints excluded: chain A residue  693 LEU
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  716 VAL
Chi-restraints excluded: chain A residue  722 GLU
Chi-restraints excluded: chain A residue  822 VAL
Chi-restraints excluded: chain B residue  483 VAL
Chi-restraints excluded: chain B residue  491 VAL
Chi-restraints excluded: chain B residue  539 LEU
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  559 LEU
Chi-restraints excluded: chain B residue  693 LEU
Chi-restraints excluded: chain B residue  698 GLU
Chi-restraints excluded: chain B residue  722 GLU
Chi-restraints excluded: chain C residue  483 VAL
Chi-restraints excluded: chain C residue  539 LEU
Chi-restraints excluded: chain C residue  550 LEU
Chi-restraints excluded: chain C residue  559 LEU
Chi-restraints excluded: chain C residue  722 GLU
Chi-restraints excluded: chain C residue  822 VAL
Chi-restraints excluded: chain D residue  483 VAL
Chi-restraints excluded: chain D residue  491 VAL
Chi-restraints excluded: chain D residue  535 VAL
Chi-restraints excluded: chain D residue  539 LEU
Chi-restraints excluded: chain D residue  559 LEU
Chi-restraints excluded: chain D residue  722 GLU
Chi-restraints excluded: chain D residue  758 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 224
   random chunks:
   chunk 141 optimal weight:    3.9990
   chunk 189 optimal weight:    2.9990
   chunk 54 optimal weight:    5.9990
   chunk 163 optimal weight:   50.0000
   chunk 26 optimal weight:    8.9990
   chunk 49 optimal weight:    8.9990
   chunk 177 optimal weight:    9.9990
   chunk 74 optimal weight:    8.9990
   chunk 182 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 32 optimal weight:   30.0000
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 573 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.059007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.043950 restraints weight = 87403.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.045732 restraints weight = 46556.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.046983 restraints weight = 30427.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.6914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18056  Z= 0.204
  Angle     :  0.814  13.407  24512  Z= 0.389
  Chirality :  0.048   0.408   2792
  Planarity :  0.004   0.078   3080
  Dihedral  :  4.381  22.640   2428
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 16.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 25.38 %
    Favored  : 72.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.18), residues: 2192
  helix:  0.45 (0.15), residues: 1224
  sheet:  0.48 (0.35), residues: 244
  loop : -0.75 (0.23), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D 585 
 HIS   0.005   0.001   HIS B 831 
 PHE   0.038   0.002   PHE A 781 
 TYR   0.016   0.001   TYR D 616 
 ARG   0.020   0.000   ARG B 681 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6570.81 seconds
wall clock time: 116 minutes 6.04 seconds (6966.04 seconds total)