Starting phenix.real_space_refine
on Wed Mar 12 07:39:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6caa_7441/03_2025/6caa_7441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6caa_7441/03_2025/6caa_7441.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6caa_7441/03_2025/6caa_7441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6caa_7441/03_2025/6caa_7441.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6caa_7441/03_2025/6caa_7441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6caa_7441/03_2025/6caa_7441.cif"
  }
  resolution = 3.9
  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=   0.010
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      42      5.16       5
     C    5044      2.51       5
     N    1158      2.21       5
     O    1264      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7508
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3754
          Classifications: {'peptide': 477}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 19, 'TRANS': 457}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 23
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 20
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.44, per 1000 atoms: 0.86
  Number of scatterers: 7508
  At special positions: 0
  Unit cell: (131.92, 77.52, 93.84, 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      42     16.00
     O    1264      8.00
     N    1158      7.00
     C    5044      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: 1.56
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1812

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 0 sheets defined
      67.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 402 through 410
      removed outlier: 4.307A  pdb=" N   ARG A 408 " --> pdb=" O   LYS A 404 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS A 409 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 418
      removed outlier: 3.708A  pdb=" N   PHE A 417 " --> pdb=" O   PHE A 413 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   TYR A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 445
      removed outlier: 3.587A  pdb=" N   SER A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE A 429 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU A 430 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU A 434 " --> pdb=" O   LEU A 430 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   GLY A 445 " --> pdb=" O   ILE A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 450
      removed outlier: 3.712A  pdb=" N   ASP A 449 " --> pdb=" O   LEU A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 470
      removed outlier: 3.813A  pdb=" N   LEU A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY A 468 " --> pdb=" O   THR A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 499
      removed outlier: 3.667A  pdb=" N   LEU A 489 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 528
      removed outlier: 3.707A  pdb=" N   TRP A 512 " --> pdb=" O   GLU A 508 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP A 516 " --> pdb=" O   TRP A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 536
    Processing helix  chain 'A' and resid 541 through 567
      removed outlier: 4.058A  pdb=" N   LEU A 547 " --> pdb=" O   GLY A 543 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   PHE A 550 " --> pdb=" O   SER A 546 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET A 560 " --> pdb=" O   ALA A 556 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LEU A 563 " --> pdb=" O   LYS A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 669
      removed outlier: 3.790A  pdb=" N   ILE A 654 " --> pdb=" O   LEU A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 672
      No H-bonds generated for 'chain 'A' and resid 670 through 672'
    Processing helix  chain 'A' and resid 676 through 684
      removed outlier: 4.194A  pdb=" N   LEU A 682 " --> pdb=" O   THR A 678 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
      removed outlier: 3.616A  pdb=" N   PHE A 695 " --> pdb=" O   SER A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 740
    Processing helix  chain 'A' and resid 740 through 764
      removed outlier: 3.542A  pdb=" N   ALA A 744 " --> pdb=" O   ALA A 740 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE A 749 " --> pdb=" O   LEU A 745 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU A 750 " --> pdb=" O   LEU A 746 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   PHE A 752 " --> pdb=" O   THR A 748 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLN A 756 " --> pdb=" O   PHE A 752 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE A 757 " --> pdb=" O   MET A 753 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE A 761 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   VAL A 762 " --> pdb=" O   THR A 758 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ARG A 764 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 776 through 792
      removed outlier: 3.635A  pdb=" N   ALA A 783 " --> pdb=" O   LEU A 779 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL A 787 " --> pdb=" O   ALA A 783 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE A 788 " --> pdb=" O   ILE A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 811
      removed outlier: 3.506A  pdb=" N   ASP A 809 " --> pdb=" O   ILE A 805 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   SER A 810 " --> pdb=" O   ALA A 806 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU A 811 " --> pdb=" O   HIS A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 845
      removed outlier: 3.958A  pdb=" N   VAL A 839 " --> pdb=" O   THR A 835 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   PHE A 840 " --> pdb=" O   GLY A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 855
      removed outlier: 4.067A  pdb=" N   PHE A 855 " --> pdb=" O   PRO A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 873
      removed outlier: 3.821A  pdb=" N   LEU A 861 " --> pdb=" O   PRO A 857 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   GLY A 863 " --> pdb=" O   PRO A 859 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   LEU A 873 " --> pdb=" O   GLY A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 883
      removed outlier: 4.041A  pdb=" N   ASP A 880 " --> pdb=" O   VAL A 876 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG A 881 " --> pdb=" O   GLN A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 902 through 926
      removed outlier: 3.816A  pdb=" N   VAL A 906 " --> pdb=" O   PRO A 902 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS A 907 " --> pdb=" O   LEU A 903 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE A 911 " --> pdb=" O   HIS A 907 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 917 " --> pdb=" O   GLN A 913 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A 919 " --> pdb=" O   LEU A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 946
      removed outlier: 3.540A  pdb=" N   ALA A 938 " --> pdb=" O   VAL A 934 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LEU A 939 " --> pdb=" O   MET A 935 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   VAL A 942 " --> pdb=" O   ALA A 938 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ARG A 943 " --> pdb=" O   LEU A 939 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS A 944 " --> pdb=" O   VAL A 940 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 949
      No H-bonds generated for 'chain 'A' and resid 947 through 949'
    Processing helix  chain 'B' and resid 402 through 410
      removed outlier: 4.307A  pdb=" N   ARG B 408 " --> pdb=" O   LYS B 404 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LYS B 409 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 418
      removed outlier: 3.707A  pdb=" N   PHE B 417 " --> pdb=" O   PHE B 413 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   TYR B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 445
      removed outlier: 3.587A  pdb=" N   SER B 427 " --> pdb=" O   ILE B 423 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE B 429 " --> pdb=" O   ALA B 425 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LEU B 430 " --> pdb=" O   LEU B 426 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU B 434 " --> pdb=" O   LEU B 430 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   PHE B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY B 445 " --> pdb=" O   ILE B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 450
      removed outlier: 3.711A  pdb=" N   ASP B 449 " --> pdb=" O   LEU B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 470
      removed outlier: 3.813A  pdb=" N   LEU B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL B 466 " --> pdb=" O   LEU B 462 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY B 468 " --> pdb=" O   THR B 464 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 485 through 499
      removed outlier: 3.668A  pdb=" N   LEU B 489 " --> pdb=" O   THR B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 528
      removed outlier: 3.708A  pdb=" N   TRP B 512 " --> pdb=" O   GLU B 508 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   TRP B 516 " --> pdb=" O   TRP B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 536
    Processing helix  chain 'B' and resid 541 through 567
      removed outlier: 4.059A  pdb=" N   LEU B 547 " --> pdb=" O   GLY B 543 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   PHE B 550 " --> pdb=" O   SER B 546 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   MET B 560 " --> pdb=" O   ALA B 556 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU B 563 " --> pdb=" O   LYS B 559 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 669
      removed outlier: 3.790A  pdb=" N   ILE B 654 " --> pdb=" O   LEU B 650 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 670 through 672
      No H-bonds generated for 'chain 'B' and resid 670 through 672'
    Processing helix  chain 'B' and resid 676 through 684
      removed outlier: 4.194A  pdb=" N   LEU B 682 " --> pdb=" O   THR B 678 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 702
      removed outlier: 3.615A  pdb=" N   PHE B 695 " --> pdb=" O   SER B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 736 through 740
    Processing helix  chain 'B' and resid 740 through 764
      removed outlier: 3.542A  pdb=" N   ALA B 744 " --> pdb=" O   ALA B 740 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   ILE B 749 " --> pdb=" O   LEU B 745 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   LEU B 750 " --> pdb=" O   LEU B 746 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   PHE B 752 " --> pdb=" O   THR B 748 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN B 756 " --> pdb=" O   PHE B 752 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   ILE B 757 " --> pdb=" O   MET B 753 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ILE B 761 " --> pdb=" O   ILE B 757 " (cutoff:3.500A)
      removed outlier: 4.883A  pdb=" N   VAL B 762 " --> pdb=" O   THR B 758 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ARG B 764 " --> pdb=" O   VAL B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 792
      removed outlier: 3.635A  pdb=" N   ALA B 783 " --> pdb=" O   LEU B 779 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL B 787 " --> pdb=" O   ALA B 783 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   ILE B 788 " --> pdb=" O   ILE B 784 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 802 through 811
      removed outlier: 3.506A  pdb=" N   ASP B 809 " --> pdb=" O   ILE B 805 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   SER B 810 " --> pdb=" O   ALA B 806 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LEU B 811 " --> pdb=" O   HIS B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 834 through 845
      removed outlier: 3.958A  pdb=" N   VAL B 839 " --> pdb=" O   THR B 835 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   PHE B 840 " --> pdb=" O   GLY B 836 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 850 through 855
      removed outlier: 4.066A  pdb=" N   PHE B 855 " --> pdb=" O   PRO B 851 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 857 through 873
      removed outlier: 3.821A  pdb=" N   LEU B 861 " --> pdb=" O   PRO B 857 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B 863 " --> pdb=" O   PRO B 859 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU B 873 " --> pdb=" O   GLY B 869 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 876 through 883
      removed outlier: 4.041A  pdb=" N   ASP B 880 " --> pdb=" O   VAL B 876 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ARG B 881 " --> pdb=" O   GLN B 877 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 902 through 926
      removed outlier: 3.816A  pdb=" N   VAL B 906 " --> pdb=" O   PRO B 902 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   HIS B 907 " --> pdb=" O   LEU B 903 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   PHE B 911 " --> pdb=" O   HIS B 907 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B 917 " --> pdb=" O   GLN B 913 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 919 " --> pdb=" O   LEU B 915 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 933 through 946
      removed outlier: 3.540A  pdb=" N   ALA B 938 " --> pdb=" O   VAL B 934 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LEU B 939 " --> pdb=" O   MET B 935 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL B 942 " --> pdb=" O   ALA B 938 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   ARG B 943 " --> pdb=" O   LEU B 939 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS B 944 " --> pdb=" O   VAL B 940 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 947 through 949
      No H-bonds generated for 'chain 'B' and resid 947 through 949'

    342 hydrogen bonds defined for protein.
    1020 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: 1.63

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2090
        1.34 -     1.45: 1412
        1.45 -     1.57: 4120
        1.57 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 7694
  Sorted by residual:
  bond pdb=" CA  ALA A 410 "
       pdb=" C   ALA A 410 "
    ideal  model  delta    sigma   weight residual
    1.522  1.554 -0.032 1.26e-02 6.30e+03 6.65e+00
  bond pdb=" CA  ALA B 410 "
       pdb=" C   ALA B 410 "
    ideal  model  delta    sigma   weight residual
    1.522  1.554 -0.032 1.26e-02 6.30e+03 6.51e+00
  bond pdb=" CG1 ILE A 432 "
       pdb=" CD1 ILE A 432 "
    ideal  model  delta    sigma   weight residual
    1.513  1.425  0.088 3.90e-02 6.57e+02 5.07e+00
  bond pdb=" CG1 ILE B 432 "
       pdb=" CD1 ILE B 432 "
    ideal  model  delta    sigma   weight residual
    1.513  1.426  0.087 3.90e-02 6.57e+02 5.03e+00
  bond pdb=" CG  MET B 560 "
       pdb=" SD  MET B 560 "
    ideal  model  delta    sigma   weight residual
    1.803  1.752  0.051 2.50e-02 1.60e+03 4.19e+00
  ... (remaining 7689 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.85: 10215
        3.85 -     7.70: 209
        7.70 -    11.55: 26
       11.55 -    15.40: 4
       15.40 -    19.26: 2
  Bond angle restraints: 10456
  Sorted by residual:
  angle pdb=" CA  LEU B 898 "
        pdb=" CB  LEU B 898 "
        pdb=" CG  LEU B 898 "
      ideal   model   delta    sigma   weight residual
     116.30  135.56  -19.26 3.50e+00 8.16e-02 3.03e+01
  angle pdb=" CA  LEU A 898 "
        pdb=" CB  LEU A 898 "
        pdb=" CG  LEU A 898 "
      ideal   model   delta    sigma   weight residual
     116.30  135.55  -19.25 3.50e+00 8.16e-02 3.02e+01
  angle pdb=" C   PRO A 646 "
        pdb=" N   ASP A 647 "
        pdb=" CA  ASP A 647 "
      ideal   model   delta    sigma   weight residual
     121.54  130.44   -8.90 1.91e+00 2.74e-01 2.17e+01
  angle pdb=" C   PRO B 646 "
        pdb=" N   ASP B 647 "
        pdb=" CA  ASP B 647 "
      ideal   model   delta    sigma   weight residual
     121.54  130.43   -8.89 1.91e+00 2.74e-01 2.17e+01
  angle pdb=" N   TYR A 897 "
        pdb=" CA  TYR A 897 "
        pdb=" CB  TYR A 897 "
      ideal   model   delta    sigma   weight residual
     114.17  108.91    5.26 1.14e+00 7.69e-01 2.13e+01
  ... (remaining 10451 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.77: 4174
       16.77 -    33.53: 256
       33.53 -    50.30: 58
       50.30 -    67.07: 2
       67.07 -    83.83: 8
  Dihedral angle restraints: 4498
    sinusoidal: 1708
      harmonic: 2790
  Sorted by residual:
  dihedral pdb=" CA  PRO B 888 "
           pdb=" C   PRO B 888 "
           pdb=" N   LEU B 889 "
           pdb=" CA  LEU B 889 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.27  -29.73     0      5.00e+00 4.00e-02 3.54e+01
  dihedral pdb=" CA  PRO A 888 "
           pdb=" C   PRO A 888 "
           pdb=" N   LEU A 889 "
           pdb=" CA  LEU A 889 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.31  -29.69     0      5.00e+00 4.00e-02 3.53e+01
  dihedral pdb=" CA  GLU B 541 "
           pdb=" C   GLU B 541 "
           pdb=" N   GLU B 542 "
           pdb=" CA  GLU B 542 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.61   29.39     0      5.00e+00 4.00e-02 3.45e+01
  ... (remaining 4495 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 1002
       0.080 -    0.159: 220
       0.159 -    0.238: 34
       0.238 -    0.318: 2
       0.318 -    0.397: 2
  Chirality restraints: 1260
  Sorted by residual:
  chirality pdb=" CB  ILE A 710 "
            pdb=" CA  ILE A 710 "
            pdb=" CG1 ILE A 710 "
            pdb=" CG2 ILE A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.40 2.00e-01 2.50e+01 3.95e+00
  chirality pdb=" CB  ILE B 710 "
            pdb=" CA  ILE B 710 "
            pdb=" CG1 ILE B 710 "
            pdb=" CG2 ILE B 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.25    0.40 2.00e-01 2.50e+01 3.95e+00
  chirality pdb=" CA  ASP A 647 "
            pdb=" N   ASP A 647 "
            pdb=" C   ASP A 647 "
            pdb=" CB  ASP A 647 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 1257 not shown)

  Planarity restraints: 1260
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 829 "    0.015 2.00e-02 2.50e+03   3.04e-02 9.26e+00
        pdb=" C   VAL A 829 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   VAL A 829 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG A 830 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 829 "    0.015 2.00e-02 2.50e+03   3.03e-02 9.15e+00
        pdb=" C   VAL B 829 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   VAL B 829 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ARG B 830 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 850 "   -0.047 5.00e-02 4.00e+02   7.02e-02 7.88e+00
        pdb=" N   PRO A 851 "    0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 851 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 851 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1257 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 32
        2.49 -     3.09: 5123
        3.09 -     3.69: 11730
        3.69 -     4.30: 15665
        4.30 -     4.90: 24962
  Nonbonded interactions: 57512
  Sorted by model distance:
  nonbonded pdb=" O   TYR B 674 "
            pdb=" CD1 PHE B 675 "
     model   vdw
     1.886 3.340
  nonbonded pdb=" O   TYR A 674 "
            pdb=" CD1 PHE A 675 "
     model   vdw
     1.886 3.340
  nonbonded pdb=" O   GLN A 424 "
            pdb=" OG  SER A 427 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" O   GLN B 424 "
            pdb=" OG  SER B 427 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   ILE A 922 "
            pdb=" OG  SER A 925 "
     model   vdw
     2.311 3.040
  ... (remaining 57507 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: 0.03
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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     20.820
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  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:2.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
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      :  0.009   0.088   7694  Z= 0.539
  Angle     :  1.328  19.256  10456  Z= 0.670
  Chirality :  0.068   0.397   1260
  Planarity :  0.009   0.070   1260
  Dihedral  : 12.406  83.834   2686
  Min Nonbonded Distance : 1.886

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.01 %
    Favored  : 86.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.36 %
    Favored  : 90.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -6.23 (0.18), residues: 938
  helix: -4.19 (0.11), residues: 546
  sheet:  None (None), residues: 0
  loop : -3.91 (0.27), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 512 
 HIS   0.017   0.004   HIS B 900 
 PHE   0.042   0.004   PHE A 855 
 TYR   0.017   0.003   TYR B 797 
 ARG   0.006   0.001   ARG A 830 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.941 
Fit side-chains
REVERT: A  430 LEU cc_start: 0.8199 (pp) cc_final: 0.7721 (tp)
REVERT: A  454 MET cc_start: 0.4217 (mmm) cc_final: 0.2570 (tmm)
REVERT: A  473 LEU cc_start: 0.7235 (mt) cc_final: 0.6835 (mt)
REVERT: A  493 ARG cc_start: 0.7963 (mtt180) cc_final: 0.7301 (mmp-170)
REVERT: A  494 LEU cc_start: 0.8783 (tp) cc_final: 0.8487 (tp)
REVERT: A  502 ASN cc_start: 0.8454 (t0) cc_final: 0.7791 (t0)
REVERT: A  506 TYR cc_start: 0.7558 (t80) cc_final: 0.7358 (t80)
REVERT: A  699 ASP cc_start: 0.8197 (t0) cc_final: 0.7865 (t0)
REVERT: A  754 ASP cc_start: 0.8774 (t0) cc_final: 0.8253 (t0)
REVERT: A  858 MET cc_start: 0.9184 (tpt) cc_final: 0.8545 (tpp)
REVERT: A  887 MET cc_start: 0.7605 (ttt) cc_final: 0.7404 (tmm)
REVERT: A  924 LYS cc_start: 0.8493 (tppp) cc_final: 0.8213 (tptt)
REVERT: B  430 LEU cc_start: 0.8241 (pp) cc_final: 0.7772 (tp)
REVERT: B  454 MET cc_start: 0.4111 (mmm) cc_final: 0.2414 (tmm)
REVERT: B  473 LEU cc_start: 0.7246 (mt) cc_final: 0.6852 (mt)
REVERT: B  493 ARG cc_start: 0.7972 (mtt180) cc_final: 0.7349 (mmp-170)
REVERT: B  494 LEU cc_start: 0.8779 (tp) cc_final: 0.8482 (tp)
REVERT: B  502 ASN cc_start: 0.8373 (t0) cc_final: 0.7690 (t0)
REVERT: B  506 TYR cc_start: 0.7494 (t80) cc_final: 0.7282 (t80)
REVERT: B  699 ASP cc_start: 0.8233 (t0) cc_final: 0.7883 (t0)
REVERT: B  754 ASP cc_start: 0.8775 (t0) cc_final: 0.8384 (t0)
REVERT: B  854 LYS cc_start: 0.8779 (tmtm) cc_final: 0.8479 (tppt)
REVERT: B  858 MET cc_start: 0.9170 (tpt) cc_final: 0.8535 (tpp)
REVERT: B  887 MET cc_start: 0.7674 (ttt) cc_final: 0.7441 (tmm)
REVERT: B  924 LYS cc_start: 0.8491 (tppp) cc_final: 0.8212 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.2236
  time to fit residues: 67.1381
Evaluate side-chains
  131 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.824 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
A 763 ASN
A 767 HIS
B 572 ASN
B 763 ASN
B 767 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.121038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.096510 restraints weight = 15016.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.098286 restraints weight = 10695.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099428 restraints weight = 8612.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7694  Z= 0.211
  Angle     :  0.808  10.000  10456  Z= 0.407
  Chirality :  0.046   0.189   1260
  Planarity :  0.007   0.061   1260
  Dihedral  :  6.546  23.624   1002
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.94 %
    Favored  : 88.06 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 13.92 %
    Favored  : 82.27 %
  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: -4.18 (0.22), residues: 938
  helix: -2.12 (0.17), residues: 586
  sheet:  None (None), residues: 0
  loop : -3.82 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 953 
 PHE   0.015   0.002   PHE B 531 
 TYR   0.035   0.002   TYR B 577 
 ARG   0.005   0.001   ARG B 830 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 167
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A  413 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7528 (m-80)
REVERT: A  430 LEU cc_start: 0.8832 (pp) cc_final: 0.8290 (tp)
REVERT: A  454 MET cc_start: 0.4368 (mmm) cc_final: 0.3857 (tpt)
REVERT: A  542 GLU cc_start: 0.7795 (mp0) cc_final: 0.6805 (mp0)
REVERT: A  699 ASP cc_start: 0.8305 (t0) cc_final: 0.8040 (t0)
REVERT: A  808 ILE cc_start: 0.9229 (pt) cc_final: 0.9001 (tp)
REVERT: A  924 LYS cc_start: 0.8412 (tppp) cc_final: 0.8087 (tptt)
REVERT: B  413 PHE cc_start: 0.8162 (OUTLIER) cc_final: 0.7489 (m-80)
REVERT: B  430 LEU cc_start: 0.8816 (pp) cc_final: 0.8296 (tp)
REVERT: B  454 MET cc_start: 0.4325 (mmm) cc_final: 0.3812 (tpt)
REVERT: B  542 GLU cc_start: 0.7822 (mp0) cc_final: 0.6723 (mp0)
REVERT: B  699 ASP cc_start: 0.8286 (t0) cc_final: 0.8010 (t0)
REVERT: B  808 ILE cc_start: 0.9216 (pt) cc_final: 0.9003 (tp)
REVERT: B  924 LYS cc_start: 0.8489 (tppp) cc_final: 0.8068 (tptt)
  outliers start: 31
  outliers final: 13
  residues processed: 190
  average time/residue: 0.1682
  time to fit residues: 44.5315
Evaluate side-chains
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  546 SER
Chi-restraints excluded: chain A residue  675 PHE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  546 SER
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  801 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.4980
   chunk 86 optimal weight:    0.5980
   chunk 52 optimal weight:    0.0270
   chunk 73 optimal weight:    0.2980
   chunk 39 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 572 ASN
B 422 ASN
B 572 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.123985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.098666 restraints weight = 14962.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100493 restraints weight = 10451.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.101951 restraints weight = 8305.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7694  Z= 0.176
  Angle     :  0.759  11.088  10456  Z= 0.372
  Chirality :  0.044   0.173   1260
  Planarity :  0.005   0.054   1260
  Dihedral  :  5.975  22.029   1002
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.55 %
    Favored  : 89.45 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 15.02 %
    Favored  : 80.30 %
  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: -2.91 (0.25), residues: 938
  helix: -1.05 (0.19), residues: 596
  sheet:  None (None), residues: 0
  loop : -3.52 (0.31), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 516 
 HIS   0.003   0.001   HIS A 953 
 PHE   0.038   0.002   PHE A 848 
 TYR   0.012   0.001   TYR B 867 
 ARG   0.002   0.000   ARG B 899 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 164
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7540 (m-80)
REVERT: A  430 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8238 (tp)
REVERT: A  454 MET cc_start: 0.4481 (mmm) cc_final: 0.3987 (tpt)
REVERT: A  754 ASP cc_start: 0.8724 (t0) cc_final: 0.8502 (t0)
REVERT: B  413 PHE cc_start: 0.8213 (OUTLIER) cc_final: 0.7548 (m-80)
REVERT: B  430 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8256 (tp)
REVERT: B  454 MET cc_start: 0.4285 (mmm) cc_final: 0.3798 (tpt)
REVERT: B  754 ASP cc_start: 0.8635 (t0) cc_final: 0.8285 (t0)
REVERT: B  757 ILE cc_start: 0.8716 (pp) cc_final: 0.8239 (pp)
  outliers start: 38
  outliers final: 11
  residues processed: 192
  average time/residue: 0.1512
  time to fit residues: 41.1149
Evaluate side-chains
  145 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  711 VAL
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  801 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 73 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 48 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
B 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.096822 restraints weight = 14970.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.098596 restraints weight = 10641.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.099875 restraints weight = 8529.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7694  Z= 0.203
  Angle     :  0.798  13.075  10456  Z= 0.382
  Chirality :  0.045   0.172   1260
  Planarity :  0.005   0.057   1260
  Dihedral  :  5.690  20.184   1002
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 17.24 %
    Favored  : 76.60 %
  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: -2.42 (0.26), residues: 938
  helix: -0.62 (0.20), residues: 598
  sheet:  None (None), residues: 0
  loop : -3.43 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 516 
 HIS   0.004   0.001   HIS A 900 
 PHE   0.038   0.002   PHE A 848 
 TYR   0.024   0.002   TYR A 577 
 ARG   0.003   0.000   ARG A 764 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 149
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7624 (m-80)
REVERT: A  430 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8163 (tp)
REVERT: A  454 MET cc_start: 0.4147 (mmm) cc_final: 0.3611 (tpt)
REVERT: A  542 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.6907 (mt-10)
REVERT: A  699 ASP cc_start: 0.8365 (t0) cc_final: 0.8069 (t0)
REVERT: A  756 GLN cc_start: 0.8089 (mp10) cc_final: 0.7501 (mp10)
REVERT: A  794 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8444 (mp)
REVERT: B  413 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7632 (m-80)
REVERT: B  430 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8199 (tp)
REVERT: B  454 MET cc_start: 0.4022 (mmm) cc_final: 0.3403 (tpt)
REVERT: B  542 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.6868 (mt-10)
REVERT: B  699 ASP cc_start: 0.8359 (t0) cc_final: 0.8021 (t0)
REVERT: B  756 GLN cc_start: 0.8246 (mp10) cc_final: 0.7633 (mp10)
REVERT: B  757 ILE cc_start: 0.8752 (pp) cc_final: 0.8345 (pp)
REVERT: B  911 PHE cc_start: 0.7947 (t80) cc_final: 0.7384 (m-80)
  outliers start: 50
  outliers final: 20
  residues processed: 187
  average time/residue: 0.1511
  time to fit residues: 40.5854
Evaluate side-chains
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  711 VAL
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  763 ASN
Chi-restraints excluded: chain A residue  794 LEU
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  804 SER
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  804 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 48 optimal weight:    0.1980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
A 900 HIS
B 572 ASN
B 900 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.123140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.097133 restraints weight = 14937.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.099305 restraints weight = 10061.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.100753 restraints weight = 7793.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7694  Z= 0.200
  Angle     :  0.784  10.720  10456  Z= 0.379
  Chirality :  0.044   0.164   1260
  Planarity :  0.005   0.053   1260
  Dihedral  :  5.470  19.964   1002
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 11.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.09 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 17.86 %
    Favored  : 76.72 %
  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: -2.08 (0.27), residues: 938
  helix: -0.38 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -3.23 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 516 
 HIS   0.003   0.001   HIS A 907 
 PHE   0.057   0.002   PHE A 848 
 TYR   0.015   0.001   TYR B 897 
 ARG   0.008   0.001   ARG A 899 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 156
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7283 (m-80)
REVERT: A  430 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8183 (tp)
REVERT: A  454 MET cc_start: 0.3952 (mmm) cc_final: 0.3410 (tpt)
REVERT: A  510 ARG cc_start: 0.8416 (mtp180) cc_final: 0.7959 (ttt-90)
REVERT: A  542 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7618 (mt-10)
REVERT: A  699 ASP cc_start: 0.8462 (t0) cc_final: 0.8139 (t0)
REVERT: A  756 GLN cc_start: 0.8324 (mp10) cc_final: 0.7657 (mp10)
REVERT: A  911 PHE cc_start: 0.8053 (t80) cc_final: 0.7501 (m-80)
REVERT: A  957 PHE cc_start: 0.7149 (p90) cc_final: 0.6531 (p90)
REVERT: B  413 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7403 (m-80)
REVERT: B  430 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8203 (tp)
REVERT: B  454 MET cc_start: 0.4148 (mmm) cc_final: 0.3500 (tpt)
REVERT: B  510 ARG cc_start: 0.8377 (mtp180) cc_final: 0.7930 (ttt-90)
REVERT: B  542 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7501 (mt-10)
REVERT: B  699 ASP cc_start: 0.8408 (t0) cc_final: 0.8078 (t0)
REVERT: B  756 GLN cc_start: 0.8441 (mp10) cc_final: 0.7746 (mp10)
REVERT: B  757 ILE cc_start: 0.8844 (pp) cc_final: 0.8591 (pp)
REVERT: B  764 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7838 (mmm-85)
REVERT: B  911 PHE cc_start: 0.8032 (t80) cc_final: 0.7482 (m-80)
  outliers start: 44
  outliers final: 21
  residues processed: 186
  average time/residue: 0.1635
  time to fit residues: 42.6871
Evaluate side-chains
  159 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  542 GLU
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  763 ASN
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  908 LEU
Chi-restraints excluded: chain B residue  949 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 51 optimal weight:    0.0050
   chunk 3 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 84 optimal weight:    0.5980
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
B 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.125402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.099640 restraints weight = 14799.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.101905 restraints weight = 9827.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.103435 restraints weight = 7542.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.4875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7694  Z= 0.184
  Angle     :  0.792  11.101  10456  Z= 0.377
  Chirality :  0.044   0.211   1260
  Planarity :  0.005   0.052   1260
  Dihedral  :  5.297  18.988   1002
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 18.10 %
    Favored  : 76.35 %
  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: -1.90 (0.27), residues: 938
  helix: -0.24 (0.21), residues: 604
  sheet:  None (None), residues: 0
  loop : -3.21 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 516 
 HIS   0.004   0.001   HIS A 900 
 PHE   0.029   0.002   PHE B 848 
 TYR   0.012   0.001   TYR B 867 
 ARG   0.004   0.000   ARG B 899 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 155
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.7963 (OUTLIER) cc_final: 0.7400 (m-80)
REVERT: A  430 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8180 (tp)
REVERT: A  454 MET cc_start: 0.4152 (mmm) cc_final: 0.3510 (tpt)
REVERT: A  510 ARG cc_start: 0.8413 (mtp180) cc_final: 0.8031 (ttt-90)
REVERT: A  911 PHE cc_start: 0.8139 (t80) cc_final: 0.7563 (m-80)
REVERT: B  413 PHE cc_start: 0.8053 (OUTLIER) cc_final: 0.7464 (m-80)
REVERT: B  430 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8217 (tp)
REVERT: B  454 MET cc_start: 0.4126 (mmm) cc_final: 0.3474 (tpt)
REVERT: B  510 ARG cc_start: 0.8387 (mtp180) cc_final: 0.8027 (ttt-90)
REVERT: B  753 MET cc_start: 0.7886 (mtt) cc_final: 0.7627 (mtm)
REVERT: B  754 ASP cc_start: 0.9093 (t0) cc_final: 0.8818 (t0)
REVERT: B  756 GLN cc_start: 0.8547 (mp10) cc_final: 0.7779 (mp10)
REVERT: B  764 ARG cc_start: 0.8045 (mmm-85) cc_final: 0.7806 (mmm-85)
REVERT: B  911 PHE cc_start: 0.8098 (t80) cc_final: 0.7502 (m-80)
REVERT: B  930 ILE cc_start: 0.8752 (pt) cc_final: 0.8458 (mp)
  outliers start: 45
  outliers final: 23
  residues processed: 187
  average time/residue: 0.1615
  time to fit residues: 42.5000
Evaluate side-chains
  167 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 140
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  865 PHE
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain B residue  908 LEU
Chi-restraints excluded: chain B residue  949 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   chunk 69 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
B 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.122680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.096822 restraints weight = 14878.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.098956 restraints weight = 9905.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.100488 restraints weight = 7673.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.4977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   7694  Z= 0.224
  Angle     :  0.812  13.915  10456  Z= 0.387
  Chirality :  0.046   0.179   1260
  Planarity :  0.005   0.052   1260
  Dihedral  :  5.312  20.031   1002
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 19.70 %
    Favored  : 75.25 %
  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: -1.64 (0.28), residues: 938
  helix: -0.07 (0.21), residues: 608
  sheet:  None (None), residues: 0
  loop : -3.04 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 516 
 HIS   0.002   0.001   HIS A 900 
 PHE   0.029   0.002   PHE B 656 
 TYR   0.010   0.001   TYR B 867 
 ARG   0.003   0.000   ARG B 899 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 155
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8353 (OUTLIER) cc_final: 0.7648 (m-80)
REVERT: A  430 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.7952 (tp)
REVERT: A  454 MET cc_start: 0.4165 (mmm) cc_final: 0.3452 (tpt)
REVERT: A  493 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7673 (mmp-170)
REVERT: A  510 ARG cc_start: 0.8463 (mtp180) cc_final: 0.8112 (ttt-90)
REVERT: A  830 ARG cc_start: 0.8305 (mmt180) cc_final: 0.7840 (mmt-90)
REVERT: A  911 PHE cc_start: 0.8156 (t80) cc_final: 0.7547 (m-80)
REVERT: B  413 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.7649 (m-80)
REVERT: B  430 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8121 (tp)
REVERT: B  454 MET cc_start: 0.4119 (mmm) cc_final: 0.3408 (tpt)
REVERT: B  493 ARG cc_start: 0.7878 (mtt180) cc_final: 0.7633 (mmp-170)
REVERT: B  510 ARG cc_start: 0.8410 (mtp180) cc_final: 0.8040 (ttt-90)
REVERT: B  699 ASP cc_start: 0.8336 (t0) cc_final: 0.8105 (t0)
REVERT: B  756 GLN cc_start: 0.8170 (mp10) cc_final: 0.7468 (mp10)
REVERT: B  911 PHE cc_start: 0.8111 (t80) cc_final: 0.7499 (m-80)
REVERT: B  930 ILE cc_start: 0.8764 (pt) cc_final: 0.8477 (mp)
  outliers start: 41
  outliers final: 32
  residues processed: 186
  average time/residue: 0.2013
  time to fit residues: 49.6216
Evaluate side-chains
  173 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  572 ASN
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  763 ASN
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  572 ASN
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  839 VAL
Chi-restraints excluded: chain B residue  865 PHE
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain B residue  908 LEU
Chi-restraints excluded: chain B residue  949 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
B 572 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.123542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.097471 restraints weight = 15052.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.099830 restraints weight = 9978.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.101266 restraints weight = 7634.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7694  Z= 0.204
  Angle     :  0.804  12.613  10456  Z= 0.380
  Chirality :  0.045   0.158   1260
  Planarity :  0.005   0.051   1260
  Dihedral  :  5.238  19.478   1002
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.98 %
    Favored  : 89.02 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 20.07 %
    Favored  : 74.88 %
  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: -1.43 (0.28), residues: 938
  helix:  0.15 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -3.00 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 516 
 HIS   0.002   0.001   HIS B 807 
 PHE   0.023   0.002   PHE B 656 
 TYR   0.010   0.001   TYR A 867 
 ARG   0.010   0.001   ARG B 881 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 149
  time to evaluate  : 0.888 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7431 (m-80)
REVERT: A  430 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.7940 (tp)
REVERT: A  454 MET cc_start: 0.4005 (mmm) cc_final: 0.3335 (tpt)
REVERT: A  510 ARG cc_start: 0.8418 (mtp180) cc_final: 0.8049 (ttt-90)
REVERT: A  911 PHE cc_start: 0.8006 (t80) cc_final: 0.7396 (m-80)
REVERT: B  413 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7498 (m-80)
REVERT: B  430 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8121 (tp)
REVERT: B  454 MET cc_start: 0.4128 (mmm) cc_final: 0.3386 (tpt)
REVERT: B  493 ARG cc_start: 0.7764 (mtt180) cc_final: 0.7542 (mmp-170)
REVERT: B  510 ARG cc_start: 0.8369 (mtp180) cc_final: 0.8043 (ttt-90)
REVERT: B  542 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8199 (mt-10)
REVERT: B  699 ASP cc_start: 0.8376 (t0) cc_final: 0.8135 (t0)
REVERT: B  756 GLN cc_start: 0.8273 (mp10) cc_final: 0.7561 (mp10)
REVERT: B  911 PHE cc_start: 0.7938 (t80) cc_final: 0.7354 (m-80)
  outliers start: 41
  outliers final: 31
  residues processed: 182
  average time/residue: 0.1582
  time to fit residues: 40.6614
Evaluate side-chains
  175 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 140
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  572 ASN
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  763 ASN
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  572 ASN
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  839 VAL
Chi-restraints excluded: chain B residue  865 PHE
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain B residue  908 LEU
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  958 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 90 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
A 913 GLN
B 477 GLN
B 572 ASN
B 763 ASN
B 913 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.123656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.098331 restraints weight = 15038.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.100342 restraints weight = 10623.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.101655 restraints weight = 8460.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7694  Z= 0.209
  Angle     :  0.810  12.105  10456  Z= 0.383
  Chirality :  0.045   0.156   1260
  Planarity :  0.005   0.051   1260
  Dihedral  :  5.186  19.618   1002
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 21.43 %
    Favored  : 73.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.28), residues: 938
  helix:  0.26 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.95 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 516 
 HIS   0.002   0.001   HIS A 807 
 PHE   0.024   0.002   PHE B 957 
 TYR   0.010   0.001   TYR B 867 
 ARG   0.008   0.001   ARG B 881 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 147
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7374 (m-80)
REVERT: A  430 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.7791 (tp)
REVERT: A  454 MET cc_start: 0.4429 (mmm) cc_final: 0.3769 (tpt)
REVERT: A  510 ARG cc_start: 0.8391 (mtp180) cc_final: 0.8122 (ttt-90)
REVERT: A  532 LEU cc_start: 0.7892 (pt) cc_final: 0.7666 (pp)
REVERT: A  675 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.8059 (m-10)
REVERT: A  911 PHE cc_start: 0.7833 (t80) cc_final: 0.7275 (m-80)
REVERT: B  413 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7544 (m-80)
REVERT: B  430 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8054 (tp)
REVERT: B  454 MET cc_start: 0.4386 (mmm) cc_final: 0.3719 (tpt)
REVERT: B  510 ARG cc_start: 0.8313 (mtp180) cc_final: 0.8046 (ttt-90)
REVERT: B  542 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8196 (mt-10)
REVERT: B  699 ASP cc_start: 0.8254 (t0) cc_final: 0.7979 (t0)
REVERT: B  756 GLN cc_start: 0.8102 (mp10) cc_final: 0.7543 (mp10)
REVERT: B  858 MET cc_start: 0.8782 (mmm) cc_final: 0.8516 (mmt)
REVERT: B  911 PHE cc_start: 0.7733 (t80) cc_final: 0.7218 (m-80)
  outliers start: 41
  outliers final: 30
  residues processed: 179
  average time/residue: 0.1656
  time to fit residues: 41.6148
Evaluate side-chains
  174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 139
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  675 PHE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  913 GLN
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  788 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  839 VAL
Chi-restraints excluded: chain B residue  865 PHE
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain B residue  908 LEU
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  958 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 66 optimal weight:    0.1980
   chunk 86 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 48 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0170
   chunk 81 optimal weight:    2.9990
   chunk 40 optimal weight:    0.5980
   chunk 77 optimal weight:    6.9990
   overall best weight:    0.5018

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 763 ASN
A 913 GLN
B 763 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.124859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.099861 restraints weight = 14932.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.101718 restraints weight = 10596.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.102987 restraints weight = 8504.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.5529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7694  Z= 0.193
  Angle     :  0.821  11.110  10456  Z= 0.385
  Chirality :  0.046   0.309   1260
  Planarity :  0.006   0.087   1260
  Dihedral  :  5.116  17.320   1002
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 22.54 %
    Favored  : 73.03 %
  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: -1.25 (0.28), residues: 938
  helix:  0.27 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.89 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 516 
 HIS   0.005   0.001   HIS A 907 
 PHE   0.019   0.002   PHE B 932 
 TYR   0.011   0.001   TYR B 867 
 ARG   0.008   0.001   ARG A 881 

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

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

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1876 Ramachandran restraints generated.
    938 Oldfield, 0 Emsley, 938 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.853 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8177 (OUTLIER) cc_final: 0.7361 (m-80)
REVERT: A  430 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.7782 (tp)
REVERT: A  454 MET cc_start: 0.4304 (mmm) cc_final: 0.3732 (tpt)
REVERT: A  510 ARG cc_start: 0.8337 (mtp180) cc_final: 0.8088 (ttt-90)
REVERT: A  532 LEU cc_start: 0.7854 (pt) cc_final: 0.7587 (pp)
REVERT: A  675 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.8055 (m-10)
REVERT: A  911 PHE cc_start: 0.7795 (t80) cc_final: 0.7325 (m-80)
REVERT: B  413 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7429 (m-80)
REVERT: B  430 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.7836 (tp)
REVERT: B  454 MET cc_start: 0.4294 (mmm) cc_final: 0.3720 (tpt)
REVERT: B  510 ARG cc_start: 0.8279 (mtp180) cc_final: 0.8061 (ttt-90)
REVERT: B  532 LEU cc_start: 0.7806 (pt) cc_final: 0.7517 (pp)
REVERT: B  542 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: B  756 GLN cc_start: 0.8077 (mp10) cc_final: 0.7535 (mp10)
REVERT: B  858 MET cc_start: 0.8693 (mmm) cc_final: 0.8487 (mmt)
REVERT: B  911 PHE cc_start: 0.7755 (t80) cc_final: 0.7254 (m-80)
  outliers start: 36
  outliers final: 28
  residues processed: 173
  average time/residue: 0.1506
  time to fit residues: 37.5514
Evaluate side-chains
  174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 0.826 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  413 PHE
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  507 LEU
Chi-restraints excluded: chain A residue  516 TRP
Chi-restraints excluded: chain A residue  537 THR
Chi-restraints excluded: chain A residue  649 THR
Chi-restraints excluded: chain A residue  675 PHE
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  801 THR
Chi-restraints excluded: chain A residue  839 VAL
Chi-restraints excluded: chain A residue  865 PHE
Chi-restraints excluded: chain A residue  889 LEU
Chi-restraints excluded: chain A residue  908 LEU
Chi-restraints excluded: chain A residue  913 GLN
Chi-restraints excluded: chain A residue  949 LEU
Chi-restraints excluded: chain A residue  958 LEU
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain B residue  516 TRP
Chi-restraints excluded: chain B residue  521 CYS
Chi-restraints excluded: chain B residue  537 THR
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  839 VAL
Chi-restraints excluded: chain B residue  865 PHE
Chi-restraints excluded: chain B residue  889 LEU
Chi-restraints excluded: chain B residue  908 LEU
Chi-restraints excluded: chain B residue  949 LEU
Chi-restraints excluded: chain B residue  958 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 87 optimal weight:    0.0370
   chunk 10 optimal weight:    1.9990
   chunk 34 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 76 optimal weight:    8.9990
   chunk 79 optimal weight:    0.6980
   chunk 25 optimal weight:   10.0000
   chunk 63 optimal weight:    0.0770
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
A 763 ASN
A 913 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.125764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.100005 restraints weight = 14936.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.102304 restraints weight = 9892.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103840 restraints weight = 7599.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.5663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7694  Z= 0.193
  Angle     :  0.826  10.858  10456  Z= 0.385
  Chirality :  0.045   0.296   1260
  Planarity :  0.005   0.075   1260
  Dihedral  :  5.029  17.769   1002
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 23.89 %
    Favored  : 71.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.16 (0.28), residues: 938
  helix:  0.31 (0.21), residues: 600
  sheet:  None (None), residues: 0
  loop : -2.80 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 516 
 HIS   0.003   0.001   HIS A 907 
 PHE   0.018   0.002   PHE A 656 
 TYR   0.011   0.001   TYR A 867 
 ARG   0.007   0.001   ARG B 881 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2272.47 seconds
wall clock time: 40 minutes 12.62 seconds (2412.62 seconds total)