Starting phenix.real_space_refine
on Thu Jun 19 19:08:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8pba_17582/06_2025/8pba_17582.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8pba_17582/06_2025/8pba_17582.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8pba_17582/06_2025/8pba_17582.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8pba_17582/06_2025/8pba_17582.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8pba_17582/06_2025/8pba_17582.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8pba_17582/06_2025/8pba_17582.cif"
  }
  resolution = 2.64
  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=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      72      5.16       5
     C    7410      2.51       5
     N    2004      2.21       5
     O    2146      1.98       5
     H   11332      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 118 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 22964
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 11482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 722, 11482
          Classifications: {'peptide': 722}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 688}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 11482
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 722, 11482
          Classifications: {'peptide': 722}
          Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 688}
          Chain breaks: 2
  Time building chain proxies: 11.28, per 1000 atoms: 0.49
  Number of scatterers: 22964
  At special positions: 0
  Unit cell: (97.175, 149.565, 104.78, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      72     16.00
     O    2146      8.00
     N    2004      7.00
     C    7410      6.00
     H   11332      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.20
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2692

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 24 sheets defined
      23.1% alpha, 42.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 2.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 60
      removed outlier: 3.547A  pdb=" N   THR A  57 " --> pdb=" O   ARG A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 63
      No H-bonds generated for 'chain 'A' and resid 61 through 63'
    Processing helix  chain 'A' and resid 102 through 108
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 380 through 385
      removed outlier: 4.630A  pdb=" N   TYR A 384 " --> pdb=" O   ASP A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 400 through 402
      No H-bonds generated for 'chain 'A' and resid 400 through 402'
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 712 through 716
      removed outlier: 3.897A  pdb=" N   GLN A 716 " --> pdb=" O   SER A 713 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 722
    Processing helix  chain 'A' and resid 739 through 744
    Processing helix  chain 'A' and resid 745 through 747
      No H-bonds generated for 'chain 'A' and resid 745 through 747'
    Processing helix  chain 'A' and resid 753 through 769
    Processing helix  chain 'A' and resid 784 through 797
    Processing helix  chain 'A' and resid 812 through 816
    Processing helix  chain 'A' and resid 817 through 826
      removed outlier: 3.800A  pdb=" N   ARG A 823 " --> pdb=" O   ALA A 819 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR A 824 " --> pdb=" O   TYR A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 837
    Processing helix  chain 'A' and resid 839 through 846
      removed outlier: 4.668A  pdb=" N   GLU A 844 " --> pdb=" O   GLY A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 880
      removed outlier: 3.978A  pdb=" N   LEU A 869 " --> pdb=" O   HIS A 865 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 897 through 917
    Processing helix  chain 'B' and resid 44 through 60
      removed outlier: 3.537A  pdb=" N   THR B  57 " --> pdb=" O   ARG B  53 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 63
      No H-bonds generated for 'chain 'B' and resid 61 through 63'
    Processing helix  chain 'B' and resid 102 through 107
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 380 through 385
      removed outlier: 4.579A  pdb=" N   TYR B 384 " --> pdb=" O   ASP B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 402
      No H-bonds generated for 'chain 'B' and resid 400 through 402'
    Processing helix  chain 'B' and resid 425 through 427
      No H-bonds generated for 'chain 'B' and resid 425 through 427'
    Processing helix  chain 'B' and resid 430 through 434
    Processing helix  chain 'B' and resid 712 through 716
      removed outlier: 3.894A  pdb=" N   GLN B 716 " --> pdb=" O   SER B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 722
    Processing helix  chain 'B' and resid 739 through 744
    Processing helix  chain 'B' and resid 745 through 747
      No H-bonds generated for 'chain 'B' and resid 745 through 747'
    Processing helix  chain 'B' and resid 753 through 769
    Processing helix  chain 'B' and resid 784 through 797
    Processing helix  chain 'B' and resid 812 through 816
    Processing helix  chain 'B' and resid 817 through 826
      removed outlier: 3.804A  pdb=" N   ARG B 823 " --> pdb=" O   ALA B 819 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   TYR B 824 " --> pdb=" O   TYR B 820 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 837
    Processing helix  chain 'B' and resid 839 through 846
      removed outlier: 4.668A  pdb=" N   GLU B 844 " --> pdb=" O   GLY B 841 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 865 through 880
      removed outlier: 3.978A  pdb=" N   LEU B 869 " --> pdb=" O   HIS B 865 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 897 through 917
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37
      removed outlier: 6.764A  pdb=" N   GLU A  36 " --> pdb=" O   LYS A 692 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   ILE A 730 " --> pdb=" O   TYR A 698 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37
      removed outlier: 6.764A  pdb=" N   GLU A  36 " --> pdb=" O   LYS A 692 " (cutoff:3.500A)
      removed outlier: 9.505A  pdb=" N   LYS A 691 " --> pdb=" O   MET A 773 " (cutoff:3.500A)
      removed outlier: 10.018A  pdb=" N   MET A 775 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 10.491A  pdb=" N   TYR A 693 " --> pdb=" O   MET A 775 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   ARG A 777 " --> pdb=" O   TYR A 693 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   TRP A 783 " --> pdb=" O   VAL A 699 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ALA A 803 " --> pdb=" O   SER A 776 " (cutoff:3.500A)
      removed outlier: 6.816A  pdb=" N   VAL A 778 " --> pdb=" O   ALA A 803 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   ILE A 805 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL A 780 " --> pdb=" O   ILE A 805 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   GLY A 807 " --> pdb=" O   VAL A 780 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   GLY A 782 " --> pdb=" O   GLY A 807 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 76
      removed outlier: 3.543A  pdb=" N   ALA A  75 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ARG A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   LEU A  80 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   THR A 100 " --> pdb=" O   LYS A 119 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   LYS A 119 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   PHE A 116 " --> pdb=" O   ASN A 646 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   THR A 648 " --> pdb=" O   PHE A 116 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   LEU A 118 " --> pdb=" O   THR A 648 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   THR A 641 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ARG A 631 " --> pdb=" O   THR A 641 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   TYR A 643 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   SER A 629 " --> pdb=" O   TYR A 643 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   CYS A 625 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 10.339A  pdb=" N   VAL A 649 " --> pdb=" O   ALA A 623 " (cutoff:3.500A)
      removed outlier: 14.695A  pdb=" N   ALA A 623 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   SER A 618 " --> pdb=" O   PRO A 622 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   TYR A 615 " --> pdb=" O   LYS A 596 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 76
      removed outlier: 3.543A  pdb=" N   ALA A  75 " --> pdb=" O   ARG A  79 " (cutoff:3.500A)
      removed outlier: 6.875A  pdb=" N   ARG A  79 " --> pdb=" O   ALA A  75 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   LEU A  80 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.042A  pdb=" N   THR A 100 " --> pdb=" O   LYS A 119 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   LYS A 119 " --> pdb=" O   THR A 100 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   PHE A 116 " --> pdb=" O   ASN A 646 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   THR A 648 " --> pdb=" O   PHE A 116 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   LEU A 118 " --> pdb=" O   THR A 648 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   THR A 641 " --> pdb=" O   ARG A 631 " (cutoff:3.500A)
      removed outlier: 6.535A  pdb=" N   ARG A 631 " --> pdb=" O   THR A 641 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   TYR A 643 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   SER A 629 " --> pdb=" O   TYR A 643 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   CYS A 625 " --> pdb=" O   ILE A 647 " (cutoff:3.500A)
      removed outlier: 10.339A  pdb=" N   VAL A 649 " --> pdb=" O   ALA A 623 " (cutoff:3.500A)
      removed outlier: 14.695A  pdb=" N   ALA A 623 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   SER A 618 " --> pdb=" O   PRO A 622 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ALA A 605 " --> pdb=" O   ALA A 613 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 258 through 260
      removed outlier: 6.746A  pdb=" N   VAL A 276 " --> pdb=" O   ARG A 287 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   ARG A 287 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   ILE A 278 " --> pdb=" O   ILE A 285 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 295 through 297
    Processing sheet with id=AA7, first strand: chain 'A' and resid 295 through 297
    Processing sheet with id=AA8, first strand: chain 'A' and resid 335 through 336
    Processing sheet with id=AA9, first strand: chain 'A' and resid 390 through 398
      removed outlier: 6.558A  pdb=" N   GLN A 408 " --> pdb=" O   THR A 394 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ALA A 396 " --> pdb=" O   TRP A 406 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   TRP A 406 " --> pdb=" O   ALA A 396 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   PHE A 398 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   THR A 404 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 5.647A  pdb=" N   GLN A 416 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 6.214A  pdb=" N   LEU A 421 " --> pdb=" O   GLN A 475 " (cutoff:3.500A)
      removed outlier: 5.739A  pdb=" N   GLN A 475 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 492 through 493
      removed outlier: 6.716A  pdb=" N   SER A 522 " --> pdb=" O   THR A 534 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   THR A 534 " --> pdb=" O   SER A 522 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLU A 524 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 492 through 493
    Processing sheet with id=AB3, first strand: chain 'A' and resid 553 through 554
      removed outlier: 4.626A  pdb=" N   GLU A 567 " --> pdb=" O   GLU A 572 " (cutoff:3.500A)
      removed outlier: 8.596A  pdb=" N   GLU A 572 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 36 through 37
      removed outlier: 6.761A  pdb=" N   GLU B  36 " --> pdb=" O   LYS B 692 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ILE B 730 " --> pdb=" O   TYR B 698 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 36 through 37
      removed outlier: 6.761A  pdb=" N   GLU B  36 " --> pdb=" O   LYS B 692 " (cutoff:3.500A)
      removed outlier: 9.508A  pdb=" N   LYS B 691 " --> pdb=" O   MET B 773 " (cutoff:3.500A)
      removed outlier: 10.021A  pdb=" N   MET B 775 " --> pdb=" O   LYS B 691 " (cutoff:3.500A)
      removed outlier: 10.494A  pdb=" N   TYR B 693 " --> pdb=" O   MET B 775 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ARG B 777 " --> pdb=" O   TYR B 693 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   TRP B 783 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   ALA B 803 " --> pdb=" O   SER B 776 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL B 778 " --> pdb=" O   ALA B 803 " (cutoff:3.500A)
      removed outlier: 8.293A  pdb=" N   ILE B 805 " --> pdb=" O   VAL B 778 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL B 780 " --> pdb=" O   ILE B 805 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLY B 807 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   GLY B 782 " --> pdb=" O   GLY B 807 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 70 through 76
      removed outlier: 3.549A  pdb=" N   ALA B  75 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ARG B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   LEU B  80 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   THR B 100 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS B 119 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   THR B 641 " --> pdb=" O   ARG B 631 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG B 631 " --> pdb=" O   THR B 641 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   TYR B 643 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   SER B 629 " --> pdb=" O   TYR B 643 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   CYS B 625 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 10.357A  pdb=" N   VAL B 649 " --> pdb=" O   ALA B 623 " (cutoff:3.500A)
      removed outlier: 14.715A  pdb=" N   ALA B 623 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   SER B 618 " --> pdb=" O   PRO B 622 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   TYR B 615 " --> pdb=" O   LYS B 596 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 70 through 76
      removed outlier: 3.549A  pdb=" N   ALA B  75 " --> pdb=" O   ARG B  79 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ARG B  79 " --> pdb=" O   ALA B  75 " (cutoff:3.500A)
      removed outlier: 4.492A  pdb=" N   LEU B  80 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 5.950A  pdb=" N   THR B 100 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS B 119 " --> pdb=" O   THR B 100 " (cutoff:3.500A)
      removed outlier: 5.559A  pdb=" N   THR B 641 " --> pdb=" O   ARG B 631 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   ARG B 631 " --> pdb=" O   THR B 641 " (cutoff:3.500A)
      removed outlier: 5.691A  pdb=" N   TYR B 643 " --> pdb=" O   SER B 629 " (cutoff:3.500A)
      removed outlier: 6.623A  pdb=" N   SER B 629 " --> pdb=" O   TYR B 643 " (cutoff:3.500A)
      removed outlier: 4.531A  pdb=" N   CYS B 625 " --> pdb=" O   ILE B 647 " (cutoff:3.500A)
      removed outlier: 10.357A  pdb=" N   VAL B 649 " --> pdb=" O   ALA B 623 " (cutoff:3.500A)
      removed outlier: 14.715A  pdb=" N   ALA B 623 " --> pdb=" O   VAL B 649 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   SER B 618 " --> pdb=" O   PRO B 622 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ALA B 605 " --> pdb=" O   ALA B 613 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 258 through 260
      removed outlier: 6.744A  pdb=" N   VAL B 276 " --> pdb=" O   ARG B 287 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ARG B 287 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE B 278 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 295 through 297
    Processing sheet with id=AC1, first strand: chain 'B' and resid 295 through 297
    Processing sheet with id=AC2, first strand: chain 'B' and resid 335 through 336
    Processing sheet with id=AC3, first strand: chain 'B' and resid 390 through 398
      removed outlier: 6.558A  pdb=" N   GLN B 408 " --> pdb=" O   THR B 394 " (cutoff:3.500A)
      removed outlier: 4.596A  pdb=" N   ALA B 396 " --> pdb=" O   TRP B 406 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   TRP B 406 " --> pdb=" O   ALA B 396 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   PHE B 398 " --> pdb=" O   THR B 404 " (cutoff:3.500A)
      removed outlier: 7.020A  pdb=" N   THR B 404 " --> pdb=" O   PHE B 398 " (cutoff:3.500A)
      removed outlier: 5.645A  pdb=" N   GLN B 416 " --> pdb=" O   SER B 411 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   LEU B 421 " --> pdb=" O   GLN B 475 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   GLN B 475 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 492 through 493
      removed outlier: 6.716A  pdb=" N   SER B 522 " --> pdb=" O   THR B 534 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   THR B 534 " --> pdb=" O   SER B 522 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   GLU B 524 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 492 through 493
    Processing sheet with id=AC6, first strand: chain 'B' and resid 553 through 554
      removed outlier: 4.626A  pdb=" N   GLU B 567 " --> pdb=" O   GLU B 572 " (cutoff:3.500A)
      removed outlier: 8.595A  pdb=" N   GLU B 572 " --> pdb=" O   GLU B 567 " (cutoff:3.500A)

    503 hydrogen bonds defined for protein.
    1359 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: 10.79

  Time building geometry restraints manager: 7.65 seconds

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

  Histogram of bond lengths:
        0.95 -     1.12: 11308
        1.12 -     1.29: 1914
        1.29 -     1.46: 5045
        1.46 -     1.64: 4879
        1.64 -     1.81: 120
  Bond restraints: 23266
  Sorted by residual:
  bond pdb=" CD2 PHE B 399 "
       pdb=" HD2 PHE B 399 "
    ideal  model  delta    sigma   weight residual
    0.930  1.096 -0.166 2.00e-02 2.50e+03 6.88e+01
  bond pdb=" CD2 PHE A 399 "
       pdb=" HD2 PHE A 399 "
    ideal  model  delta    sigma   weight residual
    0.930  1.095 -0.165 2.00e-02 2.50e+03 6.83e+01
  bond pdb=" NE2 HIS B 286 "
       pdb=" HE2 HIS B 286 "
    ideal  model  delta    sigma   weight residual
    0.860  1.025 -0.165 2.00e-02 2.50e+03 6.79e+01
  bond pdb=" CD1 PHE A 712 "
       pdb=" HD1 PHE A 712 "
    ideal  model  delta    sigma   weight residual
    0.930  1.095 -0.165 2.00e-02 2.50e+03 6.78e+01
  bond pdb=" CD2 PHE B 742 "
       pdb=" HD2 PHE B 742 "
    ideal  model  delta    sigma   weight residual
    0.930  1.094 -0.164 2.00e-02 2.50e+03 6.76e+01
  ... (remaining 23261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.73: 37743
        2.73 -     5.46: 2971
        5.46 -     8.19: 1168
        8.19 -    10.93: 0
       10.93 -    13.66: 24
  Bond angle restraints: 41906
  Sorted by residual:
  angle pdb=" C   ASP A 343 "
        pdb=" N   PRO A 344 "
        pdb=" CA  PRO A 344 "
      ideal   model   delta    sigma   weight residual
     119.66  125.32   -5.66 7.30e-01 1.88e+00 6.00e+01
  angle pdb=" C   CYS A 387 "
        pdb=" N   PRO A 388 "
        pdb=" CA  PRO A 388 "
      ideal   model   delta    sigma   weight residual
     119.56  127.39   -7.83 1.02e+00 9.61e-01 5.89e+01
  angle pdb=" C   CYS B 387 "
        pdb=" N   PRO B 388 "
        pdb=" CA  PRO B 388 "
      ideal   model   delta    sigma   weight residual
     119.56  127.36   -7.80 1.02e+00 9.61e-01 5.86e+01
  angle pdb=" C   HIS A 797 "
        pdb=" N   PRO A 798 "
        pdb=" CA  PRO A 798 "
      ideal   model   delta    sigma   weight residual
     119.56  126.76   -7.20 1.01e+00 9.80e-01 5.08e+01
  angle pdb=" C   HIS B 797 "
        pdb=" N   PRO B 798 "
        pdb=" CA  PRO B 798 "
      ideal   model   delta    sigma   weight residual
     119.56  126.72   -7.16 1.01e+00 9.80e-01 5.03e+01
  ... (remaining 41901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 10336
       17.10 -    34.20: 494
       34.20 -    51.29: 119
       51.29 -    68.39: 59
       68.39 -    85.49: 12
  Dihedral angle restraints: 11020
    sinusoidal: 5888
      harmonic: 5132
  Sorted by residual:
  dihedral pdb=" CA  TYR A 392 "
           pdb=" C   TYR A 392 "
           pdb=" N   ILE A 393 "
           pdb=" CA  ILE A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.69   20.31     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  TYR B 392 "
           pdb=" C   TYR B 392 "
           pdb=" N   ILE B 393 "
           pdb=" CA  ILE B 393 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.73   20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  LEU A 429 "
           pdb=" C   LEU A 429 "
           pdb=" N   PRO A 430 "
           pdb=" CA  PRO A 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.35   19.65     0      5.00e+00 4.00e-02 1.54e+01
  ... (remaining 11017 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1092
       0.062 -    0.124: 483
       0.124 -    0.186: 111
       0.186 -    0.248: 18
       0.248 -    0.310: 6
  Chirality restraints: 1710
  Sorted by residual:
  chirality pdb=" CA  TYR A 580 "
            pdb=" N   TYR A 580 "
            pdb=" C   TYR A 580 "
            pdb=" CB  TYR A 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.41e+00
  chirality pdb=" CA  PHE B  67 "
            pdb=" N   PHE B  67 "
            pdb=" C   PHE B  67 "
            pdb=" CB  PHE B  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.31e+00
  chirality pdb=" CA  TYR B 580 "
            pdb=" N   TYR B 580 "
            pdb=" C   TYR B 580 "
            pdb=" CB  TYR B 580 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.30e+00
  ... (remaining 1707 not shown)

  Planarity restraints: 3458
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 910 "    0.107 2.00e-02 2.50e+03   4.27e-02 5.48e+01
        pdb=" CG  TYR B 910 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 910 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 910 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 910 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 910 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 910 "    0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR B 910 "    0.072 2.00e-02 2.50e+03
        pdb=" HD1 TYR B 910 "   -0.013 2.00e-02 2.50e+03
        pdb=" HD2 TYR B 910 "   -0.021 2.00e-02 2.50e+03
        pdb=" HE1 TYR B 910 "   -0.004 2.00e-02 2.50e+03
        pdb=" HE2 TYR B 910 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 910 "   -0.106 2.00e-02 2.50e+03   4.26e-02 5.46e+01
        pdb=" CG  TYR A 910 "    0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 910 "    0.035 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 910 "    0.036 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 910 "    0.028 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 910 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 910 "   -0.005 2.00e-02 2.50e+03
        pdb=" OH  TYR A 910 "   -0.073 2.00e-02 2.50e+03
        pdb=" HD1 TYR A 910 "    0.012 2.00e-02 2.50e+03
        pdb=" HD2 TYR A 910 "    0.021 2.00e-02 2.50e+03
        pdb=" HE1 TYR A 910 "    0.004 2.00e-02 2.50e+03
        pdb=" HE2 TYR A 910 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 316 "    0.112 2.00e-02 2.50e+03   3.57e-02 5.10e+01
        pdb=" CG  TRP A 316 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 316 "   -0.034 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 316 "   -0.025 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 316 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 316 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 316 "   -0.024 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 316 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 316 "   -0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 316 "    0.012 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 316 "   -0.016 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 316 "   -0.014 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 316 "   -0.030 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 316 "    0.044 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 316 "   -0.018 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 316 "    0.024 2.00e-02 2.50e+03
  ... (remaining 3455 not shown)

  Histogram of nonbonded interaction distances:
        1.28 -     1.94: 403
        1.94 -     2.61: 26083
        2.61 -     3.27: 70176
        3.27 -     3.94: 94733
        3.94 -     4.60: 144903
  Nonbonded interactions: 336298
  Sorted by model distance:
  nonbonded pdb=" HG1 THR B  91 "
            pdb=" H   ASN B  92 "
     model   vdw
     1.281 2.100
  nonbonded pdb=" HG1 THR A  91 "
            pdb=" H   ASN A  92 "
     model   vdw
     1.283 2.100
  nonbonded pdb=" HG1 THR A 673 "
            pdb=" H   LEU A 675 "
     model   vdw
     1.293 2.100
  nonbonded pdb=" HH  TYR A 903 "
            pdb="HH11 ARG A 907 "
     model   vdw
     1.443 2.100
  nonbonded pdb=" HH  TYR B 903 "
            pdb="HH11 ARG B 907 "
     model   vdw
     1.447 2.100
  ... (remaining 336293 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.130
  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:             0.390
  Extract box with map and model:          0.850
  Check model and map are aligned:         0.160
  Set scattering table:                    0.190
  Process input model:                     54.860
  Find NCS groups from input model:        0.360
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:14.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
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      :  0.017   0.117  11934  Z= 0.893
  Angle     :  1.313   7.827  16154  Z= 0.901
  Chirality :  0.071   0.310   1710
  Planarity :  0.011   0.056   2084
  Dihedral  : 11.775  85.487   4402
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 0.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  2.31 %
    Favored  : 97.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.95 (0.22), residues: 1432
  helix: -1.95 (0.26), residues: 270
  sheet:  1.43 (0.25), residues: 428
  loop :  1.41 (0.23), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.076   0.015   TRP A 316 
 HIS   0.013   0.003   HIS B 865 
 PHE   0.069   0.010   PHE A  40 
 TYR   0.097   0.015   TYR B 910 
 ARG   0.013   0.002   ARG A  74 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17504 (  430)
  hydrogen bonds       : angle       7.94680 ( 1359)
  covalent geometry    : bond        0.01679 (11934)
  covalent geometry    : angle       1.31330 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 191
  time to evaluate  : 1.962 
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: A  616 MET cc_start: 0.8212 (mmm) cc_final: 0.7928 (mmt)
REVERT: B  616 MET cc_start: 0.8121 (mmm) cc_final: 0.7821 (mmt)
  outliers start: 4
  outliers final: 0
  residues processed: 195
  average time/residue: 3.1000
  time to fit residues: 650.6413
Evaluate side-chains
  108 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.749 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    0.8980
   chunk 109 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 84 optimal weight:    6.9990
   chunk 130 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 273 ASN
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 890 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.098765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.083636 restraints weight = 83577.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 2.44
r_work: 0.3422 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  11934  Z= 0.147
  Angle     :  0.598   7.296  16154  Z= 0.337
  Chirality :  0.046   0.180   1710
  Planarity :  0.005   0.062   2084
  Dihedral  :  5.529  24.905   1594
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.47 %
    Favored  : 88.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.89 (0.22), residues: 1432
  helix: -0.13 (0.31), residues: 252
  sheet:  0.64 (0.24), residues: 454
  loop :  1.07 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  55 
 HIS   0.004   0.001   HIS B 659 
 PHE   0.025   0.002   PHE B 772 
 TYR   0.015   0.002   TYR A 628 
 ARG   0.008   0.001   ARG A 802 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05362 (  430)
  hydrogen bonds       : angle       5.53569 ( 1359)
  covalent geometry    : bond        0.00304 (11934)
  covalent geometry    : angle       0.59812 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8382 (mm)
REVERT: A  114 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8489 (tpp80)
REVERT: A  424 TYR cc_start: 0.7904 (t80) cc_final: 0.7673 (t80)
REVERT: B   35 ASN cc_start: 0.6338 (m-40) cc_final: 0.5907 (m110)
REVERT: B  105 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8890 (tm)
REVERT: B  268 LEU cc_start: 0.8136 (mp) cc_final: 0.7925 (mm)
REVERT: B  593 ILE cc_start: 0.8560 (mt) cc_final: 0.8327 (tp)
  outliers start: 20
  outliers final: 7
  residues processed: 144
  average time/residue: 3.1774
  time to fit residues: 492.8931
Evaluate side-chains
  121 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 1.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  496 ILE
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 115 optimal weight:    5.9990
   chunk 7 optimal weight:    8.9990
   chunk 81 optimal weight:   10.0000
   chunk 39 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 868 HIS
B 890 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.094701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.078995 restraints weight = 83638.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.44
r_work: 0.3342 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  11934  Z= 0.256
  Angle     :  0.608   5.040  16154  Z= 0.336
  Chirality :  0.046   0.177   1710
  Planarity :  0.005   0.043   2084
  Dihedral  :  5.473  24.244   1594
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 11.39 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.22), residues: 1432
  helix: -0.08 (0.33), residues: 250
  sheet:  0.02 (0.23), residues: 452
  loop :  0.56 (0.23), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  55 
 HIS   0.005   0.001   HIS B 781 
 PHE   0.018   0.002   PHE A 772 
 TYR   0.014   0.002   TYR A 628 
 ARG   0.005   0.001   ARG B 907 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05037 (  430)
  hydrogen bonds       : angle       5.08521 ( 1359)
  covalent geometry    : bond        0.00556 (11934)
  covalent geometry    : angle       0.60827 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.900 
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: A   48 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8479 (mm)
REVERT: A  117 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7693 (mp0)
REVERT: B   62 MET cc_start: 0.8363 (mtp) cc_final: 0.8138 (mtm)
REVERT: B   73 MET cc_start: 0.8549 (ppp) cc_final: 0.8255 (ppp)
REVERT: B  105 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8908 (tm)
REVERT: B  332 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8814 (mptp)
  outliers start: 19
  outliers final: 9
  residues processed: 141
  average time/residue: 3.0140
  time to fit residues: 457.5258
Evaluate side-chains
  126 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 1.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ARG
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   46 SER
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  332 LYS
Chi-restraints excluded: chain B residue  497 THR
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 128 optimal weight:    0.7980
   chunk 142 optimal weight:    2.9990
   chunk 109 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 66 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 54 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.096434 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.080885 restraints weight = 83937.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.48
r_work: 0.3388 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.3595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  11934  Z= 0.109
  Angle     :  0.513   4.911  16154  Z= 0.277
  Chirality :  0.044   0.201   1710
  Planarity :  0.004   0.038   2084
  Dihedral  :  5.143  25.639   1594
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.66 %
    Favored  : 86.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.22), residues: 1432
  helix:  0.13 (0.32), residues: 268
  sheet:  0.02 (0.24), residues: 438
  loop :  0.42 (0.23), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  55 
 HIS   0.003   0.001   HIS B 501 
 PHE   0.016   0.001   PHE A 772 
 TYR   0.010   0.001   TYR B 628 
 ARG   0.002   0.000   ARG A 532 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  430)
  hydrogen bonds       : angle       4.66441 ( 1359)
  covalent geometry    : bond        0.00243 (11934)
  covalent geometry    : angle       0.51252 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 ASN cc_start: 0.6595 (m-40) cc_final: 0.6147 (m-40)
REVERT: A   48 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8401 (mm)
REVERT: A  117 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7667 (mp0)
REVERT: B   62 MET cc_start: 0.8368 (mtp) cc_final: 0.8125 (mtm)
REVERT: B  105 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8959 (tm)
  outliers start: 15
  outliers final: 5
  residues processed: 128
  average time/residue: 3.1391
  time to fit residues: 431.7295
Evaluate side-chains
  109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  497 THR
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 116 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 408 GLN
B 408 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.095412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.079898 restraints weight = 84139.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 2.42
r_work: 0.3368 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.3848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11934  Z= 0.147
  Angle     :  0.515   4.710  16154  Z= 0.276
  Chirality :  0.044   0.194   1710
  Planarity :  0.004   0.065   2084
  Dihedral  :  5.025  24.631   1594
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.14 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.22), residues: 1432
  helix:  0.32 (0.32), residues: 268
  sheet: -0.25 (0.23), residues: 450
  loop :  0.41 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.007   0.001   HIS B 610 
 PHE   0.014   0.001   PHE B 772 
 TYR   0.010   0.001   TYR A 628 
 ARG   0.008   0.001   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03951 (  430)
  hydrogen bonds       : angle       4.55283 ( 1359)
  covalent geometry    : bond        0.00330 (11934)
  covalent geometry    : angle       0.51491 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8388 (mm)
REVERT: A  117 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7679 (mp0)
REVERT: B   35 ASN cc_start: 0.6670 (t0) cc_final: 0.6123 (m-40)
REVERT: B   62 MET cc_start: 0.8434 (mtp) cc_final: 0.8168 (mtm)
REVERT: B   73 MET cc_start: 0.8497 (ppp) cc_final: 0.8208 (tmm)
REVERT: B  105 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9006 (tm)
  outliers start: 19
  outliers final: 9
  residues processed: 115
  average time/residue: 3.0062
  time to fit residues: 374.3184
Evaluate side-chains
  114 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 1.803 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ARG
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  532 ARG
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  665 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 21 optimal weight:    0.2980
   chunk 97 optimal weight:    1.9990
   chunk 26 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 6 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0020
   chunk 15 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.4592

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

Flipped N/Q/H residues before XYZ refinement:
A 832 HIS
B 857 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.095240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.079735 restraints weight = 83753.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.43
r_work: 0.3366 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.4017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  11934  Z= 0.140
  Angle     :  0.505   5.108  16154  Z= 0.270
  Chirality :  0.044   0.178   1710
  Planarity :  0.004   0.039   2084
  Dihedral  :  4.936  24.102   1594
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.82 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.08 (0.22), residues: 1432
  helix:  0.57 (0.33), residues: 256
  sheet: -0.30 (0.23), residues: 436
  loop :  0.27 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.009   0.001   HIS A 832 
 PHE   0.014   0.001   PHE A 772 
 TYR   0.011   0.001   TYR A 628 
 ARG   0.005   0.000   ARG A 287 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03788 (  430)
  hydrogen bonds       : angle       4.49119 ( 1359)
  covalent geometry    : bond        0.00315 (11934)
  covalent geometry    : angle       0.50503 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 1.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: A  114 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8457 (tpp80)
REVERT: B   35 ASN cc_start: 0.6747 (t0) cc_final: 0.6075 (m-40)
REVERT: B   62 MET cc_start: 0.8479 (mtp) cc_final: 0.8212 (mtm)
REVERT: B   73 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8208 (tmm)
REVERT: B  664 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7270 (tm-30)
  outliers start: 20
  outliers final: 9
  residues processed: 119
  average time/residue: 2.9265
  time to fit residues: 378.4958
Evaluate side-chains
  113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 1.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ARG
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  532 ARG
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  532 ARG
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  664 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 129 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 118 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0270
   overall best weight:    2.2046

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 HIS
A 857 HIS
B 797 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.093962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.078446 restraints weight = 84311.236|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.41
r_work: 0.3340 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8306
moved from start:          0.4200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11934  Z= 0.193
  Angle     :  0.539   5.038  16154  Z= 0.289
  Chirality :  0.044   0.177   1710
  Planarity :  0.004   0.042   2084
  Dihedral  :  5.035  23.859   1594
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 12.98 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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 (0.22), residues: 1432
  helix:  0.49 (0.33), residues: 256
  sheet: -0.43 (0.23), residues: 440
  loop :  0.15 (0.23), residues: 736

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  55 
 HIS   0.008   0.001   HIS A 832 
 PHE   0.018   0.002   PHE A 116 
 TYR   0.012   0.002   TYR A 628 
 ARG   0.005   0.000   ARG B 907 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  430)
  hydrogen bonds       : angle       4.58514 ( 1359)
  covalent geometry    : bond        0.00433 (11934)
  covalent geometry    : angle       0.53878 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.699 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: A  114 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8483 (tpp80)
REVERT: A  382 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8061 (p)
REVERT: B   62 MET cc_start: 0.8472 (mtp) cc_final: 0.8207 (mtm)
REVERT: B  105 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9105 (tm)
REVERT: B  664 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7355 (tm-30)
  outliers start: 23
  outliers final: 8
  residues processed: 117
  average time/residue: 3.0483
  time to fit residues: 385.3893
Evaluate side-chains
  111 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ARG
Chi-restraints excluded: chain A residue   46 SER
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   59 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  664 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 120 optimal weight:    0.7980
   chunk 116 optimal weight:    2.9990
   chunk 83 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   chunk 62 optimal weight:    0.6980
   chunk 123 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0050
   chunk 121 optimal weight:    0.9980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 337 GLN
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 HIS
A 832 HIS
B  92 ASN
B 579 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.095928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.080568 restraints weight = 83821.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 2.42
r_work: 0.3382 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.4353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  11934  Z= 0.101
  Angle     :  0.502   5.831  16154  Z= 0.265
  Chirality :  0.043   0.170   1710
  Planarity :  0.004   0.038   2084
  Dihedral  :  4.805  23.237   1594
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 13.46 %
    Favored  : 85.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.07 (0.22), residues: 1432
  helix:  0.78 (0.34), residues: 256
  sheet: -0.42 (0.24), residues: 424
  loop :  0.24 (0.23), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  55 
 HIS   0.006   0.001   HIS A 832 
 PHE   0.014   0.001   PHE B 772 
 TYR   0.009   0.001   TYR A 628 
 ARG   0.007   0.001   ARG B 114 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03426 (  430)
  hydrogen bonds       : angle       4.33518 ( 1359)
  covalent geometry    : bond        0.00230 (11934)
  covalent geometry    : angle       0.50194 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8344 (mm)
REVERT: A  114 ARG cc_start: 0.8772 (mmm-85) cc_final: 0.8460 (tpp80)
REVERT: A  117 GLU cc_start: 0.8229 (OUTLIER) cc_final: 0.7699 (mp0)
REVERT: A  382 VAL cc_start: 0.8331 (OUTLIER) cc_final: 0.8001 (p)
REVERT: B   62 MET cc_start: 0.8447 (mtp) cc_final: 0.8196 (mtm)
REVERT: B  664 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7370 (tm-30)
  outliers start: 17
  outliers final: 7
  residues processed: 117
  average time/residue: 3.0265
  time to fit residues: 382.6543
Evaluate side-chains
  113 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 1.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ARG
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  664 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 113 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 142 optimal weight:    0.0670
   chunk 138 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0270
   overall best weight:    0.7378

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

Flipped N/Q/H residues before XYZ refinement:
A 574 ASN
A 832 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.095977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.080619 restraints weight = 83874.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.42
r_work: 0.3385 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.4410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.056  11934  Z= 0.105
  Angle     :  0.501   6.307  16154  Z= 0.264
  Chirality :  0.043   0.168   1710
  Planarity :  0.004   0.055   2084
  Dihedral  :  4.693  22.532   1594
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 13.85 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.10 (0.22), residues: 1432
  helix:  0.92 (0.35), residues: 256
  sheet: -0.42 (0.24), residues: 424
  loop :  0.23 (0.24), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.007   0.001   HIS A 832 
 PHE   0.013   0.001   PHE A 116 
 TYR   0.009   0.001   TYR A 628 
 ARG   0.008   0.000   ARG B 683 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03399 (  430)
  hydrogen bonds       : angle       4.26389 ( 1359)
  covalent geometry    : bond        0.00244 (11934)
  covalent geometry    : angle       0.50130 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 107
  time to evaluate  : 2.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 ARG cc_start: 0.8737 (mmm-85) cc_final: 0.8429 (tpp80)
REVERT: A  382 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.8049 (p)
REVERT: B   62 MET cc_start: 0.8436 (mtp) cc_final: 0.8184 (mtm)
  outliers start: 11
  outliers final: 7
  residues processed: 113
  average time/residue: 3.1130
  time to fit residues: 381.7089
Evaluate side-chains
  109 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.660 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ARG
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 74 optimal weight:    0.0070
   chunk 91 optimal weight:    6.9990
   chunk 111 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 141 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0040
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5010

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 HIS
B  92 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.096650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.081199 restraints weight = 83992.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.48
r_work: 0.3392 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.4522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  11934  Z= 0.098
  Angle     :  0.506   6.406  16154  Z= 0.265
  Chirality :  0.043   0.168   1710
  Planarity :  0.004   0.054   2084
  Dihedral  :  4.600  21.901   1594
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.25 %
    Favored  : 84.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.10 (0.23), residues: 1432
  helix:  1.01 (0.35), residues: 256
  sheet: -0.45 (0.24), residues: 426
  loop :  0.20 (0.24), residues: 750

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.007   0.001   HIS A 832 
 PHE   0.014   0.001   PHE A 116 
 TYR   0.009   0.001   TYR A 628 
 ARG   0.005   0.000   ARG B 683 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03267 (  430)
  hydrogen bonds       : angle       4.20056 ( 1359)
  covalent geometry    : bond        0.00229 (11934)
  covalent geometry    : angle       0.50633 (16154)

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

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

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2864 Ramachandran restraints generated.
    1432 Oldfield, 0 Emsley, 1432 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 1.708 
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: A  114 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8424 (tpp80)
REVERT: A  382 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8160 (p)
REVERT: B   62 MET cc_start: 0.8434 (mtp) cc_final: 0.8198 (mtm)
REVERT: B  268 LEU cc_start: 0.8584 (mm) cc_final: 0.8029 (mm)
REVERT: B  664 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7463 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 114
  average time/residue: 2.9350
  time to fit residues: 363.5511
Evaluate side-chains
  115 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 1.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 PHE
Chi-restraints excluded: chain A residue  285 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain B residue   43 ARG
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  658 LEU
Chi-restraints excluded: chain B residue  664 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 141 optimal weight:    0.4980
   chunk 21 optimal weight:    0.5980
   chunk 115 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 65 optimal weight:    0.0470
   chunk 84 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.0282

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.098565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.082902 restraints weight = 83373.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.46
r_work: 0.3385 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.4591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11934  Z= 0.119
  Angle     :  0.515   6.273  16154  Z= 0.270
  Chirality :  0.043   0.169   1710
  Planarity :  0.004   0.057   2084
  Dihedral  :  4.590  21.513   1594
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.58 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 14.49 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.12 %
    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:  0.10 (0.23), residues: 1432
  helix:  0.97 (0.35), residues: 256
  sheet: -0.43 (0.24), residues: 424
  loop :  0.21 (0.24), residues: 752

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  55 
 HIS   0.007   0.001   HIS A 832 
 PHE   0.019   0.001   PHE B 506 
 TYR   0.010   0.001   TYR A 628 
 ARG   0.006   0.000   ARG B 683 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03391 (  430)
  hydrogen bonds       : angle       4.20084 ( 1359)
  covalent geometry    : bond        0.00275 (11934)
  covalent geometry    : angle       0.51518 (16154)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 17241.14 seconds
wall clock time: 295 minutes 17.52 seconds (17717.52 seconds total)