Starting phenix.real_space_refine
on Fri Feb 14 18:47:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k3x_36864/02_2025/8k3x_36864_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k3x_36864/02_2025/8k3x_36864.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.86
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k3x_36864/02_2025/8k3x_36864.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k3x_36864/02_2025/8k3x_36864.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k3x_36864/02_2025/8k3x_36864_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k3x_36864/02_2025/8k3x_36864_neut.cif"
  }
  resolution = 2.86
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.136
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      64      5.16       5
     C    6738      2.51       5
     N    1696      2.21       5
     O    1888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 74 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10386
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 693, 5158
          Classifications: {'peptide': 693}
          Incomplete info: {'truncation_to_alanine': 126}
          Link IDs: {'PTRANS': 20, 'TRANS': 672}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 492
          Unresolved non-hydrogen angles: 608
          Unresolved non-hydrogen dihedrals: 408
          Unresolved non-hydrogen chiralities: 37
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 16, 'GLU:plan': 16, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 279
    Chain: "B"
      Number of atoms: 5158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 693, 5158
          Classifications: {'peptide': 693}
          Incomplete info: {'truncation_to_alanine': 126}
          Link IDs: {'PTRANS': 20, 'TRANS': 672}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 492
          Unresolved non-hydrogen angles: 608
          Unresolved non-hydrogen dihedrals: 408
          Unresolved non-hydrogen chiralities: 37
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 10, 'ASP:plan': 6, 'PHE:plan': 16, 'GLU:plan': 16, 'ARG:plan': 11}
          Unresolved non-hydrogen planarities: 279
    Chain: "A"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'BGI': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'BGI': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.24, per 1000 atoms: 0.60
  Number of scatterers: 10386
  At special positions: 0
  Unit cell: (77.38, 136.74, 113.42, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      64     16.00
     O    1888      8.00
     N    1696      7.00
     C    6738      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2644

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 6 sheets defined
      64.5% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 392 through 401
      removed outlier: 3.641A  pdb=" N   GLN A 398 " --> pdb=" O   THR A 394 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR A 401 " --> pdb=" O   ASP A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 414
      removed outlier: 3.522A  pdb=" N   LYS A 414 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 410 through 414'
    Processing helix  chain 'A' and resid 424 through 428
      removed outlier: 4.020A  pdb=" N   LEU A 428 " --> pdb=" O   PRO A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 439
    Processing helix  chain 'A' and resid 458 through 468
      removed outlier: 3.590A  pdb=" N   LEU A 462 " --> pdb=" O   ASP A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 479
    Processing helix  chain 'A' and resid 488 through 493
      removed outlier: 3.543A  pdb=" N   LYS A 491 " --> pdb=" O   ASP A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 517
      removed outlier: 3.687A  pdb=" N   LEU A 512 " --> pdb=" O   ARG A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 588
      removed outlier: 4.072A  pdb=" N   ASN A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 581 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 594
      removed outlier: 3.536A  pdb=" N   LEU A 592 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 617
    Processing helix  chain 'A' and resid 618 through 621
      removed outlier: 3.734A  pdb=" N   ASN A 621 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 618 through 621'
    Processing helix  chain 'A' and resid 636 through 640
      removed outlier: 3.704A  pdb=" N   PHE A 639 " --> pdb=" O   GLY A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 660
      removed outlier: 3.613A  pdb=" N   GLN A 650 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 669
      removed outlier: 3.756A  pdb=" N   PHE A 668 " --> pdb=" O   THR A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 687
    Processing helix  chain 'A' and resid 688 through 696
    Processing helix  chain 'A' and resid 706 through 712
    Processing helix  chain 'A' and resid 713 through 716
      removed outlier: 3.950A  pdb=" N   GLU A 716 " --> pdb=" O   TYR A 713 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 713 through 716'
    Processing helix  chain 'A' and resid 717 through 726
      removed outlier: 4.380A  pdb=" N   CYS A 721 " --> pdb=" O   ASP A 717 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   PHE A 722 " --> pdb=" O   ARG A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 774
      removed outlier: 3.906A  pdb=" N   ARG A 759 " --> pdb=" O   LEU A 755 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TRP A 760 " --> pdb=" O   GLN A 756 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN A 762 " --> pdb=" O   ARG A 758 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 775 through 781
    Processing helix  chain 'A' and resid 784 through 807
    Processing helix  chain 'A' and resid 807 through 828
      removed outlier: 3.683A  pdb=" N   PHE A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ALA A 824 " --> pdb=" O   THR A 820 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 856
      removed outlier: 3.523A  pdb=" N   LEU A 834 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 893
    Processing helix  chain 'A' and resid 917 through 932
    Processing helix  chain 'A' and resid 936 through 941
      removed outlier: 3.781A  pdb=" N   THR A 940 " --> pdb=" O   TRP A 936 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER A 941 " --> pdb=" O   HIS A 937 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 936 through 941'
    Processing helix  chain 'A' and resid 941 through 948
      removed outlier: 3.531A  pdb=" N   TYR A 945 " --> pdb=" O   SER A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 949 through 955
    Processing helix  chain 'A' and resid 955 through 963
    Processing helix  chain 'A' and resid 997 through 1014
    Processing helix  chain 'A' and resid 1027 through 1045
      removed outlier: 3.526A  pdb=" N   SER A1041 " --> pdb=" O   ALA A1037 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   ILE A1044 " --> pdb=" O   ARG A1040 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1048 through 1060
      removed outlier: 3.811A  pdb=" N   ILE A1054 " --> pdb=" O   THR A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1075
      removed outlier: 3.523A  pdb=" N   THR A1075 " --> pdb=" O   LYS A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1128
      removed outlier: 4.241A  pdb=" N   SER A1095 " --> pdb=" O   THR A1091 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A1102 " --> pdb=" O   PHE A1098 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   SER A1108 " --> pdb=" O   LEU A1104 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA A1109 " --> pdb=" O   VAL A1105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 392 through 401
      removed outlier: 3.641A  pdb=" N   GLN B 398 " --> pdb=" O   THR B 394 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   THR B 401 " --> pdb=" O   ASP B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 414
      removed outlier: 3.522A  pdb=" N   LYS B 414 " --> pdb=" O   PRO B 410 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 410 through 414'
    Processing helix  chain 'B' and resid 424 through 428
      removed outlier: 4.020A  pdb=" N   LEU B 428 " --> pdb=" O   PRO B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 435 through 439
    Processing helix  chain 'B' and resid 458 through 468
      removed outlier: 3.591A  pdb=" N   LEU B 462 " --> pdb=" O   ASP B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 471 through 479
    Processing helix  chain 'B' and resid 488 through 493
      removed outlier: 3.543A  pdb=" N   LYS B 491 " --> pdb=" O   ASP B 488 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 517
      removed outlier: 3.687A  pdb=" N   LEU B 512 " --> pdb=" O   ARG B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 588
      removed outlier: 4.073A  pdb=" N   ASN B 580 " --> pdb=" O   GLN B 576 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER B 581 " --> pdb=" O   LYS B 577 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 594
      removed outlier: 3.535A  pdb=" N   LEU B 592 " --> pdb=" O   GLY B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 617
    Processing helix  chain 'B' and resid 618 through 621
      removed outlier: 3.734A  pdb=" N   ASN B 621 " --> pdb=" O   GLU B 618 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 618 through 621'
    Processing helix  chain 'B' and resid 636 through 640
      removed outlier: 3.704A  pdb=" N   PHE B 639 " --> pdb=" O   GLY B 636 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 644 through 660
      removed outlier: 3.613A  pdb=" N   GLN B 650 " --> pdb=" O   LEU B 646 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 669
      removed outlier: 3.755A  pdb=" N   PHE B 668 " --> pdb=" O   THR B 664 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 687
    Processing helix  chain 'B' and resid 688 through 696
    Processing helix  chain 'B' and resid 706 through 712
    Processing helix  chain 'B' and resid 713 through 716
      removed outlier: 3.950A  pdb=" N   GLU B 716 " --> pdb=" O   TYR B 713 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 713 through 716'
    Processing helix  chain 'B' and resid 717 through 726
      removed outlier: 4.381A  pdb=" N   CYS B 721 " --> pdb=" O   ASP B 717 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   PHE B 722 " --> pdb=" O   ARG B 718 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 749 through 774
      removed outlier: 3.906A  pdb=" N   ARG B 759 " --> pdb=" O   LEU B 755 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TRP B 760 " --> pdb=" O   GLN B 756 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN B 762 " --> pdb=" O   ARG B 758 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 781
    Processing helix  chain 'B' and resid 784 through 807
    Processing helix  chain 'B' and resid 807 through 828
      removed outlier: 3.683A  pdb=" N   PHE B 813 " --> pdb=" O   LEU B 809 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA B 824 " --> pdb=" O   THR B 820 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 856
      removed outlier: 3.522A  pdb=" N   LEU B 834 " --> pdb=" O   ALA B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 862 through 893
    Processing helix  chain 'B' and resid 917 through 932
    Processing helix  chain 'B' and resid 936 through 941
      removed outlier: 3.781A  pdb=" N   THR B 940 " --> pdb=" O   TRP B 936 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   SER B 941 " --> pdb=" O   HIS B 937 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 936 through 941'
    Processing helix  chain 'B' and resid 941 through 948
      removed outlier: 3.531A  pdb=" N   TYR B 945 " --> pdb=" O   SER B 941 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 949 through 955
    Processing helix  chain 'B' and resid 955 through 963
    Processing helix  chain 'B' and resid 997 through 1014
    Processing helix  chain 'B' and resid 1027 through 1045
      removed outlier: 3.525A  pdb=" N   SER B1041 " --> pdb=" O   ALA B1037 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE B1044 " --> pdb=" O   ARG B1040 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   ILE B1045 " --> pdb=" O   SER B1041 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1048 through 1060
      removed outlier: 3.811A  pdb=" N   ILE B1054 " --> pdb=" O   THR B1050 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1063 through 1075
      removed outlier: 3.524A  pdb=" N   THR B1075 " --> pdb=" O   LYS B1071 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1091 through 1128
      removed outlier: 4.241A  pdb=" N   SER B1095 " --> pdb=" O   THR B1091 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU B1102 " --> pdb=" O   PHE B1098 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   SER B1108 " --> pdb=" O   LEU B1104 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA B1109 " --> pdb=" O   VAL B1105 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 388 through 390
      removed outlier: 6.164A  pdb=" N   ILE A 497 " --> pdb=" O   CYS A 570 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LYS A 572 " --> pdb=" O   ILE A 497 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 453
      removed outlier: 3.927A  pdb=" N   THR A 453 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   PHE A 678 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLY A 629 " --> pdb=" O   PHE A 678 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLY A 625 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   LYS A 735 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA A 627 " --> pdb=" O   LYS A 735 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   CYS A 737 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY A 629 " --> pdb=" O   CYS A 737 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   SER A 739 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   ILE A 631 " --> pdb=" O   SER A 739 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   TYR A 741 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 9.932A  pdb=" N   THR A 633 " --> pdb=" O   TYR A 741 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER A 743 " --> pdb=" O   THR A 633 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 549
      removed outlier: 6.818A  pdb=" N   SER A 555 " --> pdb=" O   THR A 547 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 388 through 390
      removed outlier: 6.164A  pdb=" N   ILE B 497 " --> pdb=" O   CYS B 570 " (cutoff:3.500A)
      removed outlier: 7.394A  pdb=" N   LYS B 572 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 451 through 453
      removed outlier: 3.926A  pdb=" N   THR B 453 " --> pdb=" O   LEU B 601 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   PHE B 678 " --> pdb=" O   GLY B 629 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLY B 629 " --> pdb=" O   PHE B 678 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   GLY B 625 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   LYS B 735 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA B 627 " --> pdb=" O   LYS B 735 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   CYS B 737 " --> pdb=" O   ALA B 627 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   GLY B 629 " --> pdb=" O   CYS B 737 " (cutoff:3.500A)
      removed outlier: 8.264A  pdb=" N   SER B 739 " --> pdb=" O   GLY B 629 " (cutoff:3.500A)
      removed outlier: 10.191A  pdb=" N   ILE B 631 " --> pdb=" O   SER B 739 " (cutoff:3.500A)
      removed outlier: 8.530A  pdb=" N   TYR B 741 " --> pdb=" O   ILE B 631 " (cutoff:3.500A)
      removed outlier: 9.932A  pdb=" N   THR B 633 " --> pdb=" O   TYR B 741 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   SER B 743 " --> pdb=" O   THR B 633 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 545 through 549
      removed outlier: 6.818A  pdb=" N   SER B 555 " --> pdb=" O   THR B 547 " (cutoff:3.500A)

    604 hydrogen bonds defined for protein.
    1728 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: 3.75

  Time building geometry restraints manager: 2.96 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1634
        1.30 -     1.43: 2967
        1.43 -     1.55: 5921
        1.55 -     1.68: 6
        1.68 -     1.80: 96
  Bond restraints: 10624
  Sorted by residual:
  bond pdb=" C28 BGI A1201 "
       pdb=" N27 BGI A1201 "
    ideal  model  delta    sigma   weight residual
    1.371  1.518 -0.147 2.00e-02 2.50e+03 5.37e+01
  bond pdb=" C28 BGI B1201 "
       pdb=" N27 BGI B1201 "
    ideal  model  delta    sigma   weight residual
    1.371  1.517 -0.146 2.00e-02 2.50e+03 5.35e+01
  bond pdb=" C28 BGI A1201 "
       pdb=" N22 BGI A1201 "
    ideal  model  delta    sigma   weight residual
    1.382  1.515 -0.133 2.00e-02 2.50e+03 4.40e+01
  bond pdb=" C28 BGI B1201 "
       pdb=" N22 BGI B1201 "
    ideal  model  delta    sigma   weight residual
    1.382  1.514 -0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" C13 BGI B1201 "
       pdb=" N15 BGI B1201 "
    ideal  model  delta    sigma   weight residual
    1.343  1.472 -0.129 2.00e-02 2.50e+03 4.16e+01
  ... (remaining 10619 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 13435
        1.65 -     3.30: 851
        3.30 -     4.95: 144
        4.95 -     6.61: 42
        6.61 -     8.26: 16
  Bond angle restraints: 14488
  Sorted by residual:
  angle pdb=" N   LEU B 642 "
        pdb=" CA  LEU B 642 "
        pdb=" C   LEU B 642 "
      ideal   model   delta    sigma   weight residual
     113.02  106.05    6.97 1.20e+00 6.94e-01 3.38e+01
  angle pdb=" N   LEU A 642 "
        pdb=" CA  LEU A 642 "
        pdb=" C   LEU A 642 "
      ideal   model   delta    sigma   weight residual
     113.02  106.05    6.97 1.20e+00 6.94e-01 3.37e+01
  angle pdb=" N   THR B 422 "
        pdb=" CA  THR B 422 "
        pdb=" C   THR B 422 "
      ideal   model   delta    sigma   weight residual
     114.56  107.87    6.69 1.27e+00 6.20e-01 2.78e+01
  angle pdb=" N   THR A 422 "
        pdb=" CA  THR A 422 "
        pdb=" C   THR A 422 "
      ideal   model   delta    sigma   weight residual
     114.56  107.92    6.64 1.27e+00 6.20e-01 2.74e+01
  angle pdb=" N   TYR A 952 "
        pdb=" CA  TYR A 952 "
        pdb=" C   TYR A 952 "
      ideal   model   delta    sigma   weight residual
     112.89  107.00    5.89 1.24e+00 6.50e-01 2.25e+01
  ... (remaining 14483 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 5702
       15.94 -    31.88: 407
       31.88 -    47.83: 85
       47.83 -    63.77: 16
       63.77 -    79.71: 16
  Dihedral angle restraints: 6226
    sinusoidal: 2144
      harmonic: 4082
  Sorted by residual:
  dihedral pdb=" CA  ALA B 715 "
           pdb=" C   ALA B 715 "
           pdb=" N   GLU B 716 "
           pdb=" CA  GLU B 716 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.39  -28.61     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ALA A 715 "
           pdb=" C   ALA A 715 "
           pdb=" N   GLU A 716 "
           pdb=" CA  GLU A 716 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.40  -28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  HIS B 828 "
           pdb=" C   HIS B 828 "
           pdb=" N   SER B 829 "
           pdb=" CA  SER B 829 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.44  -20.56     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 6223 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1551
       0.100 -    0.199: 135
       0.199 -    0.299: 10
       0.299 -    0.399: 0
       0.399 -    0.498: 2
  Chirality restraints: 1698
  Sorted by residual:
  chirality pdb=" C19 BGI A1201 "
            pdb=" C18 BGI A1201 "
            pdb=" C20 BGI A1201 "
            pdb=" O30 BGI A1201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.97   -0.50 2.00e-01 2.50e+01 6.21e+00
  chirality pdb=" C19 BGI B1201 "
            pdb=" C18 BGI B1201 "
            pdb=" C20 BGI B1201 "
            pdb=" O30 BGI B1201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.97   -0.50 2.00e-01 2.50e+01 6.18e+00
  chirality pdb=" CA  MET A 416 "
            pdb=" N   MET A 416 "
            pdb=" C   MET A 416 "
            pdb=" CB  MET A 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 1695 not shown)

  Planarity restraints: 1798
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 539 "    0.014 2.00e-02 2.50e+03   2.88e-02 8.27e+00
        pdb=" C   GLU A 539 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   GLU A 539 "    0.019 2.00e-02 2.50e+03
        pdb=" N   HIS A 540 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 539 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.20e+00
        pdb=" C   GLU B 539 "    0.049 2.00e-02 2.50e+03
        pdb=" O   GLU B 539 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   HIS B 540 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A1025 "   -0.037 5.00e-02 4.00e+02   5.55e-02 4.93e+00
        pdb=" N   PRO A1026 "    0.096 5.00e-02 4.00e+02
        pdb=" CA  PRO A1026 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A1026 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1795 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1319
        2.74 -     3.28: 10267
        3.28 -     3.82: 16541
        3.82 -     4.36: 19582
        4.36 -     4.90: 34528
  Nonbonded interactions: 82237
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 602 "
            pdb=" O31 BGI B1201 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD2 ASP B 602 "
            pdb=" N15 BGI B1201 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" O   ILE A 818 "
            pdb=" OG  SER A 822 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   ILE B 818 "
            pdb=" OG  SER B 822 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OG  SER B 997 "
            pdb=" OE1 GLU B1000 "
     model   vdw
     2.371 3.040
  ... (remaining 82232 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: 0.05
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:             0.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.420
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     25.920
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7512
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      :  0.012   0.147  10624  Z= 0.762
  Angle     :  0.935   8.257  14488  Z= 0.580
  Chirality :  0.061   0.498   1698
  Planarity :  0.005   0.056   1798
  Dihedral  : 12.853  79.710   3582
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.22), residues: 1346
  helix:  0.48 (0.19), residues: 736
  sheet: -2.28 (0.33), residues: 150
  loop : -1.49 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 806 
 HIS   0.005   0.002   HIS B 965 
 PHE   0.021   0.002   PHE B 864 
 TYR   0.020   0.002   TYR A1008 
 ARG   0.005   0.001   ARG B 817 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 226
  time to evaluate  : 1.108 
Fit side-chains
REVERT: A  458 ASP cc_start: 0.8416 (p0) cc_final: 0.7894 (p0)
REVERT: A  466 LEU cc_start: 0.8415 (mt) cc_final: 0.8022 (mm)
REVERT: A  514 SER cc_start: 0.8389 (t) cc_final: 0.8011 (p)
REVERT: A  538 TYR cc_start: 0.7880 (m-80) cc_final: 0.7265 (m-80)
REVERT: A  548 ASN cc_start: 0.7618 (t0) cc_final: 0.6465 (p0)
REVERT: A  555 SER cc_start: 0.7594 (m) cc_final: 0.6852 (p)
REVERT: A  653 GLU cc_start: 0.8261 (tt0) cc_final: 0.8031 (tt0)
REVERT: A  745 ASP cc_start: 0.7872 (p0) cc_final: 0.7658 (p0)
REVERT: A  766 PHE cc_start: 0.7460 (m-10) cc_final: 0.7021 (t80)
REVERT: A  862 GLU cc_start: 0.8301 (tt0) cc_final: 0.8026 (tt0)
REVERT: A  936 TRP cc_start: 0.7925 (m100) cc_final: 0.7704 (m100)
REVERT: A 1067 TYR cc_start: 0.8317 (t80) cc_final: 0.7947 (t80)
REVERT: A 1088 PRO cc_start: 0.8397 (Cg_endo) cc_final: 0.8177 (Cg_exo)
REVERT: A 1103 TRP cc_start: 0.7698 (m100) cc_final: 0.7479 (m100)
REVERT: B  428 LEU cc_start: 0.8171 (mm) cc_final: 0.7961 (mm)
REVERT: B  433 PHE cc_start: 0.6810 (m-80) cc_final: 0.6371 (m-80)
REVERT: B  466 LEU cc_start: 0.8343 (mt) cc_final: 0.8080 (mp)
REVERT: B  471 ASP cc_start: 0.8134 (m-30) cc_final: 0.7597 (m-30)
REVERT: B  514 SER cc_start: 0.8419 (t) cc_final: 0.7770 (p)
REVERT: B  889 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7568 (mptt)
REVERT: B 1114 ILE cc_start: 0.8393 (mt) cc_final: 0.8144 (mm)
  outliers start: 2
  outliers final: 0
  residues processed: 228
  average time/residue: 1.0012
  time to fit residues: 249.7855
Evaluate side-chains
  144 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 116 optimal weight:    0.9980
   chunk 104 optimal weight:    5.9990
   chunk 58 optimal weight:    9.9990
   chunk 35 optimal weight:   10.0000
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 80 optimal weight:    0.9990
   chunk 125 optimal weight:    0.8980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
A 520 GLN
A 614 GLN
A 644 ASN
A 783 HIS
A 828 HIS
A 892 GLN
A 977 ASN
B 419 GLN
** B 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 783 HIS
B 828 HIS
B 977 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.155041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.121574 restraints weight = 12891.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3366 rms_B_bonded: 2.07
r_work: 0.3268 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10624  Z= 0.179
  Angle     :  0.490   6.476  14488  Z= 0.268
  Chirality :  0.040   0.174   1698
  Planarity :  0.004   0.064   1798
  Dihedral  :  5.157  32.061   1562
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  9.84 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.23), residues: 1346
  helix:  1.41 (0.19), residues: 770
  sheet: -1.37 (0.38), residues: 144
  loop : -1.46 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 840 
 HIS   0.008   0.001   HIS B 828 
 PHE   0.015   0.001   PHE B 766 
 TYR   0.020   0.001   TYR B 827 
 ARG   0.003   0.000   ARG A 759 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 163
  time to evaluate  : 1.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  466 LEU cc_start: 0.8425 (mt) cc_final: 0.8172 (mm)
REVERT: A  514 SER cc_start: 0.8643 (t) cc_final: 0.8356 (p)
REVERT: A  548 ASN cc_start: 0.8085 (t0) cc_final: 0.6672 (p0)
REVERT: A  555 SER cc_start: 0.7639 (m) cc_final: 0.6654 (p)
REVERT: A  745 ASP cc_start: 0.8094 (p0) cc_final: 0.7880 (p0)
REVERT: A  766 PHE cc_start: 0.7858 (m-10) cc_final: 0.7056 (t80)
REVERT: A  963 ASN cc_start: 0.8771 (m-40) cc_final: 0.8568 (m-40)
REVERT: A  977 ASN cc_start: 0.4654 (OUTLIER) cc_final: 0.3517 (t0)
REVERT: A 1060 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8646 (mt-10)
REVERT: A 1088 PRO cc_start: 0.8479 (Cg_endo) cc_final: 0.8259 (Cg_exo)
REVERT: B  428 LEU cc_start: 0.8175 (mm) cc_final: 0.7927 (mm)
REVERT: B  433 PHE cc_start: 0.7023 (m-80) cc_final: 0.6629 (m-80)
REVERT: B  454 MET cc_start: 0.8659 (ptm) cc_final: 0.8442 (ptm)
REVERT: B  466 LEU cc_start: 0.8098 (mt) cc_final: 0.7842 (mm)
REVERT: B  488 ASP cc_start: 0.8416 (p0) cc_final: 0.8195 (p0)
REVERT: B  553 GLU cc_start: 0.7629 (pt0) cc_final: 0.7303 (pp20)
REVERT: B  735 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8424 (ttmt)
REVERT: B  977 ASN cc_start: 0.4969 (OUTLIER) cc_final: 0.4468 (t0)
REVERT: B 1105 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7591 (p)
  outliers start: 22
  outliers final: 6
  residues processed: 176
  average time/residue: 0.8674
  time to fit residues: 169.1602
Evaluate side-chains
  137 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  977 ASN
Chi-restraints excluded: chain A residue 1060 GLU
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  537 VAL
Chi-restraints excluded: chain B residue  735 LYS
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue  977 ASN
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1117 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 88 optimal weight:    5.9990
   chunk 69 optimal weight:   20.0000
   chunk 94 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 86 optimal weight:    9.9990
   chunk 53 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 459 HIS
A 892 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.154581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.121122 restraints weight = 13030.255|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.05
r_work: 0.3230 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.060  10624  Z= 0.152
  Angle     :  0.454   8.843  14488  Z= 0.245
  Chirality :  0.039   0.166   1698
  Planarity :  0.004   0.051   1798
  Dihedral  :  4.886  33.936   1562
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.33 %
    Favored  : 85.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.23), residues: 1346
  helix:  1.76 (0.19), residues: 784
  sheet: -0.83 (0.41), residues: 142
  loop : -1.31 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B1103 
 HIS   0.005   0.001   HIS B 536 
 PHE   0.015   0.001   PHE B 881 
 TYR   0.019   0.001   TYR B 827 
 ARG   0.004   0.000   ARG A 759 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  466 LEU cc_start: 0.8330 (mt) cc_final: 0.8118 (mm)
REVERT: A  514 SER cc_start: 0.8652 (t) cc_final: 0.8352 (p)
REVERT: A  548 ASN cc_start: 0.8191 (t0) cc_final: 0.6710 (p0)
REVERT: A  555 SER cc_start: 0.7670 (m) cc_final: 0.6662 (p)
REVERT: A  892 GLN cc_start: 0.6918 (OUTLIER) cc_final: 0.6709 (mt0)
REVERT: A  963 ASN cc_start: 0.8705 (m-40) cc_final: 0.8499 (m-40)
REVERT: A 1060 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8551 (mt-10)
REVERT: A 1088 PRO cc_start: 0.8415 (Cg_endo) cc_final: 0.8152 (Cg_exo)
REVERT: B  433 PHE cc_start: 0.7006 (m-80) cc_final: 0.6764 (m-80)
REVERT: B  454 MET cc_start: 0.8645 (ptm) cc_final: 0.8407 (ptm)
REVERT: B  466 LEU cc_start: 0.8120 (mt) cc_final: 0.7869 (mm)
REVERT: B  553 GLU cc_start: 0.7628 (pt0) cc_final: 0.7302 (pp20)
REVERT: B  934 GLN cc_start: 0.7974 (tt0) cc_final: 0.7750 (mt0)
REVERT: B 1067 TYR cc_start: 0.8459 (t80) cc_final: 0.8173 (t80)
REVERT: B 1071 LYS cc_start: 0.7672 (OUTLIER) cc_final: 0.7404 (mttm)
REVERT: B 1105 VAL cc_start: 0.7957 (OUTLIER) cc_final: 0.7639 (p)
  outliers start: 26
  outliers final: 10
  residues processed: 140
  average time/residue: 0.8856
  time to fit residues: 137.3900
Evaluate side-chains
  128 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  892 GLN
Chi-restraints excluded: chain A residue 1060 GLU
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  735 LYS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1059 LEU
Chi-restraints excluded: chain B residue 1071 LYS
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1117 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 52 optimal weight:    0.0970
   chunk 136 optimal weight:    2.9990
   chunk 124 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 1 optimal weight:   10.0000
   chunk 21 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    1.2184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.152554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.118768 restraints weight = 12947.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.10
r_work: 0.3253 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10624  Z= 0.170
  Angle     :  0.442   5.983  14488  Z= 0.240
  Chirality :  0.039   0.162   1698
  Planarity :  0.003   0.050   1798
  Dihedral  :  4.764  35.343   1562
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.22 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.07 (0.23), residues: 1346
  helix:  1.93 (0.19), residues: 784
  sheet: -0.49 (0.41), residues: 142
  loop : -1.23 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 779 
 HIS   0.006   0.001   HIS B 536 
 PHE   0.014   0.001   PHE B 766 
 TYR   0.019   0.001   TYR B 827 
 ARG   0.002   0.000   ARG B 464 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 LEU cc_start: 0.8694 (mt) cc_final: 0.8474 (mm)
REVERT: A  514 SER cc_start: 0.8800 (t) cc_final: 0.8512 (p)
REVERT: A  548 ASN cc_start: 0.8339 (t0) cc_final: 0.7015 (p0)
REVERT: A  555 SER cc_start: 0.7816 (m) cc_final: 0.6869 (p)
REVERT: A  679 SER cc_start: 0.8966 (t) cc_final: 0.8732 (p)
REVERT: A  859 LYS cc_start: 0.8476 (mmmt) cc_final: 0.8070 (mppt)
REVERT: A  892 GLN cc_start: 0.6679 (OUTLIER) cc_final: 0.6218 (mp10)
REVERT: A 1060 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8666 (mt-10)
REVERT: A 1088 PRO cc_start: 0.8387 (Cg_endo) cc_final: 0.8104 (Cg_exo)
REVERT: B  466 LEU cc_start: 0.8406 (mt) cc_final: 0.8173 (mm)
REVERT: B  471 ASP cc_start: 0.8570 (m-30) cc_final: 0.8075 (m-30)
REVERT: B  516 LEU cc_start: 0.8331 (mm) cc_final: 0.8087 (mm)
REVERT: B  553 GLU cc_start: 0.7807 (pt0) cc_final: 0.7484 (pp20)
REVERT: B 1067 TYR cc_start: 0.8662 (t80) cc_final: 0.8409 (t80)
REVERT: B 1105 VAL cc_start: 0.8127 (OUTLIER) cc_final: 0.7797 (p)
  outliers start: 26
  outliers final: 14
  residues processed: 138
  average time/residue: 0.9101
  time to fit residues: 139.2094
Evaluate side-chains
  134 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  892 GLN
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1060 GLU
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  508 ARG
Chi-restraints excluded: chain B residue  537 VAL
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  735 LYS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue  938 MET
Chi-restraints excluded: chain B residue 1059 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 86 optimal weight:    2.9990
   chunk 69 optimal weight:   20.0000
   chunk 128 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0980
   chunk 130 optimal weight:    0.9980
   chunk 137 optimal weight:    3.9990
   chunk 16 optimal weight:   10.0000
   chunk 55 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   chunk 11 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A 706 HIS
A 892 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.118317 restraints weight = 12957.264|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.06
r_work: 0.3228 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10624  Z= 0.164
  Angle     :  0.435   5.903  14488  Z= 0.235
  Chirality :  0.039   0.162   1698
  Planarity :  0.003   0.050   1798
  Dihedral  :  4.677  35.359   1562
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.62 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.31 (0.23), residues: 1346
  helix:  2.16 (0.19), residues: 776
  sheet: -0.24 (0.42), residues: 142
  loop : -1.20 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 936 
 HIS   0.006   0.001   HIS B 536 
 PHE   0.019   0.001   PHE B 881 
 TYR   0.019   0.001   TYR B 827 
 ARG   0.002   0.000   ARG B 464 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  466 LEU cc_start: 0.8488 (mt) cc_final: 0.8258 (mm)
REVERT: A  514 SER cc_start: 0.8718 (t) cc_final: 0.8447 (p)
REVERT: A  548 ASN cc_start: 0.8362 (t0) cc_final: 0.6985 (p0)
REVERT: A  555 SER cc_start: 0.7724 (m) cc_final: 0.6694 (p)
REVERT: A  679 SER cc_start: 0.9035 (t) cc_final: 0.8776 (p)
REVERT: A  859 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8084 (mttp)
REVERT: A  892 GLN cc_start: 0.6714 (OUTLIER) cc_final: 0.6452 (mt0)
REVERT: A 1060 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8531 (mt-10)
REVERT: A 1088 PRO cc_start: 0.8297 (Cg_endo) cc_final: 0.8021 (Cg_exo)
REVERT: B  471 ASP cc_start: 0.8447 (m-30) cc_final: 0.7939 (m-30)
REVERT: B  516 LEU cc_start: 0.8238 (mm) cc_final: 0.8028 (mt)
REVERT: B  553 GLU cc_start: 0.7739 (pt0) cc_final: 0.7372 (pp20)
REVERT: B  684 GLU cc_start: 0.7903 (mp0) cc_final: 0.7639 (mp0)
REVERT: B  934 GLN cc_start: 0.8441 (mt0) cc_final: 0.8142 (mt0)
REVERT: B 1067 TYR cc_start: 0.8598 (t80) cc_final: 0.8342 (t80)
  outliers start: 29
  outliers final: 20
  residues processed: 143
  average time/residue: 0.8548
  time to fit residues: 136.1126
Evaluate side-chains
  140 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue  892 GLN
Chi-restraints excluded: chain A residue 1060 GLU
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  537 VAL
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  735 LYS
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1059 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 124 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 108 optimal weight:    8.9990
   chunk 86 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 132 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 34 optimal weight:    5.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 545 ASN
A 856 ASN
A 892 GLN
A 965 HIS
B 540 HIS
B 706 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.147231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.113514 restraints weight = 12768.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.99
r_work: 0.3230 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3112 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10624  Z= 0.329
  Angle     :  0.519   6.124  14488  Z= 0.280
  Chirality :  0.042   0.166   1698
  Planarity :  0.004   0.052   1798
  Dihedral  :  5.246  40.564   1562
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.31 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.23), residues: 1346
  helix:  1.98 (0.18), residues: 766
  sheet: -0.21 (0.41), residues: 142
  loop : -1.16 (0.27), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 490 
 HIS   0.007   0.002   HIS B 536 
 PHE   0.032   0.002   PHE A 881 
 TYR   0.020   0.002   TYR B 827 
 ARG   0.003   0.000   ARG B 464 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
REVERT: A  391 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6564 (pp)
REVERT: A  396 LEU cc_start: 0.2978 (OUTLIER) cc_final: 0.2739 (mm)
REVERT: A  440 TYR cc_start: 0.8076 (m-80) cc_final: 0.7671 (m-10)
REVERT: A  466 LEU cc_start: 0.8791 (mt) cc_final: 0.8587 (mm)
REVERT: A  514 SER cc_start: 0.9087 (t) cc_final: 0.8845 (p)
REVERT: A  548 ASN cc_start: 0.8614 (t0) cc_final: 0.7522 (p0)
REVERT: A  555 SER cc_start: 0.7759 (m) cc_final: 0.7133 (p)
REVERT: A  689 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7047 (tm-30)
REVERT: A  883 SER cc_start: 0.8979 (OUTLIER) cc_final: 0.8671 (m)
REVERT: A 1030 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6507 (tp30)
REVERT: A 1088 PRO cc_start: 0.8394 (Cg_endo) cc_final: 0.8096 (Cg_exo)
REVERT: B  471 ASP cc_start: 0.8508 (m-30) cc_final: 0.8118 (m-30)
REVERT: B  516 LEU cc_start: 0.8422 (mm) cc_final: 0.8168 (mt)
REVERT: B  934 GLN cc_start: 0.8779 (mt0) cc_final: 0.8527 (mt0)
REVERT: B 1067 TYR cc_start: 0.8783 (t80) cc_final: 0.8459 (t80)
  outliers start: 35
  outliers final: 19
  residues processed: 143
  average time/residue: 0.8786
  time to fit residues: 139.2100
Evaluate side-chains
  145 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  518 CYS
Chi-restraints excluded: chain A residue  689 GLN
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  883 SER
Chi-restraints excluded: chain A residue  888 VAL
Chi-restraints excluded: chain A residue 1105 VAL
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  735 LYS
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1059 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1120 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 106 optimal weight:    0.8980
   chunk 25 optimal weight:    0.2980
   chunk 16 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 11 optimal weight:    7.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.117774 restraints weight = 12770.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3388 rms_B_bonded: 2.03
r_work: 0.3289 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10624  Z= 0.130
  Angle     :  0.432   5.778  14488  Z= 0.232
  Chirality :  0.038   0.162   1698
  Planarity :  0.003   0.049   1798
  Dihedral  :  4.503  30.324   1562
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.90 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.56 (0.23), residues: 1346
  helix:  2.31 (0.18), residues: 766
  sheet:  0.04 (0.43), residues: 142
  loop : -0.97 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 779 
 HIS   0.005   0.001   HIS B 536 
 PHE   0.020   0.001   PHE B 881 
 TYR   0.018   0.001   TYR B 827 
 ARG   0.002   0.000   ARG A 759 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A  391 ILE cc_start: 0.6896 (OUTLIER) cc_final: 0.6684 (pp)
REVERT: A  396 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2664 (mm)
REVERT: A  440 TYR cc_start: 0.7781 (m-80) cc_final: 0.7484 (m-10)
REVERT: A  466 LEU cc_start: 0.8857 (mt) cc_final: 0.8625 (mm)
REVERT: A  514 SER cc_start: 0.9023 (t) cc_final: 0.8787 (p)
REVERT: A  548 ASN cc_start: 0.8527 (t0) cc_final: 0.7399 (p0)
REVERT: A  555 SER cc_start: 0.7842 (m) cc_final: 0.7032 (p)
REVERT: A  700 MET cc_start: 0.3670 (tmt) cc_final: 0.2478 (tpt)
REVERT: A  735 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8620 (mmmt)
REVERT: A  883 SER cc_start: 0.8948 (OUTLIER) cc_final: 0.8742 (m)
REVERT: A 1088 PRO cc_start: 0.8351 (Cg_endo) cc_final: 0.8065 (Cg_exo)
REVERT: B  458 ASP cc_start: 0.8447 (p0) cc_final: 0.8081 (p0)
REVERT: B  471 ASP cc_start: 0.8608 (m-30) cc_final: 0.8109 (m-30)
REVERT: B  516 LEU cc_start: 0.8443 (mm) cc_final: 0.8184 (mm)
REVERT: B  934 GLN cc_start: 0.8744 (mt0) cc_final: 0.8515 (mt0)
REVERT: B 1067 TYR cc_start: 0.8797 (t80) cc_final: 0.8503 (t80)
  outliers start: 28
  outliers final: 14
  residues processed: 149
  average time/residue: 0.8708
  time to fit residues: 143.9195
Evaluate side-chains
  144 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  543 MET
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  883 SER
Chi-restraints excluded: chain A residue 1121 ILE
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1105 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 78 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 23 optimal weight:    7.9990
   chunk 15 optimal weight:    5.9990
   chunk 55 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 856 ASN
A 892 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.115476 restraints weight = 12688.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.02
r_work: 0.3267 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3813

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10624  Z= 0.198
  Angle     :  0.462   7.644  14488  Z= 0.247
  Chirality :  0.039   0.159   1698
  Planarity :  0.003   0.050   1798
  Dihedral  :  4.761  37.116   1562
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.00 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.23), residues: 1346
  helix:  2.31 (0.18), residues: 766
  sheet:  0.13 (0.43), residues: 142
  loop : -0.95 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 806 
 HIS   0.006   0.001   HIS B 536 
 PHE   0.024   0.001   PHE A 881 
 TYR   0.018   0.001   TYR B 827 
 ARG   0.003   0.000   ARG A 759 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 129
  time to evaluate  : 1.296 
Fit side-chains
   revert: symmetry clash
REVERT: A  391 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6637 (pp)
REVERT: A  396 LEU cc_start: 0.3007 (OUTLIER) cc_final: 0.2788 (mm)
REVERT: A  440 TYR cc_start: 0.7843 (m-80) cc_final: 0.7510 (m-10)
REVERT: A  466 LEU cc_start: 0.8836 (mt) cc_final: 0.8609 (mm)
REVERT: A  514 SER cc_start: 0.9004 (t) cc_final: 0.8790 (p)
REVERT: A  543 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.7483 (ttt)
REVERT: A  548 ASN cc_start: 0.8542 (t0) cc_final: 0.7621 (p0)
REVERT: A  555 SER cc_start: 0.7782 (m) cc_final: 0.7160 (p)
REVERT: A  700 MET cc_start: 0.3645 (tmt) cc_final: 0.2473 (tpt)
REVERT: A  735 LYS cc_start: 0.8881 (ttmm) cc_final: 0.8586 (mmmt)
REVERT: A  883 SER cc_start: 0.8998 (OUTLIER) cc_final: 0.8690 (m)
REVERT: A 1030 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6599 (tp30)
REVERT: A 1088 PRO cc_start: 0.8382 (Cg_endo) cc_final: 0.8097 (Cg_exo)
REVERT: B  458 ASP cc_start: 0.8531 (p0) cc_final: 0.8192 (p0)
REVERT: B  466 LEU cc_start: 0.8700 (mm) cc_final: 0.8381 (mm)
REVERT: B  471 ASP cc_start: 0.8511 (m-30) cc_final: 0.8132 (m-30)
REVERT: B  516 LEU cc_start: 0.8446 (mm) cc_final: 0.8183 (mm)
REVERT: B 1067 TYR cc_start: 0.8779 (t80) cc_final: 0.8507 (t80)
  outliers start: 30
  outliers final: 16
  residues processed: 146
  average time/residue: 0.9073
  time to fit residues: 146.9082
Evaluate side-chains
  147 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  543 MET
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain A residue  883 SER
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  412 GLU
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1059 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 12 optimal weight:    6.9990
   chunk 83 optimal weight:    4.9990
   chunk 122 optimal weight:    0.0670
   chunk 105 optimal weight:    3.9990
   chunk 50 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 132 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 9 optimal weight:    9.9990
   overall best weight:    1.9922

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

Flipped N/Q/H residues before XYZ refinement:
A 892 GLN
B 658 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.145849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112332 restraints weight = 12832.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3309 rms_B_bonded: 2.05
r_work: 0.3210 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3092 rms_B_bonded: 4.19 restraints_weight: 0.2500
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10624  Z= 0.243
  Angle     :  0.491   7.616  14488  Z= 0.263
  Chirality :  0.040   0.163   1698
  Planarity :  0.003   0.050   1798
  Dihedral  :  4.998  38.398   1562
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 16.90 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.23), residues: 1346
  helix:  2.21 (0.19), residues: 768
  sheet:  0.22 (0.42), residues: 142
  loop : -0.95 (0.27), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 806 
 HIS   0.006   0.001   HIS B 536 
 PHE   0.028   0.001   PHE B 881 
 TYR   0.024   0.001   TYR A1067 
 ARG   0.005   0.000   ARG A 759 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  391 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6602 (pp)
REVERT: A  396 LEU cc_start: 0.3030 (OUTLIER) cc_final: 0.2789 (mm)
REVERT: A  440 TYR cc_start: 0.8113 (m-80) cc_final: 0.7686 (m-10)
REVERT: A  466 LEU cc_start: 0.8821 (mt) cc_final: 0.8620 (mm)
REVERT: A  514 SER cc_start: 0.9111 (t) cc_final: 0.8909 (p)
REVERT: A  543 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7114 (mtp)
REVERT: A  548 ASN cc_start: 0.8526 (t0) cc_final: 0.8054 (p0)
REVERT: A  700 MET cc_start: 0.3607 (tmt) cc_final: 0.2432 (tpt)
REVERT: A  735 LYS cc_start: 0.8886 (ttmm) cc_final: 0.8559 (mmmt)
REVERT: A  883 SER cc_start: 0.8946 (p) cc_final: 0.8633 (m)
REVERT: A 1030 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6572 (tp30)
REVERT: A 1088 PRO cc_start: 0.8393 (Cg_endo) cc_final: 0.8126 (Cg_exo)
REVERT: B  471 ASP cc_start: 0.8495 (m-30) cc_final: 0.8113 (m-30)
REVERT: B  516 LEU cc_start: 0.8466 (mm) cc_final: 0.8198 (mm)
REVERT: B 1067 TYR cc_start: 0.8842 (t80) cc_final: 0.8535 (t80)
  outliers start: 23
  outliers final: 16
  residues processed: 142
  average time/residue: 0.8693
  time to fit residues: 137.5433
Evaluate side-chains
  137 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  396 LEU
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  543 MET
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  764 SER
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  543 MET
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1059 LEU
Chi-restraints excluded: chain B residue 1105 VAL
Chi-restraints excluded: chain B residue 1120 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 129 optimal weight:    7.9990
   chunk 56 optimal weight:    0.7980
   chunk 66 optimal weight:    0.9980
   chunk 107 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
A 892 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.117231 restraints weight = 12723.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 2.02
r_work: 0.3284 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3167 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10624  Z= 0.149
  Angle     :  0.448   7.959  14488  Z= 0.239
  Chirality :  0.039   0.158   1698
  Planarity :  0.003   0.047   1798
  Dihedral  :  4.517  31.995   1562
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.40 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.23), residues: 1346
  helix:  2.42 (0.18), residues: 766
  sheet:  0.45 (0.44), residues: 142
  loop : -0.89 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 806 
 HIS   0.005   0.001   HIS B 536 
 PHE   0.026   0.001   PHE A 881 
 TYR   0.019   0.001   TYR B 827 
 ARG   0.003   0.000   ARG A 759 

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

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

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2692 Ramachandran restraints generated.
    1346 Oldfield, 0 Emsley, 1346 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  440 TYR cc_start: 0.7885 (m-80) cc_final: 0.7553 (m-10)
REVERT: A  466 LEU cc_start: 0.8852 (mt) cc_final: 0.8611 (mm)
REVERT: A  514 SER cc_start: 0.9018 (t) cc_final: 0.8813 (p)
REVERT: A  543 MET cc_start: 0.7752 (OUTLIER) cc_final: 0.7185 (mtp)
REVERT: A  548 ASN cc_start: 0.8594 (t0) cc_final: 0.8143 (p0)
REVERT: A  700 MET cc_start: 0.3754 (tmt) cc_final: 0.2444 (tpt)
REVERT: A  735 LYS cc_start: 0.8942 (ttmm) cc_final: 0.8666 (mmmt)
REVERT: A  883 SER cc_start: 0.8975 (p) cc_final: 0.8710 (m)
REVERT: A 1030 GLU cc_start: 0.7267 (mt-10) cc_final: 0.6610 (tp30)
REVERT: A 1088 PRO cc_start: 0.8382 (Cg_endo) cc_final: 0.8137 (Cg_exo)
REVERT: B  458 ASP cc_start: 0.8489 (p0) cc_final: 0.8140 (p0)
REVERT: B  466 LEU cc_start: 0.8693 (mm) cc_final: 0.8400 (mm)
REVERT: B  471 ASP cc_start: 0.8498 (m-30) cc_final: 0.8138 (m-30)
REVERT: B  516 LEU cc_start: 0.8462 (mm) cc_final: 0.8189 (mm)
REVERT: B 1067 TYR cc_start: 0.8805 (t80) cc_final: 0.8517 (t80)
  outliers start: 19
  outliers final: 13
  residues processed: 143
  average time/residue: 0.8669
  time to fit residues: 137.9016
Evaluate side-chains
  136 residues out of total 1258 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  543 MET
Chi-restraints excluded: chain A residue  656 MET
Chi-restraints excluded: chain A residue  673 VAL
Chi-restraints excluded: chain A residue  861 THR
Chi-restraints excluded: chain B residue  391 ILE
Chi-restraints excluded: chain B residue  446 THR
Chi-restraints excluded: chain B residue  601 LEU
Chi-restraints excluded: chain B residue  649 SER
Chi-restraints excluded: chain B residue  673 VAL
Chi-restraints excluded: chain B residue  828 HIS
Chi-restraints excluded: chain B residue  833 VAL
Chi-restraints excluded: chain B residue  861 THR
Chi-restraints excluded: chain B residue 1105 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 47 optimal weight:    0.0270
   chunk 36 optimal weight:    0.5980
   chunk 117 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 27 optimal weight:    4.9990
   chunk 120 optimal weight:    6.9990
   chunk 62 optimal weight:    0.5980
   chunk 73 optimal weight:    0.0980
   overall best weight:    0.3438

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

Flipped N/Q/H residues before XYZ refinement:
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 892 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.157428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.125753 restraints weight = 12853.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 1.92
r_work: 0.3342 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10624  Z= 0.111
  Angle     :  0.424   8.166  14488  Z= 0.226
  Chirality :  0.038   0.147   1698
  Planarity :  0.003   0.046   1798
  Dihedral  :  4.114  25.173   1562
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 17.89 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.23), residues: 1346
  helix:  2.50 (0.18), residues: 778
  sheet:  0.64 (0.44), residues: 142
  loop : -0.84 (0.28), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 806 
 HIS   0.004   0.001   HIS A 536 
 PHE   0.030   0.001   PHE B 881 
 TYR   0.022   0.001   TYR A1067 
 ARG   0.001   0.000   ARG B 464 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7036.92 seconds
wall clock time: 124 minutes 50.86 seconds (7490.86 seconds total)