Starting phenix.real_space_refine
on Sun Sep 29 15:36:03 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/09_2024/8pba_17582.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/09_2024/8pba_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/09_2024/8pba_17582.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/09_2024/8pba_17582.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/09_2024/8pba_17582.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pba_17582/09_2024/8pba_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-5461/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: 11.25, 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: 5.85
  Conformation dependent library (CDL) restraints added in 1.8 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: 2.76
  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: 9.87

  Time building geometry restraints manager: 7.10 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: 0.00
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:             1.930
  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:             0.380
  Extract box with map and model:          0.840
  Check model and map are aligned:         0.180
  Set scattering table:                    0.200
  Process input model:                     51.480
  Find NCS groups from input model:        0.450
  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:             0.010
  Load rotamer database and sin/cos tables:10.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   66.260
-------------------------------------------------------------------------------
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= 1.095
  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 

*********************** 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 fitting.
    rotamer outliers: 4
    poor density    : 191
  time to evaluate  : 1.800 
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: 2.9947
  time to fit residues: 627.4973
Evaluate side-chains
  108 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 1.798 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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= 0.198
  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 

*********************** 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 fitting.
    rotamer outliers: 20
    poor density    : 131
  time to evaluate  : 1.827 
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  114 ARG cc_start: 0.8933 (mmm-85) cc_final: 0.8730 (tpp80)
REVERT: A  616 MET cc_start: 0.8183 (mmm) cc_final: 0.7853 (mmt)
REVERT: B  105 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8222 (tm)
REVERT: B  616 MET cc_start: 0.8117 (mmm) cc_final: 0.7908 (mmt)
  outliers start: 20
  outliers final: 7
  residues processed: 144
  average time/residue: 3.0842
  time to fit residues: 477.6202
Evaluate side-chains
  117 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 1.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 72 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 108 optimal weight:    3.9990
   chunk 89 optimal weight:    4.9990
   chunk 36 optimal weight:    3.9990
   chunk 131 optimal weight:    3.9990
   chunk 141 optimal weight:    0.7980
   chunk 116 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   chunk 44 optimal weight:   20.0000
   chunk 105 optimal weight:    0.0870
   overall best weight:    1.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 574 ASN
B 890 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11934  Z= 0.260
  Angle     :  0.562   5.350  16154  Z= 0.309
  Chirality :  0.045   0.168   1710
  Planarity :  0.004   0.041   2084
  Dihedral  :  5.290  24.058   1594
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 11.46 %
    Favored  : 87.50 %
  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:  0.45 (0.22), residues: 1432
  helix:  0.01 (0.32), residues: 264
  sheet:  0.23 (0.24), residues: 452
  loop :  0.68 (0.23), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  55 
 HIS   0.004   0.001   HIS B 579 
 PHE   0.019   0.002   PHE A 772 
 TYR   0.013   0.002   TYR A 628 
 ARG   0.003   0.000   ARG A  60 

*********************** 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
  136 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7945 (mp0)
REVERT: A  616 MET cc_start: 0.8201 (mmm) cc_final: 0.7551 (mmt)
REVERT: B  105 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8268 (tm)
REVERT: B  616 MET cc_start: 0.8098 (mmm) cc_final: 0.7858 (mmt)
  outliers start: 13
  outliers final: 7
  residues processed: 134
  average time/residue: 3.1157
  time to fit residues: 448.4828
Evaluate side-chains
  119 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 1.927 
-------------------------------------------------------------------------------
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  117 GLU
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  105 LEU
Chi-restraints excluded: chain B residue  496 ILE
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 129 optimal weight:    5.9990
   chunk 98 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 14 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 87 optimal weight:    5.9990
   chunk 131 optimal weight:    3.9990
   chunk 139 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 124 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  11934  Z= 0.264
  Angle     :  0.548   4.987  16154  Z= 0.297
  Chirality :  0.045   0.209   1710
  Planarity :  0.004   0.040   2084
  Dihedral  :  5.223  25.826   1594
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 11.94 %
    Favored  : 86.46 %
  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:  0.01 (0.31), residues: 268
  sheet: -0.12 (0.23), residues: 446
  loop :  0.37 (0.23), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  55 
 HIS   0.003   0.001   HIS A 579 
 PHE   0.015   0.002   PHE A 772 
 TYR   0.013   0.002   TYR B 390 
 ARG   0.006   0.001   ARG A 114 

*********************** 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 fitting.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.846 
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  117 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7923 (mp0)
REVERT: A  616 MET cc_start: 0.8075 (mmm) cc_final: 0.7663 (mmt)
REVERT: B  105 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8351 (tm)
REVERT: B  616 MET cc_start: 0.8118 (mmm) cc_final: 0.7702 (mmt)
REVERT: B  680 MET cc_start: 0.8142 (ttp) cc_final: 0.7911 (ttp)
  outliers start: 20
  outliers final: 8
  residues processed: 126
  average time/residue: 3.0760
  time to fit residues: 417.5108
Evaluate side-chains
  110 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 1.793 
-------------------------------------------------------------------------------
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   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  497 THR
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 115 optimal weight:    3.9990
   chunk 79 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 103 optimal weight:    2.9990
   chunk 57 optimal weight:    5.9990
   chunk 118 optimal weight:    0.0040
   chunk 96 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   chunk 124 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.5196

-------------------------------------------------------------------------------
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
B 857 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11934  Z= 0.211
  Angle     :  0.515   4.775  16154  Z= 0.277
  Chirality :  0.044   0.174   1710
  Planarity :  0.004   0.041   2084
  Dihedral  :  5.064  24.725   1594
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 12.34 %
    Favored  : 86.31 %
  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:  0.05 (0.22), residues: 1432
  helix:  0.27 (0.32), residues: 268
  sheet: -0.29 (0.23), residues: 450
  loop :  0.36 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  55 
 HIS   0.009   0.001   HIS B 610 
 PHE   0.015   0.001   PHE A 772 
 TYR   0.011   0.001   TYR A 628 
 ARG   0.004   0.001   ARG A 287 

*********************** 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 fitting.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 1.776 
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  117 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7902 (mp0)
REVERT: A  616 MET cc_start: 0.8060 (mmm) cc_final: 0.7639 (mmt)
REVERT: B  105 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8372 (tm)
REVERT: B  616 MET cc_start: 0.8089 (mmm) cc_final: 0.7648 (mmt)
  outliers start: 17
  outliers final: 9
  residues processed: 118
  average time/residue: 2.8863
  time to fit residues: 368.3660
Evaluate side-chains
  112 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 1.759 
-------------------------------------------------------------------------------
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   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  658 LEU
Chi-restraints excluded: chain B residue   46 SER
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  665 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    0.4980
   chunk 125 optimal weight:    0.8980
   chunk 27 optimal weight:    0.2980
   chunk 81 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 139 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 832 HIS
A 857 HIS
B  35 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  11934  Z= 0.142
  Angle     :  0.485   5.003  16154  Z= 0.258
  Chirality :  0.043   0.174   1710
  Planarity :  0.004   0.060   2084
  Dihedral  :  4.830  23.957   1594
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.26 %
    Favored  : 86.54 %
  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:  0.16 (0.22), residues: 1432
  helix:  0.67 (0.34), residues: 256
  sheet: -0.25 (0.23), residues: 436
  loop :  0.31 (0.23), residues: 740

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  55 
 HIS   0.008   0.001   HIS A 832 
 PHE   0.015   0.001   PHE A 116 
 TYR   0.010   0.001   TYR B 628 
 ARG   0.005   0.000   ARG A 892 

*********************** 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
  121 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.823 
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: A  117 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7858 (mp0)
REVERT: A  616 MET cc_start: 0.8020 (mmm) cc_final: 0.7654 (mmt)
REVERT: B  616 MET cc_start: 0.8081 (mmm) cc_final: 0.7625 (mmt)
  outliers start: 15
  outliers final: 7
  residues processed: 116
  average time/residue: 2.9658
  time to fit residues: 370.6824
Evaluate side-chains
  109 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 1.698 
-------------------------------------------------------------------------------
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  117 GLU
Chi-restraints excluded: chain A residue  532 ARG
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  658 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0980
   chunk 101 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 117 optimal weight:    9.9990
   chunk 77 optimal weight:    3.9990
   chunk 138 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 84 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    1.3786

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11934  Z= 0.194
  Angle     :  0.495   5.244  16154  Z= 0.265
  Chirality :  0.043   0.172   1710
  Planarity :  0.004   0.053   2084
  Dihedral  :  4.812  23.306   1594
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  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:  0.14 (0.22), residues: 1432
  helix:  0.72 (0.34), residues: 256
  sheet: -0.28 (0.23), residues: 436
  loop :  0.29 (0.24), residues: 740

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 712 
 TYR   0.011   0.001   TYR A 628 
 ARG   0.006   0.000   ARG A 892 

*********************** 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
  120 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 1.732 
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: A  117 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7879 (mp0)
REVERT: A  616 MET cc_start: 0.8000 (mmm) cc_final: 0.7708 (mmt)
REVERT: B  105 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8452 (tm)
REVERT: B  616 MET cc_start: 0.8072 (mmm) cc_final: 0.7625 (mmt)
  outliers start: 15
  outliers final: 8
  residues processed: 113
  average time/residue: 2.8449
  time to fit residues: 349.0222
Evaluate side-chains
  112 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 2.016 
-------------------------------------------------------------------------------
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   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
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   67 PHE
Chi-restraints excluded: chain B residue  105 LEU
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    3.9990
   chunk 88 optimal weight:    4.9990
   chunk 94 optimal weight:    6.9990
   chunk 68 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 109 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   overall best weight:    3.3990

-------------------------------------------------------------------------------
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 475 GLN
A 832 HIS
A 868 HIS
B 610 HIS
B 797 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.4326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  11934  Z= 0.389
  Angle     :  0.582   5.493  16154  Z= 0.315
  Chirality :  0.046   0.178   1710
  Planarity :  0.005   0.054   2084
  Dihedral  :  5.197  23.662   1594
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.58 %
    Favored  : 85.83 %
  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: -0.28 (0.22), residues: 1432
  helix:  0.15 (0.32), residues: 266
  sheet: -0.50 (0.23), residues: 440
  loop :  0.08 (0.24), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  55 
 HIS   0.008   0.001   HIS A 832 
 PHE   0.019   0.002   PHE B 506 
 TYR   0.015   0.002   TYR A 325 
 ARG   0.007   0.001   ARG B 683 

*********************** 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
  126 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 1.667 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7908 (mp0)
REVERT: A  616 MET cc_start: 0.8080 (mmm) cc_final: 0.7683 (mmt)
REVERT: B  616 MET cc_start: 0.8090 (mmm) cc_final: 0.7656 (mmt)
  outliers start: 20
  outliers final: 9
  residues processed: 120
  average time/residue: 2.9667
  time to fit residues: 385.2820
Evaluate side-chains
  105 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.777 
-------------------------------------------------------------------------------
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   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
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   59 VAL
Chi-restraints excluded: chain B residue   67 PHE
Chi-restraints excluded: chain B residue  658 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 132 optimal weight:    3.9990
   chunk 121 optimal weight:    0.7980
   chunk 129 optimal weight:    0.7980
   chunk 77 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   chunk 122 optimal weight:    0.7980
   chunk 128 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 579 HIS
A 832 HIS
B  92 ASN
B 610 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.4470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11934  Z= 0.181
  Angle     :  0.529   6.550  16154  Z= 0.281
  Chirality :  0.044   0.174   1710
  Planarity :  0.004   0.049   2084
  Dihedral  :  4.969  23.436   1594
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 13.22 %
    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: -0.13 (0.22), residues: 1432
  helix:  0.56 (0.33), residues: 256
  sheet: -0.52 (0.24), residues: 420
  loop :  0.12 (0.23), residues: 756

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   0.016   0.001   PHE B 506 
 TYR   0.010   0.001   TYR A 483 
 ARG   0.010   0.001   ARG B 114 

*********************** 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
  114 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 99
  time to evaluate  : 2.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7904 (mp0)
REVERT: A  616 MET cc_start: 0.8008 (mmm) cc_final: 0.7706 (mmt)
REVERT: B  105 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8546 (tm)
REVERT: B  616 MET cc_start: 0.8072 (mmm) cc_final: 0.7611 (mmt)
  outliers start: 15
  outliers final: 9
  residues processed: 111
  average time/residue: 2.7584
  time to fit residues: 332.8155
Evaluate side-chains
  108 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 1.689 
-------------------------------------------------------------------------------
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   67 PHE
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  285 ILE
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   67 PHE
Chi-restraints excluded: chain B residue  105 LEU
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 136 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 64 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 143 optimal weight:    2.9990
   chunk 132 optimal weight:    3.9990
   chunk 114 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 88 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11934  Z= 0.189
  Angle     :  0.523   6.522  16154  Z= 0.277
  Chirality :  0.043   0.172   1710
  Planarity :  0.004   0.047   2084
  Dihedral  :  4.873  22.868   1594
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 13.46 %
    Favored  : 85.67 %
  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:  0.68 (0.34), residues: 256
  sheet: -0.51 (0.24), residues: 420
  loop :  0.10 (0.23), residues: 756

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   0.017   0.001   PHE B 506 
 TYR   0.010   0.001   TYR A 628 
 ARG   0.005   0.001   ARG B 114 

********************** 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
  113 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 2.068 
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  616 MET cc_start: 0.8012 (mmm) cc_final: 0.7723 (mmt)
REVERT: B  616 MET cc_start: 0.8091 (mmm) cc_final: 0.7634 (mmt)
  outliers start: 11
  outliers final: 9
  residues processed: 110
  average time/residue: 2.8422
  time to fit residues: 338.8629
Evaluate side-chains
  111 residues out of total 1256 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 1.837 
-------------------------------------------------------------------------------
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   67 PHE
Chi-restraints excluded: chain A residue  285 ILE
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   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 121 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 16 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 47 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 100 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 652 HIS ** 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 = 0.3745 r_free = 0.3745 target = 0.096237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.080669 restraints weight = 83686.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 2.43
r_work: 0.3339 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.4596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11934  Z= 0.253
  Angle     :  0.547   6.593  16154  Z= 0.291
  Chirality :  0.044   0.174   1710
  Planarity :  0.004   0.048   2084
  Dihedral  :  4.956  22.722   1594
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.00 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 13.69 %
    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: -0.22 (0.22), residues: 1432
  helix:  0.57 (0.33), residues: 256
  sheet: -0.58 (0.24), residues: 424
  loop :  0.03 (0.23), 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   0.021   0.002   PHE B 506 
 TYR   0.011   0.002   TYR A 628 
 ARG   0.005   0.001   ARG B 683 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8402.72 seconds
wall clock time: 145 minutes 41.45 seconds (8741.45 seconds total)