Starting phenix.real_space_refine
on Mon Nov 17 18:23:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6caa_7441/11_2025/6caa_7441.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6caa_7441/11_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6caa_7441/11_2025/6caa_7441.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6caa_7441/11_2025/6caa_7441.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6caa_7441/11_2025/6caa_7441.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6caa_7441/11_2025/6caa_7441.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 2.49, per 1000 atoms: 0.33
  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: 0.62
  Conformation dependent library (CDL) restraints added in 330.0 milliseconds
  

  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: 0.22
  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: 0.87

  Time building geometry restraints manager: 0.84 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: 0.02
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:             0.600
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.550
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.560
-------------------------------------------------------------------------------
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= 0.372
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  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
 ARG   0.006   0.001   ARG A 830 
 TYR   0.017   0.003   TYR B 797 
 PHE   0.042   0.004   PHE A 855 
 TRP   0.021   0.003   TRP A 512 
 HIS   0.017   0.004   HIS B 900 

Details of bonding type rmsd
  covalent geometry    : bond        0.00863 ( 7694)
  covalent geometry    : angle       1.32757 (10456)
  hydrogen bonds       : bond        0.30968 (  342)
  hydrogen bonds       : angle       9.83516 ( 1020)

*********************** 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  : 0.273 
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: 0.0947
  time to fit residues: 28.7907
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  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3639 r_free = 0.3639 target = 0.120432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.095564 restraints weight = 15076.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.097444 restraints weight = 10422.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.098647 restraints weight = 8223.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.099554 restraints weight = 7092.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.099924 restraints weight = 6436.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.3047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7694  Z= 0.157
  Angle     :  0.817   9.667  10456  Z= 0.411
  Chirality :  0.046   0.191   1260
  Planarity :  0.007   0.061   1260
  Dihedral  :  6.620  23.821   1002
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.83 %
    Favored  : 88.17 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 13.79 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.24 (0.22), residues: 938
  helix: -2.16 (0.17), residues: 586
  sheet:  None (None), residues: 0
  loop : -3.86 (0.29), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 830 
 TYR   0.035   0.002   TYR B 577 
 PHE   0.016   0.002   PHE A 855 
 TRP   0.010   0.001   TRP A 512 
 HIS   0.003   0.001   HIS B 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 7694)
  covalent geometry    : angle       0.81676 (10456)
  hydrogen bonds       : bond        0.05289 (  342)
  hydrogen bonds       : angle       4.98596 ( 1020)

*********************** 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
  194 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  413 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7516 (m-80)
REVERT: A  430 LEU cc_start: 0.8804 (pp) cc_final: 0.8218 (tp)
REVERT: A  454 MET cc_start: 0.4169 (mmm) cc_final: 0.3713 (tpt)
REVERT: A  542 GLU cc_start: 0.7864 (mp0) cc_final: 0.6903 (mp0)
REVERT: A  699 ASP cc_start: 0.8286 (t0) cc_final: 0.8018 (t0)
REVERT: A  808 ILE cc_start: 0.9225 (pt) cc_final: 0.8997 (tp)
REVERT: A  874 ASN cc_start: 0.7892 (t0) cc_final: 0.7678 (t0)
REVERT: A  924 LYS cc_start: 0.8332 (tppp) cc_final: 0.8044 (tptt)
REVERT: B  413 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7472 (m-80)
REVERT: B  430 LEU cc_start: 0.8805 (pp) cc_final: 0.8255 (tp)
REVERT: B  454 MET cc_start: 0.4229 (mmm) cc_final: 0.3830 (tpt)
REVERT: B  542 GLU cc_start: 0.7888 (mp0) cc_final: 0.6857 (mp0)
REVERT: B  699 ASP cc_start: 0.8273 (t0) cc_final: 0.7956 (t0)
REVERT: B  808 ILE cc_start: 0.9213 (pt) cc_final: 0.9005 (tp)
REVERT: B  858 MET cc_start: 0.8711 (tpt) cc_final: 0.8429 (tpp)
REVERT: B  924 LYS cc_start: 0.8417 (tppp) cc_final: 0.8020 (tptt)
  outliers start: 28
  outliers final: 13
  residues processed: 186
  average time/residue: 0.0755
  time to fit residues: 19.6565
Evaluate side-chains
  150 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 135
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
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 18 optimal weight:    6.9990
   chunk 79 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0030
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 477 GLN
A 572 ASN
A 763 ASN
B 422 ASN
B 477 GLN
B 763 ASN
** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.122757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.097407 restraints weight = 14917.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.099245 restraints weight = 10478.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.100483 restraints weight = 8361.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.101128 restraints weight = 7249.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.101727 restraints weight = 6661.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.3806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7694  Z= 0.136
  Angle     :  0.778  11.666  10456  Z= 0.382
  Chirality :  0.044   0.178   1260
  Planarity :  0.006   0.057   1260
  Dihedral  :  6.039  21.782   1002
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 15.27 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.89 (0.25), residues: 938
  helix: -0.93 (0.20), residues: 584
  sheet:  None (None), residues: 0
  loop : -3.63 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 899 
 TYR   0.011   0.001   TYR B 867 
 PHE   0.039   0.002   PHE A 848 
 TRP   0.008   0.001   TRP A 516 
 HIS   0.003   0.001   HIS A 953 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 7694)
  covalent geometry    : angle       0.77800 (10456)
  hydrogen bonds       : bond        0.03922 (  342)
  hydrogen bonds       : angle       4.43149 ( 1020)

*********************** 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
  197 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 161
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7583 (m-80)
REVERT: A  430 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8234 (tp)
REVERT: A  454 MET cc_start: 0.4568 (mmm) cc_final: 0.4033 (tpt)
REVERT: A  542 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7795 (mp0)
REVERT: A  754 ASP cc_start: 0.8654 (t0) cc_final: 0.8438 (t0)
REVERT: A  757 ILE cc_start: 0.8702 (pt) cc_final: 0.8493 (mm)
REVERT: A  874 ASN cc_start: 0.7895 (t0) cc_final: 0.7689 (t0)
REVERT: B  413 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7582 (m-80)
REVERT: B  430 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8246 (tp)
REVERT: B  454 MET cc_start: 0.4354 (mmm) cc_final: 0.3843 (tpt)
REVERT: B  542 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7757 (mp0)
REVERT: B  699 ASP cc_start: 0.8283 (t0) cc_final: 0.7940 (t0)
REVERT: B  754 ASP cc_start: 0.8688 (t0) cc_final: 0.8370 (t0)
REVERT: B  757 ILE cc_start: 0.8731 (pp) cc_final: 0.8236 (pp)
REVERT: B  874 ASN cc_start: 0.7985 (t0) cc_final: 0.7773 (t0)
REVERT: B  924 LYS cc_start: 0.8370 (tppp) cc_final: 0.8046 (tptt)
  outliers start: 36
  outliers final: 13
  residues processed: 186
  average time/residue: 0.0688
  time to fit residues: 18.3609
Evaluate side-chains
  153 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  542 GLU
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  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  542 GLU
Chi-restraints excluded: chain B residue  546 SER
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
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 74 optimal weight:    0.6980
   chunk 26 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0000
   chunk 81 optimal weight:    6.9990
   chunk 82 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    0.6184

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
A 572 ASN
A 763 ASN
B 477 GLN
B 763 ASN
** B 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.122857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.097681 restraints weight = 15145.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.099585 restraints weight = 10647.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.100841 restraints weight = 8475.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.101698 restraints weight = 7301.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.102141 restraints weight = 6651.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   7694  Z= 0.135
  Angle     :  0.794  13.597  10456  Z= 0.380
  Chirality :  0.044   0.168   1260
  Planarity :  0.005   0.057   1260
  Dihedral  :  5.737  18.866   1002
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.66 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 17.73 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.45 (0.26), residues: 938
  helix: -0.68 (0.20), residues: 602
  sheet:  None (None), residues: 0
  loop : -3.37 (0.32), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 830 
 TYR   0.031   0.002   TYR A 577 
 PHE   0.040   0.002   PHE B 848 
 TRP   0.010   0.001   TRP B 516 
 HIS   0.003   0.001   HIS B 900 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7694)
  covalent geometry    : angle       0.79390 (10456)
  hydrogen bonds       : bond        0.03642 (  342)
  hydrogen bonds       : angle       4.32365 ( 1020)

*********************** 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
  193 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7582 (m-80)
REVERT: A  430 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8190 (tp)
REVERT: A  454 MET cc_start: 0.4124 (mmm) cc_final: 0.3563 (tpt)
REVERT: A  542 GLU cc_start: 0.7924 (mp0) cc_final: 0.7560 (mt-10)
REVERT: B  413 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7589 (m-80)
REVERT: B  430 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8215 (tp)
REVERT: B  454 MET cc_start: 0.4002 (mmm) cc_final: 0.3434 (tpt)
REVERT: B  542 GLU cc_start: 0.7856 (mp0) cc_final: 0.7299 (mt-10)
REVERT: B  699 ASP cc_start: 0.8305 (t0) cc_final: 0.7962 (t0)
REVERT: B  757 ILE cc_start: 0.8736 (pp) cc_final: 0.8388 (pp)
REVERT: B  911 PHE cc_start: 0.7890 (t80) cc_final: 0.7650 (m-80)
  outliers start: 39
  outliers final: 17
  residues processed: 183
  average time/residue: 0.0652
  time to fit residues: 17.3562
Evaluate side-chains
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
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  649 THR
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 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  546 SER
Chi-restraints excluded: chain B residue  649 THR
Chi-restraints excluded: chain B residue  742 ILE
Chi-restraints excluded: chain B residue  801 THR
Chi-restraints excluded: chain B residue  908 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 69 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 57 optimal weight:   10.0000
   chunk 2 optimal weight:    0.0470
   chunk 78 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 900 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.124215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.098932 restraints weight = 15015.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.100762 restraints weight = 10707.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.102029 restraints weight = 8596.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.102667 restraints weight = 7475.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.103173 restraints weight = 6853.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7694  Z= 0.134
  Angle     :  0.762  10.363  10456  Z= 0.371
  Chirality :  0.044   0.164   1260
  Planarity :  0.006   0.054   1260
  Dihedral  :  5.432  20.318   1002
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.77 %
    Favored  : 89.23 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 18.23 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.12 (0.27), residues: 938
  helix: -0.30 (0.21), residues: 586
  sheet:  None (None), residues: 0
  loop : -3.38 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 899 
 TYR   0.014   0.001   TYR A 897 
 PHE   0.057   0.002   PHE B 848 
 TRP   0.010   0.001   TRP B 516 
 HIS   0.002   0.001   HIS A 900 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 7694)
  covalent geometry    : angle       0.76169 (10456)
  hydrogen bonds       : bond        0.03389 (  342)
  hydrogen bonds       : angle       4.16819 ( 1020)

*********************** 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: 46
    poor density    : 154
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8272 (OUTLIER) cc_final: 0.7571 (m-80)
REVERT: A  430 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8141 (tp)
REVERT: A  454 MET cc_start: 0.4130 (mmm) cc_final: 0.3579 (tpt)
REVERT: A  510 ARG cc_start: 0.8359 (mtp180) cc_final: 0.8025 (ttt-90)
REVERT: A  542 GLU cc_start: 0.7919 (mp0) cc_final: 0.7582 (mt-10)
REVERT: A  756 GLN cc_start: 0.8026 (mp10) cc_final: 0.7494 (mp10)
REVERT: A  911 PHE cc_start: 0.7894 (t80) cc_final: 0.7400 (m-80)
REVERT: B  413 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7628 (m-80)
REVERT: B  430 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8147 (tp)
REVERT: B  454 MET cc_start: 0.4090 (mmm) cc_final: 0.3554 (tpt)
REVERT: B  510 ARG cc_start: 0.8331 (mtp180) cc_final: 0.8059 (ttt-90)
REVERT: B  699 ASP cc_start: 0.8190 (t0) cc_final: 0.7858 (t0)
REVERT: B  757 ILE cc_start: 0.8809 (pp) cc_final: 0.8586 (pp)
REVERT: B  911 PHE cc_start: 0.7892 (t80) cc_final: 0.7379 (m-80)
  outliers start: 46
  outliers final: 19
  residues processed: 188
  average time/residue: 0.0653
  time to fit residues: 17.7913
Evaluate side-chains
  156 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  649 THR
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 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  649 THR
Chi-restraints excluded: chain B residue  742 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 33 optimal weight:    0.0980
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 80 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 37 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.6380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.124608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.098888 restraints weight = 14806.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.101108 restraints weight = 9791.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102588 restraints weight = 7528.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.103530 restraints weight = 6365.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.103871 restraints weight = 5720.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.4822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7694  Z= 0.138
  Angle     :  0.794  11.825  10456  Z= 0.380
  Chirality :  0.045   0.209   1260
  Planarity :  0.005   0.053   1260
  Dihedral  :  5.285  19.658   1002
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.09 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 18.97 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.80 (0.27), residues: 938
  helix: -0.09 (0.21), residues: 582
  sheet:  None (None), residues: 0
  loop : -3.14 (0.32), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 899 
 TYR   0.020   0.001   TYR A 577 
 PHE   0.051   0.002   PHE A 848 
 TRP   0.012   0.001   TRP B 516 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 7694)
  covalent geometry    : angle       0.79439 (10456)
  hydrogen bonds       : bond        0.03307 (  342)
  hydrogen bonds       : angle       4.22601 ( 1020)

*********************** 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
  192 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 151
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8323 (OUTLIER) cc_final: 0.7398 (m-80)
REVERT: A  430 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8098 (tp)
REVERT: A  454 MET cc_start: 0.4143 (mmm) cc_final: 0.3540 (tpt)
REVERT: A  510 ARG cc_start: 0.8433 (mtp180) cc_final: 0.8063 (ttt-90)
REVERT: A  756 GLN cc_start: 0.8123 (mp10) cc_final: 0.7472 (mp10)
REVERT: A  911 PHE cc_start: 0.8107 (t80) cc_final: 0.7541 (m-80)
REVERT: B  413 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.7327 (m-80)
REVERT: B  430 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8188 (tp)
REVERT: B  454 MET cc_start: 0.4131 (mmm) cc_final: 0.3520 (tpt)
REVERT: B  510 ARG cc_start: 0.8433 (mtp180) cc_final: 0.8073 (ttt-90)
REVERT: B  542 GLU cc_start: 0.8431 (mt-10) cc_final: 0.8196 (mt-10)
REVERT: B  699 ASP cc_start: 0.8319 (t0) cc_final: 0.7960 (t0)
REVERT: B  756 GLN cc_start: 0.8510 (mp10) cc_final: 0.7727 (mp10)
REVERT: B  911 PHE cc_start: 0.7970 (t80) cc_final: 0.7365 (m-80)
  outliers start: 41
  outliers final: 22
  residues processed: 179
  average time/residue: 0.0716
  time to fit residues: 18.1950
Evaluate side-chains
  167 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
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  711 VAL
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  742 ILE
Chi-restraints excluded: chain B residue  801 THR
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 18 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 24 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 58 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 37 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0570
   overall best weight:    0.5898

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.125729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.100813 restraints weight = 14920.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.102823 restraints weight = 10385.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.104042 restraints weight = 8219.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.104548 restraints weight = 7090.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.105465 restraints weight = 6575.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.5087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7694  Z= 0.133
  Angle     :  0.780  13.275  10456  Z= 0.370
  Chirality :  0.044   0.165   1260
  Planarity :  0.005   0.052   1260
  Dihedral  :  5.203  19.515   1002
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.09 %
    Favored  : 88.91 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 19.83 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.71 (0.27), residues: 938
  helix: -0.07 (0.21), residues: 602
  sheet:  None (None), residues: 0
  loop : -3.16 (0.33), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 899 
 TYR   0.011   0.001   TYR A 867 
 PHE   0.030   0.002   PHE A 848 
 TRP   0.013   0.001   TRP B 516 
 HIS   0.003   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 7694)
  covalent geometry    : angle       0.78014 (10456)
  hydrogen bonds       : bond        0.03148 (  342)
  hydrogen bonds       : angle       4.11387 ( 1020)

*********************** 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
  191 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 152
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7526 (m-80)
REVERT: A  430 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8014 (tp)
REVERT: A  454 MET cc_start: 0.3965 (mmm) cc_final: 0.3524 (tpt)
REVERT: A  510 ARG cc_start: 0.8308 (mtp180) cc_final: 0.8092 (ttt-90)
REVERT: A  756 GLN cc_start: 0.7882 (mp10) cc_final: 0.7292 (mp10)
REVERT: A  911 PHE cc_start: 0.7864 (t80) cc_final: 0.7289 (m-80)
REVERT: B  413 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7493 (m-80)
REVERT: B  430 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8027 (tp)
REVERT: B  454 MET cc_start: 0.3979 (mmm) cc_final: 0.3511 (tpt)
REVERT: B  510 ARG cc_start: 0.8288 (mtp180) cc_final: 0.8070 (ttt-90)
REVERT: B  541 GLU cc_start: 0.8205 (pm20) cc_final: 0.7993 (pm20)
REVERT: B  699 ASP cc_start: 0.8159 (t0) cc_final: 0.7831 (t0)
REVERT: B  756 GLN cc_start: 0.8058 (mp10) cc_final: 0.7453 (mp10)
REVERT: B  911 PHE cc_start: 0.7837 (t80) cc_final: 0.7258 (m-80)
  outliers start: 39
  outliers final: 25
  residues processed: 181
  average time/residue: 0.0750
  time to fit residues: 18.9567
Evaluate side-chains
  167 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 138
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
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  711 VAL
Chi-restraints excluded: chain A residue  742 ILE
Chi-restraints excluded: chain A residue  763 ASN
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  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  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 79 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 28 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 93 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.125356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.100236 restraints weight = 14953.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.102077 restraints weight = 10771.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.103267 restraints weight = 8700.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.103978 restraints weight = 7597.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.104295 restraints weight = 6985.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.5231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7694  Z= 0.131
  Angle     :  0.780  11.790  10456  Z= 0.370
  Chirality :  0.044   0.172   1260
  Planarity :  0.005   0.052   1260
  Dihedral  :  5.158  19.012   1002
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.19 %
    Favored  : 88.81 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 20.69 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.53 (0.28), residues: 938
  helix:  0.09 (0.21), residues: 590
  sheet:  None (None), residues: 0
  loop : -3.00 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 881 
 TYR   0.010   0.001   TYR B 867 
 PHE   0.026   0.002   PHE A 957 
 TRP   0.015   0.001   TRP B 516 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7694)
  covalent geometry    : angle       0.77960 (10456)
  hydrogen bonds       : bond        0.03162 (  342)
  hydrogen bonds       : angle       4.09205 ( 1020)

*********************** 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
  187 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 151
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7490 (m-80)
REVERT: A  430 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.7906 (tp)
REVERT: A  454 MET cc_start: 0.4167 (mmm) cc_final: 0.3589 (tpt)
REVERT: A  541 GLU cc_start: 0.8162 (pm20) cc_final: 0.7896 (pm20)
REVERT: A  756 GLN cc_start: 0.7772 (mp10) cc_final: 0.7299 (mp10)
REVERT: A  911 PHE cc_start: 0.7758 (t80) cc_final: 0.7308 (m-80)
REVERT: B  413 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7692 (m-80)
REVERT: B  430 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.7995 (tp)
REVERT: B  454 MET cc_start: 0.4070 (mmm) cc_final: 0.3511 (tpt)
REVERT: B  699 ASP cc_start: 0.8149 (t0) cc_final: 0.7839 (t0)
REVERT: B  756 GLN cc_start: 0.8059 (mp10) cc_final: 0.7452 (mp10)
REVERT: B  858 MET cc_start: 0.8700 (mmm) cc_final: 0.8498 (mmt)
REVERT: B  911 PHE cc_start: 0.7787 (t80) cc_final: 0.7221 (m-80)
  outliers start: 36
  outliers final: 22
  residues processed: 181
  average time/residue: 0.0670
  time to fit residues: 17.5809
Evaluate side-chains
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 134
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
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  742 ILE
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  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  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
Chi-restraints excluded: chain B residue  801 THR
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 6 optimal weight:    0.9980
   chunk 2 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 60 optimal weight:    0.6980
   chunk 91 optimal weight:    6.9990
   chunk 72 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 28 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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.124485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.099091 restraints weight = 14865.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100813 restraints weight = 10870.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.101958 restraints weight = 8895.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.102349 restraints weight = 7823.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.102945 restraints weight = 7342.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.5365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7694  Z= 0.137
  Angle     :  0.807  12.285  10456  Z= 0.378
  Chirality :  0.044   0.157   1260
  Planarity :  0.005   0.052   1260
  Dihedral  :  5.111  18.971   1002
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.51 %
    Favored  : 88.49 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.04 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.34 (0.28), residues: 938
  helix:  0.23 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.98 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 881 
 TYR   0.010   0.001   TYR B 867 
 PHE   0.033   0.002   PHE A 848 
 TRP   0.027   0.002   TRP B 796 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7694)
  covalent geometry    : angle       0.80680 (10456)
  hydrogen bonds       : bond        0.03193 (  342)
  hydrogen bonds       : angle       4.14247 ( 1020)

*********************** 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
  174 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 141
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8246 (OUTLIER) cc_final: 0.7478 (m-80)
REVERT: A  430 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.7908 (tp)
REVERT: A  454 MET cc_start: 0.4003 (mmm) cc_final: 0.3448 (tpt)
REVERT: A  756 GLN cc_start: 0.7970 (mp10) cc_final: 0.7337 (mp10)
REVERT: A  911 PHE cc_start: 0.7815 (t80) cc_final: 0.7310 (m-80)
REVERT: B  413 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7508 (m-80)
REVERT: B  430 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.7998 (tp)
REVERT: B  454 MET cc_start: 0.4013 (mmm) cc_final: 0.3489 (tpt)
REVERT: B  699 ASP cc_start: 0.8217 (t0) cc_final: 0.7907 (t0)
REVERT: B  745 LEU cc_start: 0.9315 (pp) cc_final: 0.8766 (tp)
REVERT: B  756 GLN cc_start: 0.8167 (mp10) cc_final: 0.7502 (mp10)
REVERT: B  858 MET cc_start: 0.8704 (mmm) cc_final: 0.8461 (mmt)
REVERT: B  911 PHE cc_start: 0.7822 (t80) cc_final: 0.7206 (m-80)
  outliers start: 33
  outliers final: 25
  residues processed: 169
  average time/residue: 0.0585
  time to fit residues: 14.6317
Evaluate side-chains
  158 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  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  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  742 ILE
Chi-restraints excluded: chain B residue  763 ASN
Chi-restraints excluded: chain B residue  801 THR
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  957 PHE
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 76 optimal weight:    0.6980
   chunk 49 optimal weight:    3.9990
   chunk 87 optimal weight:    0.3980
   chunk 39 optimal weight:    3.9990
   chunk 84 optimal weight:    0.5980
   chunk 65 optimal weight:    9.9990
   chunk 10 optimal weight:    0.8980
   chunk 63 optimal weight:    0.7980
   chunk 30 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 572 ASN
** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.124548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.099206 restraints weight = 14784.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.101085 restraints weight = 10547.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.102249 restraints weight = 8451.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.102789 restraints weight = 7351.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.103622 restraints weight = 6817.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.5398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.110   7694  Z= 0.183
  Angle     :  1.085  59.199  10456  Z= 0.589
  Chirality :  0.047   0.426   1260
  Planarity :  0.006   0.063   1260
  Dihedral  :  5.160  19.000   1002
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 22.29 %
    Favored  : 73.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.28), residues: 938
  helix:  0.24 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.97 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 881 
 TYR   0.010   0.001   TYR B 867 
 PHE   0.035   0.002   PHE A 848 
 TRP   0.025   0.002   TRP B 796 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 ( 7694)
  covalent geometry    : angle       1.08470 (10456)
  hydrogen bonds       : bond        0.03219 (  342)
  hydrogen bonds       : angle       4.16447 ( 1020)

********************** 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
  166 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 131
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7473 (m-80)
REVERT: A  430 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.7899 (tp)
REVERT: A  454 MET cc_start: 0.3996 (mmm) cc_final: 0.3484 (tpt)
REVERT: A  572 ASN cc_start: 0.7876 (OUTLIER) cc_final: 0.6507 (p0)
REVERT: A  756 GLN cc_start: 0.7960 (mp10) cc_final: 0.7343 (mp10)
REVERT: A  911 PHE cc_start: 0.7801 (t80) cc_final: 0.7301 (m-80)
REVERT: B  413 PHE cc_start: 0.8284 (OUTLIER) cc_final: 0.7495 (m-80)
REVERT: B  430 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.7989 (tp)
REVERT: B  454 MET cc_start: 0.4002 (mmm) cc_final: 0.3556 (tpt)
REVERT: B  699 ASP cc_start: 0.8194 (t0) cc_final: 0.7887 (t0)
REVERT: B  745 LEU cc_start: 0.9308 (pp) cc_final: 0.8744 (tp)
REVERT: B  858 MET cc_start: 0.8704 (mmm) cc_final: 0.8459 (mmt)
REVERT: B  911 PHE cc_start: 0.7778 (t80) cc_final: 0.7185 (m-80)
  outliers start: 35
  outliers final: 26
  residues processed: 161
  average time/residue: 0.0595
  time to fit residues: 14.1912
Evaluate side-chains
  160 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
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  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  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  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
Chi-restraints excluded: chain B residue  957 PHE
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 53 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 76 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.124559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.099291 restraints weight = 14652.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.101123 restraints weight = 10477.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.102339 restraints weight = 8425.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.103019 restraints weight = 7337.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.103602 restraints weight = 6749.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.153   7694  Z= 0.209
  Angle     :  0.911  24.449  10456  Z= 0.489
  Chirality :  0.047   0.426   1260
  Planarity :  0.006   0.101   1260
  Dihedral  :  5.160  19.000   1002
  Min Nonbonded Distance : 2.073

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.62 %
    Favored  : 88.38 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 22.66 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.31 (0.28), residues: 938
  helix:  0.24 (0.21), residues: 598
  sheet:  None (None), residues: 0
  loop : -2.97 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 881 
 TYR   0.010   0.001   TYR B 867 
 PHE   0.035   0.002   PHE A 848 
 TRP   0.025   0.002   TRP B 796 
 HIS   0.002   0.001   HIS B 807 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 7694)
  covalent geometry    : angle       0.91080 (10456)
  hydrogen bonds       : bond        0.03219 (  342)
  hydrogen bonds       : angle       4.16447 ( 1020)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1212.72 seconds
wall clock time: 21 minutes 43.81 seconds (1303.81 seconds total)