Starting phenix.real_space_refine
on Thu Sep 18 08:31:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yag_33711/09_2025/7yag_33711_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yag_33711/09_2025/7yag_33711.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yag_33711/09_2025/7yag_33711.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yag_33711/09_2025/7yag_33711.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yag_33711/09_2025/7yag_33711_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yag_33711/09_2025/7yag_33711_trim.cif"
  }
  resolution = 3.1
  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=   0.005 sd=   0.048
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: 7
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       3      5.49       5
     S      55      5.16       5
     C    4872      2.51       5
     N    1285      2.21       5
     O    1450      1.98       5
     H    7790      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15456
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 13594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 876, 13594
          Classifications: {'peptide': 876}
          Link IDs: {'PTRANS': 34, 'TRANS': 841}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 1830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 1830
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 2, 'TRANS': 120}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' CA': 1, 'ACP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.19, per 1000 atoms: 0.21
  Number of scatterers: 15456
  At special positions: 0
  Unit cell: (85.695, 83.725, 134.945, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      1     19.99
     S      55     16.00
     P       3     15.00
     O    1450      8.00
     N    1285      7.00
     C    4872      6.00
     H    7790      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C 128 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.45
  Conformation dependent library (CDL) restraints added in 434.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1846

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 8 sheets defined
      51.7% alpha, 23.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 29
    Processing helix  chain 'A' and resid 30 through 39
    Processing helix  chain 'A' and resid 47 through 59
      removed outlier: 3.618A  pdb=" N   PHE A  57 " --> pdb=" O   HIS A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 78
      removed outlier: 3.649A  pdb=" N   GLN A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 99 through 134
      removed outlier: 3.722A  pdb=" N   LEU A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.897A  pdb=" N   SER A 239 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 250
      removed outlier: 4.177A  pdb=" N   PHE A 245 " --> pdb=" O   PHE A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 288
    Processing helix  chain 'A' and resid 290 through 306
    Processing helix  chain 'A' and resid 308 through 328
      removed outlier: 4.214A  pdb=" N   ILE A 312 " --> pdb=" O   GLU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 342
      removed outlier: 4.305A  pdb=" N   GLU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   THR A 340 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   GLY A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 411
      removed outlier: 3.532A  pdb=" N   CYS A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.502A  pdb=" N   LEU A 442 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 489
      removed outlier: 3.705A  pdb=" N   TYR A 489 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 520
    Processing helix  chain 'A' and resid 551 through 562
    Processing helix  chain 'A' and resid 573 through 585
    Processing helix  chain 'A' and resid 596 through 602
    Processing helix  chain 'A' and resid 603 through 611
    Processing helix  chain 'A' and resid 621 through 635
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 666 through 673
    Processing helix  chain 'A' and resid 682 through 692
      removed outlier: 3.598A  pdb=" N   MET A 686 " --> pdb=" O   PHE A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 694 through 723
    Processing helix  chain 'A' and resid 730 through 743
    Processing helix  chain 'A' and resid 743 through 751
      removed outlier: 4.308A  pdb=" N   LEU A 749 " --> pdb=" O   PRO A 745 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   GLY A 750 " --> pdb=" O   ALA A 746 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   VAL A 751 " --> pdb=" O   GLN A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 755 through 761
      removed outlier: 4.221A  pdb=" N   ILE A 759 " --> pdb=" O   ASP A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 798
    Processing helix  chain 'A' and resid 804 through 827
      removed outlier: 3.523A  pdb=" N   THR A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 837
      removed outlier: 3.526A  pdb=" N   ILE A 836 " --> pdb=" O   SER A 832 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 861
    Processing helix  chain 'A' and resid 861 through 869
    Processing helix  chain 'A' and resid 874 through 904
      removed outlier: 4.038A  pdb=" N   SER A 887 " --> pdb=" O   GLY A 883 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   VAL A 888 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   CYS A 889 " --> pdb=" O   THR A 885 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 123
      removed outlier: 4.194A  pdb=" N   THR C 123 " --> pdb=" O   PRO C 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151
      removed outlier: 4.495A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A 222 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 151
      removed outlier: 4.495A  pdb=" N   HIS A 140 " --> pdb=" O   CYS A 162 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   THR A 160 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LEU A 222 " --> pdb=" O   ASP A 184 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 7.172A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 5.855A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 330 through 332
      removed outlier: 6.254A  pdb=" N   GLY A 658 " --> pdb=" O   MET A 675 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   LEU A 677 " --> pdb=" O   GLY A 658 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ALA A 660 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)
      removed outlier: 6.478A  pdb=" N   VAL A 639 " --> pdb=" O   ILE A 657 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   VAL A 659 " --> pdb=" O   VAL A 639 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   MET A 641 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 8.268A  pdb=" N   MET A 661 " --> pdb=" O   MET A 641 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   CYS A 344 " --> pdb=" O   VAL A 638 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ALA A 640 " --> pdb=" O   CYS A 344 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   VAL A 346 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
      removed outlier: 7.635A  pdb=" N   THR A 642 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   CYS A 348 " --> pdb=" O   THR A 642 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   ASN A 345 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   LYS A 567 " --> pdb=" O   ASN A 345 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ILE A 347 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   ILE A 569 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   SER A 349 " --> pdb=" O   ILE A 569 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   ILE A 566 " --> pdb=" O   ALA A 615 " (cutoff:3.500A)
      removed outlier: 8.207A  pdb=" N   PHE A 617 " --> pdb=" O   ILE A 566 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   MET A 568 " --> pdb=" O   PHE A 617 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   GLN A 592 " --> pdb=" O   ALA A 615 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   PHE A 617 " --> pdb=" O   GLN A 592 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   VAL A 594 " --> pdb=" O   PHE A 617 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392
      removed outlier: 4.696A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ILE A 545 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   LEU A 536 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   PHE A 538 " --> pdb=" O   SER A 529 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   SER A 529 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLY A 540 " --> pdb=" O   LEU A 527 " (cutoff:3.500A)
      removed outlier: 4.047A  pdb=" N   ALA A 450 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   VAL A 466 " --> pdb=" O   ARG A 448 " (cutoff:3.500A)
      removed outlier: 6.099A  pdb=" N   ARG A 448 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392
      removed outlier: 4.696A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   VAL A 362 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   ILE A 545 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   PHE A 538 " --> pdb=" O   CYS A 490 " (cutoff:3.500A)
      removed outlier: 7.420A  pdb=" N   THR A 492 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 8.494A  pdb=" N   GLY A 540 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
      removed outlier: 9.780A  pdb=" N   GLN A 494 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 14.074A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 37 through 40
    Processing sheet with id=AA7, first strand: chain 'C' and resid 90 through 92
      removed outlier: 6.543A  pdb=" N   TRP C  69 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLY C  83 " --> pdb=" O   MET C  67 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   MET C  67 " --> pdb=" O   GLY C  83 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C 131 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 90 through 92
      removed outlier: 6.543A  pdb=" N   TRP C  69 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   GLY C  83 " --> pdb=" O   MET C  67 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   MET C  67 " --> pdb=" O   GLY C  83 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TRP C  66 " --> pdb=" O   GLN C 131 " (cutoff:3.500A)

    467 hydrogen bonds defined for protein.
    1356 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: 4.24

  Time building geometry restraints manager: 1.98 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7770
        1.03 -     1.23: 42
        1.23 -     1.43: 3083
        1.43 -     1.62: 4598
        1.62 -     1.82: 90
  Bond restraints: 15583
  Sorted by residual:
  bond pdb=" O3A ACP A1001 "
       pdb=" PB  ACP A1001 "
    ideal  model  delta    sigma   weight residual
    1.698  1.605  0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C3B ACP A1001 "
       pdb=" PG  ACP A1001 "
    ideal  model  delta    sigma   weight residual
    1.875  1.793  0.082 2.00e-02 2.50e+03 1.67e+01
  bond pdb=" O5' ACP A1001 "
       pdb=" PA  ACP A1001 "
    ideal  model  delta    sigma   weight residual
    1.659  1.580  0.079 2.00e-02 2.50e+03 1.57e+01
  bond pdb=" N   ASP A 290 "
       pdb=" H   ASP A 290 "
    ideal  model  delta    sigma   weight residual
    0.860  0.915 -0.055 2.00e-02 2.50e+03 7.55e+00
  bond pdb=" N   TRP A 285 "
       pdb=" H   TRP A 285 "
    ideal  model  delta    sigma   weight residual
    0.860  0.914 -0.054 2.00e-02 2.50e+03 7.35e+00
  ... (remaining 15578 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 28123
        3.41 -     6.83: 124
        6.83 -    10.24: 7
       10.24 -    13.66: 1
       13.66 -    17.07: 1
  Bond angle restraints: 28256
  Sorted by residual:
  angle pdb=" PA  ACP A1001 "
        pdb=" O3A ACP A1001 "
        pdb=" PB  ACP A1001 "
      ideal   model   delta    sigma   weight residual
     125.06  107.99   17.07 3.00e+00 1.11e-01 3.24e+01
  angle pdb=" CA  ASP A 290 "
        pdb=" C   ASP A 290 "
        pdb=" O   ASP A 290 "
      ideal   model   delta    sigma   weight residual
     120.80  116.55    4.25 1.08e+00 8.57e-01 1.55e+01
  angle pdb=" C3B ACP A1001 "
        pdb=" PB  ACP A1001 "
        pdb=" O3A ACP A1001 "
      ideal   model   delta    sigma   weight residual
      98.05  108.41  -10.36 3.00e+00 1.11e-01 1.19e+01
  angle pdb=" N   ASP A 290 "
        pdb=" CA  ASP A 290 "
        pdb=" C   ASP A 290 "
      ideal   model   delta    sigma   weight residual
     110.30  105.20    5.10 1.50e+00 4.44e-01 1.15e+01
  angle pdb=" N   VAL A 179 "
        pdb=" CA  VAL A 179 "
        pdb=" C   VAL A 179 "
      ideal   model   delta    sigma   weight residual
     110.30  107.01    3.29 9.70e-01 1.06e+00 1.15e+01
  ... (remaining 28251 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.91: 6826
       24.91 -    49.83: 391
       49.83 -    74.74: 80
       74.74 -    99.65: 9
       99.65 -   124.56: 2
  Dihedral angle restraints: 7308
    sinusoidal: 4055
      harmonic: 3253
  Sorted by residual:
  dihedral pdb=" CA  MET A  97 "
           pdb=" C   MET A  97 "
           pdb=" N   HIS A  98 "
           pdb=" CA  HIS A  98 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.96  -24.04     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  VAL C 111 "
           pdb=" C   VAL C 111 "
           pdb=" N   TYR C 112 "
           pdb=" CA  TYR C 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.34  -22.66     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CB  CYS C  55 "
           pdb=" SG  CYS C  55 "
           pdb=" SG  CYS C 128 "
           pdb=" CB  CYS C 128 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.30   37.70     1      1.00e+01 1.00e-02 2.00e+01
  ... (remaining 7305 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1109
       0.070 -    0.141: 133
       0.141 -    0.211: 4
       0.211 -    0.281: 1
       0.281 -    0.351: 1
  Chirality restraints: 1248
  Sorted by residual:
  chirality pdb=" C3' ACP A1001 "
            pdb=" C2' ACP A1001 "
            pdb=" C4' ACP A1001 "
            pdb=" O3' ACP A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.92    0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" C2' ACP A1001 "
            pdb=" C1' ACP A1001 "
            pdb=" C3' ACP A1001 "
            pdb=" O2' ACP A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.99    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" C4' ACP A1001 "
            pdb=" C3' ACP A1001 "
            pdb=" C5' ACP A1001 "
            pdb=" O4' ACP A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.70    0.19 2.00e-01 2.50e+01 9.09e-01
  ... (remaining 1245 not shown)

  Planarity restraints: 2286
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 391 "   -0.015 2.00e-02 2.50e+03   2.84e-02 8.08e+00
        pdb=" N   VAL A 392 "    0.049 2.00e-02 2.50e+03
        pdb=" CA  VAL A 392 "   -0.013 2.00e-02 2.50e+03
        pdb=" H   VAL A 392 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 902 "    0.215 9.50e-02 1.11e+02   7.21e-02 6.63e+00
        pdb=" NE  ARG A 902 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 902 "    0.015 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 902 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 902 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG A 902 "   -0.005 2.00e-02 2.50e+03
        pdb="HH12 ARG A 902 "    0.001 2.00e-02 2.50e+03
        pdb="HH21 ARG A 902 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A 902 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 862 "    0.041 5.00e-02 4.00e+02   6.18e-02 6.12e+00
        pdb=" N   PRO A 863 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 863 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 863 "    0.035 5.00e-02 4.00e+02
  ... (remaining 2283 not shown)

  Histogram of nonbonded interaction distances:
        1.69 -     2.27: 2308
        2.27 -     2.85: 35765
        2.85 -     3.44: 40790
        3.44 -     4.02: 55884
        4.02 -     4.60: 86495
  Nonbonded interactions: 221242
  Sorted by model distance:
  nonbonded pdb=" H   VAL A 833 "
            pdb=" OE2 GLU A 893 "
     model   vdw
     1.688 2.450
  nonbonded pdb=" OE1 GLU A  33 "
            pdb=" H   GLU A  33 "
     model   vdw
     1.719 2.450
  nonbonded pdb=" O   TRP A 285 "
            pdb=" HD1 TRP A 285 "
     model   vdw
     1.726 2.450
  nonbonded pdb=" OE1 GLU A 374 "
            pdb=" H   GLN C 134 "
     model   vdw
     1.740 2.450
  nonbonded pdb=" O   THR A 570 "
            pdb=" H   ALA A 620 "
     model   vdw
     1.746 2.450
  ... (remaining 221237 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.580
  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:             0.110
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     17.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.010
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7314
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      :  0.005   0.093   7794  Z= 0.219
  Angle     :  0.807  17.070  10557  Z= 0.418
  Chirality :  0.046   0.351   1248
  Planarity :  0.006   0.096   1328
  Dihedral  : 15.720 124.564   2884
  Min Nonbonded Distance : 2.259

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 11.47 %
    Favored  : 88.42 %
  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 aren not related in a simple way.
  whole:  0.92 (0.26), residues: 989
  helix:  1.54 (0.23), residues: 484
  sheet: -0.61 (0.43), residues: 131
  loop : -0.03 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 902 
 TYR   0.027   0.002   TYR A 397 
 PHE   0.020   0.001   PHE C  80 
 TRP   0.007   0.001   TRP A 460 
 HIS   0.010   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 ( 7793)
  covalent geometry    : angle       0.80749 (10555)
  SS BOND              : bond        0.00363 (    1)
  SS BOND              : angle       0.71708 (    2)
  hydrogen bonds       : bond        0.11837 (  432)
  hydrogen bonds       : angle       6.00161 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 146
  average time/residue: 0.1848
  time to fit residues: 38.2547
Evaluate side-chains
  138 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  285 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.181756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.141820 restraints weight = 24394.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3714 rms_B_bonded: 2.39
r_work: 0.3533 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3386 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.0924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7794  Z= 0.144
  Angle     :  0.502   5.792  10557  Z= 0.269
  Chirality :  0.041   0.183   1248
  Planarity :  0.004   0.056   1328
  Dihedral  :  8.289 109.397   1092
  Min Nonbonded Distance : 2.137

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 11.47 %
    Favored  : 87.47 %
  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 aren not related in a simple way.
  whole:  1.25 (0.26), residues: 989
  helix:  1.80 (0.23), residues: 497
  sheet: -0.47 (0.41), residues: 148
  loop :  0.13 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  54 
 TYR   0.010   0.001   TYR A 696 
 PHE   0.014   0.001   PHE A 702 
 TRP   0.004   0.001   TRP C  69 
 HIS   0.003   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 7793)
  covalent geometry    : angle       0.50170 (10555)
  SS BOND              : bond        0.00057 (    1)
  SS BOND              : angle       0.25523 (    2)
  hydrogen bonds       : bond        0.03931 (  432)
  hydrogen bonds       : angle       4.76903 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 143
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.7842 (tp30) cc_final: 0.7491 (tm-30)
REVERT: A  262 MET cc_start: 0.8262 (mmt) cc_final: 0.8017 (mmp)
REVERT: A  398 ASN cc_start: 0.8047 (t0) cc_final: 0.7821 (t0)
REVERT: A  671 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6827 (mm-30)
REVERT: A  899 GLU cc_start: 0.6594 (mp0) cc_final: 0.6362 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 148
  average time/residue: 0.1860
  time to fit residues: 38.8819
Evaluate side-chains
  143 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 72 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 97 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN
A 855 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.181226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.140820 restraints weight = 24408.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.55
r_work: 0.3544 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7349
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7794  Z= 0.123
  Angle     :  0.477   5.511  10557  Z= 0.254
  Chirality :  0.040   0.173   1248
  Planarity :  0.004   0.057   1328
  Dihedral  :  8.020 107.423   1090
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.82 %
    Favored  : 86.88 %
  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 aren not related in a simple way.
  whole:  1.45 (0.27), residues: 989
  helix:  1.99 (0.23), residues: 498
  sheet: -0.44 (0.43), residues: 137
  loop :  0.17 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 468 
 TYR   0.010   0.001   TYR A 696 
 PHE   0.014   0.001   PHE A 818 
 TRP   0.007   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 7793)
  covalent geometry    : angle       0.47675 (10555)
  SS BOND              : bond        0.00101 (    1)
  SS BOND              : angle       0.20968 (    2)
  hydrogen bonds       : bond        0.03702 (  432)
  hydrogen bonds       : angle       4.48285 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  158 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.7829 (tp30) cc_final: 0.7467 (tm-30)
REVERT: A  398 ASN cc_start: 0.8028 (t0) cc_final: 0.7826 (t0)
REVERT: A  671 GLU cc_start: 0.7281 (mt-10) cc_final: 0.7019 (tm-30)
REVERT: A  899 GLU cc_start: 0.6552 (mp0) cc_final: 0.6317 (mp0)
  outliers start: 11
  outliers final: 8
  residues processed: 155
  average time/residue: 0.1907
  time to fit residues: 41.3546
Evaluate side-chains
  150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  437 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 18 optimal weight:    7.9990
   chunk 40 optimal weight:    0.7980
   chunk 81 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.181395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.139897 restraints weight = 24474.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.26
r_work: 0.3553 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3402 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7794  Z= 0.117
  Angle     :  0.465   5.357  10557  Z= 0.248
  Chirality :  0.040   0.171   1248
  Planarity :  0.004   0.055   1328
  Dihedral  :  7.821 104.573   1090
  Min Nonbonded Distance : 2.186

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.17 %
    Favored  : 86.52 %
  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 aren not related in a simple way.
  whole:  1.58 (0.27), residues: 989
  helix:  2.12 (0.23), residues: 498
  sheet: -0.34 (0.44), residues: 138
  loop :  0.17 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 213 
 TYR   0.010   0.001   TYR A 696 
 PHE   0.013   0.001   PHE A 818 
 TRP   0.007   0.001   TRP A  72 
 HIS   0.002   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7793)
  covalent geometry    : angle       0.46495 (10555)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       0.25170 (    2)
  hydrogen bonds       : bond        0.03512 (  432)
  hydrogen bonds       : angle       4.32174 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  159 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 148
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7288 (mmt) cc_final: 0.6758 (mmp)
REVERT: A  671 GLU cc_start: 0.7350 (mt-10) cc_final: 0.7086 (tm-30)
REVERT: A  899 GLU cc_start: 0.6568 (mp0) cc_final: 0.6304 (mp0)
  outliers start: 11
  outliers final: 8
  residues processed: 155
  average time/residue: 0.1890
  time to fit residues: 41.4087
Evaluate side-chains
  150 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 142
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 86 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 84 optimal weight:    0.6980
   chunk 80 optimal weight:    7.9990
   chunk 60 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A  61 ASN
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
A 606 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.177924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.140447 restraints weight = 24814.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.17
r_work: 0.3516 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   7794  Z= 0.183
  Angle     :  0.515   6.102  10557  Z= 0.275
  Chirality :  0.041   0.180   1248
  Planarity :  0.004   0.056   1328
  Dihedral  :  7.997 104.615   1090
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.53 %
    Favored  : 85.70 %
  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 aren not related in a simple way.
  whole:  1.35 (0.27), residues: 989
  helix:  1.89 (0.23), residues: 486
  sheet: -0.16 (0.43), residues: 147
  loop :  0.09 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 213 
 TYR   0.011   0.001   TYR C 143 
 PHE   0.017   0.002   PHE A 818 
 TRP   0.008   0.001   TRP A  72 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7793)
  covalent geometry    : angle       0.51506 (10555)
  SS BOND              : bond        0.00036 (    1)
  SS BOND              : angle       0.09738 (    2)
  hydrogen bonds       : bond        0.03837 (  432)
  hydrogen bonds       : angle       4.45835 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  162 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 147
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7454 (mmt) cc_final: 0.6917 (mmp)
REVERT: A  605 GLN cc_start: 0.7876 (tp40) cc_final: 0.7617 (tp40)
REVERT: A  671 GLU cc_start: 0.7503 (mt-10) cc_final: 0.7265 (tm-30)
REVERT: A  899 GLU cc_start: 0.6557 (mp0) cc_final: 0.6249 (mp0)
  outliers start: 15
  outliers final: 13
  residues processed: 157
  average time/residue: 0.1855
  time to fit residues: 41.4975
Evaluate side-chains
  155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 93 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 46 optimal weight:    6.9990
   chunk 27 optimal weight:    0.8980
   chunk 18 optimal weight:    6.9990
   chunk 30 optimal weight:    1.9990
   chunk 95 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
C  86 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.178548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.141132 restraints weight = 24783.671|
|-----------------------------------------------------------------------------|
r_work (start): 0.3722 rms_B_bonded: 2.19
r_work: 0.3525 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7794  Z= 0.151
  Angle     :  0.490   5.436  10557  Z= 0.262
  Chirality :  0.040   0.175   1248
  Planarity :  0.004   0.055   1328
  Dihedral  :  7.872 103.497   1090
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 5.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 14.30 %
    Favored  : 84.04 %
  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 aren not related in a simple way.
  whole:  1.43 (0.27), residues: 989
  helix:  2.00 (0.23), residues: 483
  sheet: -0.20 (0.43), residues: 149
  loop :  0.11 (0.34), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 213 
 TYR   0.009   0.001   TYR A 483 
 PHE   0.019   0.001   PHE A 818 
 TRP   0.005   0.001   TRP A  72 
 HIS   0.003   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 7793)
  covalent geometry    : angle       0.48970 (10555)
  SS BOND              : bond        0.00079 (    1)
  SS BOND              : angle       0.15034 (    2)
  hydrogen bonds       : bond        0.03637 (  432)
  hydrogen bonds       : angle       4.35368 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  160 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 146
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7328 (mmt) cc_final: 0.6809 (mmp)
REVERT: A  671 GLU cc_start: 0.7526 (mt-10) cc_final: 0.7278 (tm-30)
  outliers start: 14
  outliers final: 12
  residues processed: 156
  average time/residue: 0.1855
  time to fit residues: 41.0684
Evaluate side-chains
  155 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 89 optimal weight:   10.0000
   chunk 36 optimal weight:    6.9990
   chunk 58 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 83 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN
C  86 HIS
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.179543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.142284 restraints weight = 24607.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 2.17
r_work: 0.3538 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7794  Z= 0.126
  Angle     :  0.479   5.379  10557  Z= 0.254
  Chirality :  0.040   0.172   1248
  Planarity :  0.004   0.055   1328
  Dihedral  :  7.761 102.408   1090
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 14.18 %
    Favored  : 84.04 %
  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 aren not related in a simple way.
  whole:  1.58 (0.27), residues: 989
  helix:  2.17 (0.23), residues: 483
  sheet: -0.18 (0.45), residues: 135
  loop :  0.12 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 213 
 TYR   0.010   0.001   TYR A 483 
 PHE   0.021   0.001   PHE A 818 
 TRP   0.004   0.001   TRP A  72 
 HIS   0.003   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7793)
  covalent geometry    : angle       0.47859 (10555)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.12295 (    2)
  hydrogen bonds       : bond        0.03487 (  432)
  hydrogen bonds       : angle       4.24504 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  163 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 148
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7265 (mmt) cc_final: 0.6750 (mmp)
REVERT: A  671 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7273 (tm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 158
  average time/residue: 0.1787
  time to fit residues: 40.5210
Evaluate side-chains
  153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 141
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 88 optimal weight:   30.0000
   chunk 60 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
C  86 HIS
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.176668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.136898 restraints weight = 25133.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.3667 rms_B_bonded: 2.33
r_work: 0.3489 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3349 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3349
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7479
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   7794  Z= 0.206
  Angle     :  0.537   5.718  10557  Z= 0.288
  Chirality :  0.042   0.176   1248
  Planarity :  0.005   0.054   1328
  Dihedral  :  8.016 102.593   1090
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.25 %
    Favored  : 83.22 %
  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 aren not related in a simple way.
  whole:  1.24 (0.27), residues: 989
  helix:  1.77 (0.23), residues: 482
  sheet: -0.08 (0.43), residues: 147
  loop :  0.04 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 213 
 TYR   0.013   0.001   TYR C 143 
 PHE   0.022   0.002   PHE A 818 
 TRP   0.004   0.001   TRP C  66 
 HIS   0.003   0.001   HIS A 467 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 7793)
  covalent geometry    : angle       0.53733 (10555)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.05974 (    2)
  hydrogen bonds       : bond        0.03935 (  432)
  hydrogen bonds       : angle       4.45584 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7301 (mmt) cc_final: 0.6789 (mmp)
REVERT: A  605 GLN cc_start: 0.7875 (tp40) cc_final: 0.7631 (tp40)
REVERT: A  671 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7291 (tm-30)
REVERT: A  899 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5468 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 147
  average time/residue: 0.1920
  time to fit residues: 39.6889
Evaluate side-chains
  146 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 89 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 94 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 134 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.177897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.136539 restraints weight = 24829.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.25
r_work: 0.3507 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7794  Z= 0.158
  Angle     :  0.518   7.683  10557  Z= 0.274
  Chirality :  0.040   0.174   1248
  Planarity :  0.004   0.056   1328
  Dihedral  :  7.875 102.153   1090
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.72 %
    Favored  : 82.74 %
  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 aren not related in a simple way.
  whole:  1.35 (0.27), residues: 989
  helix:  1.89 (0.23), residues: 484
  sheet:  0.01 (0.44), residues: 142
  loop :  0.01 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 213 
 TYR   0.009   0.001   TYR A 483 
 PHE   0.028   0.001   PHE A 818 
 TRP   0.009   0.001   TRP A 766 
 HIS   0.003   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 7793)
  covalent geometry    : angle       0.51759 (10555)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       0.03071 (    2)
  hydrogen bonds       : bond        0.03683 (  432)
  hydrogen bonds       : angle       4.35701 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.457 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7256 (mmt) cc_final: 0.6748 (mmp)
REVERT: A  323 MET cc_start: 0.7609 (mtp) cc_final: 0.7377 (mtp)
REVERT: A  671 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7155 (tm-30)
REVERT: A  899 GLU cc_start: 0.6291 (mm-30) cc_final: 0.5291 (mp0)
  outliers start: 13
  outliers final: 11
  residues processed: 149
  average time/residue: 0.1632
  time to fit residues: 34.5711
Evaluate side-chains
  147 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 96 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
C 109 ASN
C 134 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.177354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.137734 restraints weight = 24968.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3676 rms_B_bonded: 2.44
r_work: 0.3502 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   7794  Z= 0.178
  Angle     :  0.535   8.729  10557  Z= 0.283
  Chirality :  0.041   0.174   1248
  Planarity :  0.004   0.055   1328
  Dihedral  :  7.932 102.709   1090
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.84 %
    Favored  : 82.62 %
  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 aren not related in a simple way.
  whole:  1.25 (0.27), residues: 989
  helix:  1.81 (0.23), residues: 483
  sheet:  0.02 (0.44), residues: 142
  loop : -0.06 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 174 
 TYR   0.010   0.001   TYR C 143 
 PHE   0.028   0.002   PHE A 818 
 TRP   0.004   0.001   TRP A 766 
 HIS   0.003   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 7793)
  covalent geometry    : angle       0.53518 (10555)
  SS BOND              : bond        0.00026 (    1)
  SS BOND              : angle       0.04803 (    2)
  hydrogen bonds       : bond        0.03778 (  432)
  hydrogen bonds       : angle       4.40029 ( 1356)

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

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

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1978 Ramachandran restraints generated.
    989 Oldfield, 0 Emsley, 989 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  246 is missing expected H atoms. Skipping.
Evaluate side-chains
  149 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 MET cc_start: 0.7280 (mmt) cc_final: 0.6765 (mmp)
REVERT: A  323 MET cc_start: 0.7707 (mtp) cc_final: 0.7492 (mtp)
REVERT: A  605 GLN cc_start: 0.7717 (tp40) cc_final: 0.7512 (tp40)
REVERT: A  671 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7281 (tm-30)
REVERT: A  899 GLU cc_start: 0.6450 (mm-30) cc_final: 0.5459 (mp0)
  outliers start: 13
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1933
  time to fit residues: 39.1324
Evaluate side-chains
  146 residues out of total 849 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 ASP
Chi-restraints excluded: chain A residue  141 CYS
Chi-restraints excluded: chain A residue  167 ASP
Chi-restraints excluded: chain A residue  232 VAL
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  564 VAL
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  870 THR
Chi-restraints excluded: chain A residue  871 GLU
Chi-restraints excluded: chain C residue  109 ASN
Chi-restraints excluded: chain C residue  123 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0570
   chunk 94 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0770
   overall best weight:    0.5456

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

Flipped N/Q/H residues before XYZ refinement:
** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 419 ASN
C 109 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.177997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.139063 restraints weight = 24728.367|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 2.37
r_work: 0.3515 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3366 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.171   7794  Z= 0.169
  Angle     :  0.893  59.195  10557  Z= 0.525
  Chirality :  0.040   0.238   1248
  Planarity :  0.004   0.054   1328
  Dihedral  :  7.907 101.331   1090
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 15.84 %
    Favored  : 82.74 %
  Cbeta Deviations :  0.11 %
  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 aren not related in a simple way.
  whole:  1.30 (0.27), residues: 989
  helix:  1.86 (0.23), residues: 483
  sheet:  0.02 (0.44), residues: 142
  loop : -0.05 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 174 
 TYR   0.009   0.001   TYR A 483 
 PHE   0.026   0.001   PHE A 818 
 TRP   0.004   0.001   TRP A 766 
 HIS   0.002   0.001   HIS C  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 7793)
  covalent geometry    : angle       0.89270 (10555)
  SS BOND              : bond        0.00020 (    1)
  SS BOND              : angle       0.06057 (    2)
  hydrogen bonds       : bond        0.03690 (  432)
  hydrogen bonds       : angle       4.36848 ( 1356)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4658.68 seconds
wall clock time: 79 minutes 48.09 seconds (4788.09 seconds total)