Starting phenix.real_space_refine
on Fri Jul  3 03:20:18 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9o1q_70017/07_2026/9o1q_70017.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9o1q_70017/07_2026/9o1q_70017.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9o1q_70017/07_2026/9o1q_70017.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9o1q_70017/07_2026/9o1q_70017.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9o1q_70017/07_2026/9o1q_70017.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9o1q_70017/07_2026/9o1q_70017.map"
  }
  resolution = 4.2
  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=   0.003 sd=   0.014
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      74      5.16       5
     C    7586      2.51       5
     N    1868      2.21       5
     O    2022      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11556
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5775
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 709, 5775
          Classifications: {'peptide': 709}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 32, 'TRANS': 676}
          Chain breaks: 7
          Unresolved non-hydrogen bonds: 75
          Unresolved non-hydrogen angles: 94
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 0
          Ad-hoc single atom residues: {' CA': 3}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.76, per 1000 atoms: 0.50
  Number of scatterers: 11556
  At special positions: 0
  Unit cell: (122.925, 111.375, 111.375, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      74     16.00
     O    2022      8.00
     N    1868      7.00
     C    7586      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=10, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 352 " - pdb=" SG  CYS A 356 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 331 " - pdb=" SG  CYS B 372 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 349 " - pdb=" SG  CYS B 807 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 352 " - pdb=" SG  CYS B 356 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 601 " 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: 1.14
  Conformation dependent library (CDL) restraints added in 491.6 milliseconds
  

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2696

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 4 sheets defined
      62.2% alpha, 2.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 109
    Processing helix  chain 'A' and resid 131 through 142
      removed outlier: 3.687A  pdb=" N   MET A 142 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 220
      removed outlier: 4.114A  pdb=" N   ARG A 219 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 264 through 273
      removed outlier: 3.507A  pdb=" N   LEU A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 292
    Processing helix  chain 'A' and resid 296 through 326
      removed outlier: 4.764A  pdb=" N   LEU A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA A 313 " --> pdb=" O   MET A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 338
      removed outlier: 3.580A  pdb=" N   LYS A 335 " --> pdb=" O   CYS A 331 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   CYS A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 363
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 4.068A  pdb=" N   LYS A 370 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE A 373 " --> pdb=" O   LYS A 369 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE A 374 " --> pdb=" O   LYS A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 408
      removed outlier: 4.036A  pdb=" N   LEU A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   THR A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 480
      removed outlier: 3.862A  pdb=" N   THR A 454 " --> pdb=" O   CYS A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 537
    Processing helix  chain 'A' and resid 543 through 573
      removed outlier: 3.854A  pdb=" N   SER A 565 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 613
      removed outlier: 3.754A  pdb=" N   GLU A 604 " --> pdb=" O   GLY A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 639
      Proline residue:  A 628  - end of helix
    Processing helix  chain 'A' and resid 648 through 656
      removed outlier: 3.851A  pdb=" N   GLN A 652 " --> pdb=" O   PRO A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 681
      removed outlier: 3.674A  pdb=" N   TYR A 666 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU A 667 " --> pdb=" O   GLY A 663 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN A 674 " --> pdb=" O   GLU A 670 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE A 681 " --> pdb=" O   PHE A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 710
      removed outlier: 4.445A  pdb=" N   LEU A 698 " --> pdb=" O   VAL A 694 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR A 709 " --> pdb=" O   TRP A 705 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN A 710 " --> pdb=" O   LYS A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 732
      removed outlier: 4.197A  pdb=" N   MET A 729 " --> pdb=" O   TRP A 725 " (cutoff:3.500A)
      removed outlier: 4.349A  pdb=" N   GLN A 730 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 746
    Processing helix  chain 'A' and resid 749 through 759
    Processing helix  chain 'A' and resid 775 through 780
    Processing helix  chain 'A' and resid 825 through 857
      removed outlier: 3.590A  pdb=" N   ILE A 857 " --> pdb=" O   ILE A 853 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 875
      removed outlier: 4.521A  pdb=" N   THR A 864 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LYS A 865 " --> pdb=" O   SER A 861 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   THR A 875 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 109
    Processing helix  chain 'B' and resid 131 through 142
      removed outlier: 3.688A  pdb=" N   MET B 142 " --> pdb=" O   TYR B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 205 through 220
      removed outlier: 4.114A  pdb=" N   ARG B 219 " --> pdb=" O   PHE B 215 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   VAL B 220 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 232 through 240
    Processing helix  chain 'B' and resid 264 through 273
      removed outlier: 3.507A  pdb=" N   LEU B 268 " --> pdb=" O   SER B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 292
    Processing helix  chain 'B' and resid 296 through 326
      removed outlier: 4.763A  pdb=" N   LEU B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ALA B 313 " --> pdb=" O   MET B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 338
      removed outlier: 3.580A  pdb=" N   LYS B 335 " --> pdb=" O   CYS B 331 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   CYS B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 360 through 363
    Processing helix  chain 'B' and resid 364 through 374
      removed outlier: 4.067A  pdb=" N   LYS B 370 " --> pdb=" O   GLU B 366 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ILE B 373 " --> pdb=" O   LYS B 369 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE B 374 " --> pdb=" O   LYS B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 408
      removed outlier: 4.036A  pdb=" N   LEU B 380 " --> pdb=" O   SER B 376 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   THR B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 480
      removed outlier: 3.861A  pdb=" N   THR B 454 " --> pdb=" O   CYS B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 537
    Processing helix  chain 'B' and resid 543 through 573
      removed outlier: 3.853A  pdb=" N   SER B 565 " --> pdb=" O   VAL B 561 " (cutoff:3.500A)
      removed outlier: 5.298A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 613
      removed outlier: 3.754A  pdb=" N   GLU B 604 " --> pdb=" O   GLY B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 614 through 639
      Proline residue:  B 628  - end of helix
    Processing helix  chain 'B' and resid 648 through 656
      removed outlier: 3.851A  pdb=" N   GLN B 652 " --> pdb=" O   PRO B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 681
      removed outlier: 3.674A  pdb=" N   TYR B 666 " --> pdb=" O   LEU B 662 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLU B 667 " --> pdb=" O   GLY B 663 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 674 " --> pdb=" O   GLU B 670 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   PHE B 681 " --> pdb=" O   PHE B 677 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 710
      removed outlier: 4.445A  pdb=" N   LEU B 698 " --> pdb=" O   VAL B 694 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ILE B 700 " --> pdb=" O   ASN B 696 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   THR B 709 " --> pdb=" O   TRP B 705 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 710 " --> pdb=" O   LYS B 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 732
      removed outlier: 4.197A  pdb=" N   MET B 729 " --> pdb=" O   TRP B 725 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLN B 730 " --> pdb=" O   GLN B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 732 through 746
    Processing helix  chain 'B' and resid 749 through 759
    Processing helix  chain 'B' and resid 775 through 780
    Processing helix  chain 'B' and resid 825 through 857
      removed outlier: 3.590A  pdb=" N   ILE B 857 " --> pdb=" O   ILE B 853 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 860 through 875
      removed outlier: 4.521A  pdb=" N   THR B 864 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   LYS B 865 " --> pdb=" O   SER B 861 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   THR B 875 " --> pdb=" O   GLU B 871 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116
      removed outlier: 3.563A  pdb=" N   THR A 115 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ILE A  74 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 246 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL A  76 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA A 244 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 782 through 784
    Processing sheet with id=AA3, first strand: chain 'B' and resid 115 through 116
      removed outlier: 3.563A  pdb=" N   THR B 115 " --> pdb=" O   PHE B 125 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ILE B  74 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   PHE B 246 " --> pdb=" O   ILE B  74 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   VAL B  76 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   ALA B 244 " --> pdb=" O   VAL B  76 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 782 through 784

    628 hydrogen bonds defined for protein.
    1866 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.76

  Time building geometry restraints manager: 1.49 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: 3517
        1.34 -     1.46: 2471
        1.46 -     1.58: 5760
        1.58 -     1.69: 0
        1.69 -     1.81: 112
  Bond restraints: 11860
  Sorted by residual:
  bond pdb=" CB  TRP A 397 "
       pdb=" CG  TRP A 397 "
    ideal  model  delta    sigma   weight residual
    1.498  1.457  0.041 3.10e-02 1.04e+03 1.73e+00
  bond pdb=" CB  TRP B 397 "
       pdb=" CG  TRP B 397 "
    ideal  model  delta    sigma   weight residual
    1.498  1.458  0.040 3.10e-02 1.04e+03 1.70e+00
  bond pdb=" N   ILE B 786 "
       pdb=" CA  ILE B 786 "
    ideal  model  delta    sigma   weight residual
    1.474  1.456  0.018 1.57e-02 4.06e+03 1.38e+00
  bond pdb=" N   ILE A 786 "
       pdb=" CA  ILE A 786 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.018 1.57e-02 4.06e+03 1.29e+00
  bond pdb=" CG  MET A 309 "
       pdb=" SD  MET A 309 "
    ideal  model  delta    sigma   weight residual
    1.803  1.776  0.027 2.50e-02 1.60e+03 1.17e+00
  ... (remaining 11855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 15572
        1.55 -     3.11: 377
        3.11 -     4.66: 79
        4.66 -     6.21: 54
        6.21 -     7.77: 10
  Bond angle restraints: 16092
  Sorted by residual:
  angle pdb=" C   GLN A 308 "
        pdb=" N   MET A 309 "
        pdb=" CA  MET A 309 "
      ideal   model   delta    sigma   weight residual
     122.54  114.93    7.61 1.65e+00 3.67e-01 2.13e+01
  angle pdb=" C   GLN B 308 "
        pdb=" N   MET B 309 "
        pdb=" CA  MET B 309 "
      ideal   model   delta    sigma   weight residual
     122.54  114.95    7.59 1.65e+00 3.67e-01 2.12e+01
  angle pdb=" N   GLU A 529 "
        pdb=" CA  GLU A 529 "
        pdb=" CB  GLU A 529 "
      ideal   model   delta    sigma   weight residual
     110.28  115.72   -5.44 1.55e+00 4.16e-01 1.23e+01
  angle pdb=" N   GLU B 529 "
        pdb=" CA  GLU B 529 "
        pdb=" CB  GLU B 529 "
      ideal   model   delta    sigma   weight residual
     110.28  115.69   -5.41 1.55e+00 4.16e-01 1.22e+01
  angle pdb=" N   MET B 842 "
        pdb=" CA  MET B 842 "
        pdb=" CB  MET B 842 "
      ideal   model   delta    sigma   weight residual
     110.01  114.95   -4.94 1.45e+00 4.76e-01 1.16e+01
  ... (remaining 16087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.69: 6266
       16.69 -    33.38: 557
       33.38 -    50.07: 141
       50.07 -    66.76: 22
       66.76 -    83.45: 12
  Dihedral angle restraints: 6998
    sinusoidal: 2810
      harmonic: 4188
  Sorted by residual:
  dihedral pdb=" CB  CYS B 338 "
           pdb=" SG  CYS B 338 "
           pdb=" SG  CYS B 365 "
           pdb=" CB  CYS B 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.67  -82.33     1      1.00e+01 1.00e-02 8.32e+01
  dihedral pdb=" CB  CYS A 338 "
           pdb=" SG  CYS A 338 "
           pdb=" SG  CYS A 365 "
           pdb=" CB  CYS A 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.68  -82.32     1      1.00e+01 1.00e-02 8.32e+01
  dihedral pdb=" CB  CYS A 596 "
           pdb=" SG  CYS A 596 "
           pdb=" SG  CYS A 601 "
           pdb=" CB  CYS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -30.66  -55.34     1      1.00e+01 1.00e-02 4.14e+01
  ... (remaining 6995 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1184
       0.039 -    0.079: 447
       0.079 -    0.118: 119
       0.118 -    0.158: 20
       0.158 -    0.197: 2
  Chirality restraints: 1772
  Sorted by residual:
  chirality pdb=" CB  ILE A 857 "
            pdb=" CA  ILE A 857 "
            pdb=" CG1 ILE A 857 "
            pdb=" CG2 ILE A 857 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.71e-01
  chirality pdb=" CB  ILE B 857 "
            pdb=" CA  ILE B 857 "
            pdb=" CG1 ILE B 857 "
            pdb=" CG2 ILE B 857 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.59e-01
  chirality pdb=" CA  MET B 309 "
            pdb=" N   MET B 309 "
            pdb=" C   MET B 309 "
            pdb=" CB  MET B 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.79e-01
  ... (remaining 1769 not shown)

  Planarity restraints: 2000
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 302 "    0.010 2.00e-02 2.50e+03   1.32e-02 4.32e+00
        pdb=" CG  TRP A 302 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 302 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 302 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 302 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 302 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 302 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 302 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 302 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 302 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 302 "   -0.011 2.00e-02 2.50e+03   1.31e-02 4.30e+00
        pdb=" CG  TRP B 302 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 302 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 302 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 302 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 302 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 302 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 302 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 302 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 302 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 763 "    0.034 5.00e-02 4.00e+02   5.05e-02 4.09e+00
        pdb=" N   PRO B 764 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO B 764 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 764 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1997 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1042
        2.74 -     3.28: 13100
        3.28 -     3.82: 20208
        3.82 -     4.36: 23052
        4.36 -     4.90: 36471
  Nonbonded interactions: 93873
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 667 "
            pdb="CA    CA B1002 "
     model   vdw
     2.199 3.250
  nonbonded pdb=" OE2 GLU A 667 "
            pdb="CA    CA A1002 "
     model   vdw
     2.200 3.250
  nonbonded pdb=" O   ILE B 744 "
            pdb=" OG  SER B 748 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   ILE A 744 "
            pdb=" OG  SER A 748 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   TYR B 776 "
            pdb=" OG1 THR B 780 "
     model   vdw
     2.202 3.040
  ... (remaining 93868 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.340
  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:             0.020
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.330
  Find NCS groups from input model:        0.100
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7062
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      :  0.003   0.041  11870  Z= 0.137
  Angle     :  0.688   7.766  16112  Z= 0.373
  Chirality :  0.043   0.197   1772
  Planarity :  0.004   0.051   2000
  Dihedral  : 13.763  83.453   4272
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 17.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  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: -0.41 (0.23), residues: 1386
  helix:  0.40 (0.19), residues: 800
  sheet: -1.37 (0.75), residues: 52
  loop : -1.09 (0.28), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 701 
 TYR   0.025   0.001   TYR B 305 
 PHE   0.030   0.001   PHE A 677 
 TRP   0.033   0.002   TRP B 302 
 HIS   0.004   0.001   HIS A 844 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.14 (11860)
  covalent geometry    : angle       0.68656 /  0.37 (16092)
  SS BOND              : bond        0.00135 /  0.06 (   10)
  SS BOND              : angle       1.36077 /  0.88 (   20)
  hydrogen bonds       : bond        0.13755 /  8.76 (  628)
  hydrogen bonds       : angle       6.33089 /  4.37 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 282
  time to evaluate  : 0.463 
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  273 TRP cc_start: 0.8390 (t-100) cc_final: 0.8021 (t-100)
REVERT: A  553 MET cc_start: 0.8606 (pmm) cc_final: 0.8250 (pmm)
REVERT: A  559 GLN cc_start: 0.8531 (tp-100) cc_final: 0.6644 (tp-100)
REVERT: A  672 ILE cc_start: 0.8862 (mm) cc_final: 0.8387 (mm)
REVERT: A  722 ILE cc_start: 0.7176 (mm) cc_final: 0.6963 (mm)
REVERT: A  808 ARG cc_start: 0.8754 (tpp80) cc_final: 0.8318 (tpp80)
REVERT: B  298 ILE cc_start: 0.8245 (pt) cc_final: 0.8032 (pt)
REVERT: B  309 MET cc_start: 0.7644 (pmm) cc_final: 0.7280 (pmm)
REVERT: B  546 ASP cc_start: 0.8228 (t0) cc_final: 0.8008 (t70)
REVERT: B  553 MET cc_start: 0.8660 (pmm) cc_final: 0.8291 (pmm)
REVERT: B  559 GLN cc_start: 0.8586 (tp-100) cc_final: 0.6347 (tp-100)
REVERT: B  563 TYR cc_start: 0.7574 (m-10) cc_final: 0.7372 (m-10)
REVERT: B  672 ILE cc_start: 0.9001 (mm) cc_final: 0.8503 (mm)
REVERT: B  701 ARG cc_start: 0.8984 (mmp-170) cc_final: 0.8559 (mmp80)
REVERT: B  850 LYS cc_start: 0.8666 (mmtm) cc_final: 0.8124 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 282
  average time/residue: 0.0921
  time to fit residues: 39.4043
Evaluate side-chains
  219 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   overall best weight:    2.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 549 ASN
A 621 ASN
A 818 HIS
B 549 ASN
B 621 ASN
B 818 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4434 r_free = 0.4434 target = 0.115049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.083564 restraints weight = 43391.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.086484 restraints weight = 28483.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.088515 restraints weight = 21347.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.089966 restraints weight = 17380.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.090757 restraints weight = 14967.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.1279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11870  Z= 0.143
  Angle     :  0.614   7.818  16112  Z= 0.325
  Chirality :  0.043   0.179   1772
  Planarity :  0.004   0.048   2000
  Dihedral  :  4.144  18.254   1562
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  5.64 %
    Favored  : 94.28 %
  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: -0.21 (0.23), residues: 1386
  helix:  0.51 (0.18), residues: 848
  sheet: -1.29 (0.78), residues: 52
  loop : -1.05 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 701 
 TYR   0.025   0.001   TYR B 305 
 PHE   0.025   0.002   PHE B 677 
 TRP   0.011   0.001   TRP A 302 
 HIS   0.003   0.001   HIS A 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 (11860)
  covalent geometry    : angle       0.61217 /  0.32 (16092)
  SS BOND              : bond        0.00379 /  0.16 (   10)
  SS BOND              : angle       1.35061 /  0.85 (   20)
  hydrogen bonds       : bond        0.03884 /  2.46 (  628)
  hydrogen bonds       : angle       4.94893 /  3.38 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 274
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  523 ILE cc_start: 0.9306 (pt) cc_final: 0.9054 (pt)
REVERT: A  546 ASP cc_start: 0.8437 (t0) cc_final: 0.8101 (t70)
REVERT: A  559 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8478 (tp-100)
REVERT: A  672 ILE cc_start: 0.9030 (mm) cc_final: 0.8650 (mm)
REVERT: A  722 ILE cc_start: 0.7309 (mm) cc_final: 0.6977 (mm)
REVERT: A  729 MET cc_start: 0.8611 (mpp) cc_final: 0.8202 (mpp)
REVERT: A  742 MET cc_start: 0.9319 (mmp) cc_final: 0.9093 (mmm)
REVERT: B  302 TRP cc_start: 0.8546 (t60) cc_final: 0.8258 (t60)
REVERT: B  309 MET cc_start: 0.7698 (pmm) cc_final: 0.7211 (pmm)
REVERT: B  333 TRP cc_start: 0.8683 (p-90) cc_final: 0.8463 (p-90)
REVERT: B  523 ILE cc_start: 0.9312 (pt) cc_final: 0.9056 (pt)
REVERT: B  546 ASP cc_start: 0.8293 (t0) cc_final: 0.7938 (t70)
REVERT: B  559 GLN cc_start: 0.8775 (tp-100) cc_final: 0.8472 (tp-100)
REVERT: B  672 ILE cc_start: 0.9101 (mm) cc_final: 0.8642 (mm)
REVERT: B  701 ARG cc_start: 0.8935 (mmp-170) cc_final: 0.8016 (mmp80)
REVERT: B  729 MET cc_start: 0.8709 (mpp) cc_final: 0.8348 (mpp)
REVERT: B  740 ASN cc_start: 0.8848 (m110) cc_final: 0.8647 (m110)
REVERT: B  742 MET cc_start: 0.9366 (mmp) cc_final: 0.8996 (mmm)
REVERT: B  808 ARG cc_start: 0.8721 (tpp80) cc_final: 0.8259 (tpp80)
REVERT: B  850 LYS cc_start: 0.8937 (mmtm) cc_final: 0.8406 (tptp)
  outliers start: 1
  outliers final: 0
  residues processed: 275
  average time/residue: 0.0974
  time to fit residues: 39.5283
Evaluate side-chains
  224 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 53 optimal weight:    0.7980
   chunk 47 optimal weight:    9.9990
   chunk 104 optimal weight:   20.0000
   chunk 6 optimal weight:   30.0000
   chunk 33 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0670
   chunk 130 optimal weight:    3.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.3720

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 710 GLN
A 814 ASN
B 710 GLN
B 814 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.115752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.083741 restraints weight = 42715.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.086712 restraints weight = 28004.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.088833 restraints weight = 20909.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.090339 restraints weight = 16936.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.091411 restraints weight = 14515.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11870  Z= 0.119
  Angle     :  0.623   8.288  16112  Z= 0.323
  Chirality :  0.043   0.208   1772
  Planarity :  0.004   0.045   2000
  Dihedral  :  4.106  16.335   1562
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  4.11 %
    Favored  : 95.73 %
  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: -0.23 (0.23), residues: 1386
  helix:  0.49 (0.18), residues: 852
  sheet: -1.25 (0.78), residues: 52
  loop : -1.07 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 701 
 TYR   0.022   0.001   TYR A 305 
 PHE   0.039   0.002   PHE A 838 
 TRP   0.021   0.001   TRP A 302 
 HIS   0.002   0.001   HIS B 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00250 /  0.12 (11860)
  covalent geometry    : angle       0.62189 /  0.32 (16092)
  SS BOND              : bond        0.00282 /  0.12 (   10)
  SS BOND              : angle       1.27870 /  0.81 (   20)
  hydrogen bonds       : bond        0.03651 /  2.30 (  628)
  hydrogen bonds       : angle       4.83176 /  3.30 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 279
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.8632 (mmm) cc_final: 0.8409 (mmm)
REVERT: A  523 ILE cc_start: 0.9302 (pt) cc_final: 0.9061 (pt)
REVERT: A  546 ASP cc_start: 0.8472 (t0) cc_final: 0.8103 (t70)
REVERT: A  559 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8322 (tp-100)
REVERT: A  672 ILE cc_start: 0.9140 (mm) cc_final: 0.8791 (mm)
REVERT: A  729 MET cc_start: 0.8580 (mpp) cc_final: 0.8111 (mpp)
REVERT: A  734 ILE cc_start: 0.8682 (mp) cc_final: 0.8455 (mp)
REVERT: A  742 MET cc_start: 0.9342 (mmp) cc_final: 0.9120 (mmm)
REVERT: A  808 ARG cc_start: 0.8908 (tpp80) cc_final: 0.8406 (tpp80)
REVERT: B  302 TRP cc_start: 0.8515 (t60) cc_final: 0.8186 (t60)
REVERT: B  309 MET cc_start: 0.7618 (pmm) cc_final: 0.7188 (pmm)
REVERT: B  333 TRP cc_start: 0.8692 (p-90) cc_final: 0.8460 (p-90)
REVERT: B  523 ILE cc_start: 0.9304 (pt) cc_final: 0.9054 (pt)
REVERT: B  546 ASP cc_start: 0.8317 (t0) cc_final: 0.7934 (t70)
REVERT: B  559 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8285 (tp-100)
REVERT: B  672 ILE cc_start: 0.9193 (mm) cc_final: 0.8870 (mm)
REVERT: B  729 MET cc_start: 0.8711 (mpp) cc_final: 0.8316 (mpp)
REVERT: B  742 MET cc_start: 0.9380 (mmp) cc_final: 0.8979 (mmm)
REVERT: B  808 ARG cc_start: 0.8845 (tpp80) cc_final: 0.8299 (tpp80)
REVERT: B  839 ILE cc_start: 0.9098 (pt) cc_final: 0.8669 (pt)
REVERT: B  842 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8591 (mpp)
REVERT: B  847 TYR cc_start: 0.7865 (t80) cc_final: 0.7240 (t80)
REVERT: B  850 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8460 (tptp)
  outliers start: 2
  outliers final: 0
  residues processed: 279
  average time/residue: 0.1007
  time to fit residues: 41.3759
Evaluate side-chains
  218 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 217
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 118 optimal weight:    9.9990
   chunk 129 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 123 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 80 optimal weight:    9.9990
   chunk 8 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0020
   chunk 86 optimal weight:   10.0000
   overall best weight:    4.3996

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 655 HIS
A 657 GLN
A 726 GLN
B 657 GLN
B 720 GLN
** B 726 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 = 0.4347 r_free = 0.4347 target = 0.108974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.078252 restraints weight = 44698.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.080907 restraints weight = 29564.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.082731 restraints weight = 22246.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.083980 restraints weight = 18167.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.084563 restraints weight = 15785.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  11870  Z= 0.201
  Angle     :  0.684   7.510  16112  Z= 0.366
  Chirality :  0.045   0.252   1772
  Planarity :  0.005   0.049   2000
  Dihedral  :  4.536  21.917   1562
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 18.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  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: -0.44 (0.23), residues: 1386
  helix:  0.22 (0.18), residues: 844
  sheet:  0.58 (1.05), residues: 32
  loop : -1.08 (0.29), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 712 
 TYR   0.030   0.002   TYR A 305 
 PHE   0.041   0.002   PHE B 851 
 TRP   0.017   0.002   TRP B 273 
 HIS   0.008   0.001   HIS B 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.20 (11860)
  covalent geometry    : angle       0.68182 /  0.37 (16092)
  SS BOND              : bond        0.00513 /  0.29 (   10)
  SS BOND              : angle       1.71088 /  1.06 (   20)
  hydrogen bonds       : bond        0.04073 /  2.61 (  628)
  hydrogen bonds       : angle       5.00523 /  3.42 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 MET cc_start: 0.8227 (pmm) cc_final: 0.7809 (pmm)
REVERT: A  385 PHE cc_start: 0.8657 (t80) cc_final: 0.8410 (t80)
REVERT: A  558 PHE cc_start: 0.9291 (m-80) cc_final: 0.9044 (m-80)
REVERT: A  559 GLN cc_start: 0.8541 (tp-100) cc_final: 0.8163 (tp-100)
REVERT: A  573 PHE cc_start: 0.7842 (m-80) cc_final: 0.7324 (m-80)
REVERT: A  672 ILE cc_start: 0.9115 (mm) cc_final: 0.8705 (mm)
REVERT: A  729 MET cc_start: 0.8785 (mpp) cc_final: 0.8385 (mpp)
REVERT: A  742 MET cc_start: 0.9330 (mmp) cc_final: 0.9120 (mmm)
REVERT: B  273 TRP cc_start: 0.8665 (t-100) cc_final: 0.8330 (t-100)
REVERT: B  309 MET cc_start: 0.8081 (pmm) cc_final: 0.7506 (pmm)
REVERT: B  385 PHE cc_start: 0.8740 (t80) cc_final: 0.8455 (t80)
REVERT: B  386 MET cc_start: 0.8306 (mmp) cc_final: 0.8028 (mmp)
REVERT: B  398 LYS cc_start: 0.9463 (tppt) cc_final: 0.9176 (tptp)
REVERT: B  546 ASP cc_start: 0.8382 (t0) cc_final: 0.8015 (t70)
REVERT: B  559 GLN cc_start: 0.8533 (tp-100) cc_final: 0.8142 (tp-100)
REVERT: B  573 PHE cc_start: 0.7810 (m-80) cc_final: 0.7290 (m-80)
REVERT: B  608 GLN cc_start: 0.9310 (tm-30) cc_final: 0.9065 (tm-30)
REVERT: B  672 ILE cc_start: 0.9172 (mm) cc_final: 0.8804 (mm)
REVERT: B  729 MET cc_start: 0.8822 (mpp) cc_final: 0.8408 (mpp)
REVERT: B  742 MET cc_start: 0.9384 (mmp) cc_final: 0.9135 (mmm)
REVERT: B  808 ARG cc_start: 0.8812 (tpp80) cc_final: 0.8521 (mmt90)
REVERT: B  847 TYR cc_start: 0.7639 (t80) cc_final: 0.7296 (t80)
REVERT: B  850 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8368 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1015
  time to fit residues: 38.3063
Evaluate side-chains
  220 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 121 optimal weight:    5.9990
   chunk 135 optimal weight:    6.9990
   chunk 109 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 116 optimal weight:    2.9990
   chunk 110 optimal weight:    7.9990
   chunk 117 optimal weight:   20.0000
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 720 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.113067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.081069 restraints weight = 42949.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.084018 restraints weight = 28016.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.086080 restraints weight = 20848.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.087316 restraints weight = 16930.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.088484 restraints weight = 14828.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7200
moved from start:          0.2589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11870  Z= 0.122
  Angle     :  0.646   9.298  16112  Z= 0.333
  Chirality :  0.044   0.231   1772
  Planarity :  0.004   0.078   2000
  Dihedral  :  4.299  18.778   1562
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.46 %
    Favored  : 96.38 %
  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: -0.29 (0.23), residues: 1386
  helix:  0.40 (0.18), residues: 852
  sheet:  0.40 (1.03), residues: 32
  loop : -1.15 (0.29), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 712 
 TYR   0.027   0.001   TYR A 847 
 PHE   0.031   0.002   PHE A 851 
 TRP   0.021   0.001   TRP B 302 
 HIS   0.012   0.001   HIS B 655 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 (11860)
  covalent geometry    : angle       0.64417 /  0.33 (16092)
  SS BOND              : bond        0.00335 /  0.14 (   10)
  SS BOND              : angle       1.43475 /  0.88 (   20)
  hydrogen bonds       : bond        0.03574 /  2.30 (  628)
  hydrogen bonds       : angle       4.71929 /  3.23 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  271 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 269
  time to evaluate  : 0.518 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  273 TRP cc_start: 0.8720 (t-100) cc_final: 0.8317 (t-100)
REVERT: A  298 ILE cc_start: 0.8538 (pt) cc_final: 0.8307 (pt)
REVERT: A  309 MET cc_start: 0.8038 (pmm) cc_final: 0.7719 (pmm)
REVERT: A  385 PHE cc_start: 0.8697 (t80) cc_final: 0.8446 (t80)
REVERT: A  523 ILE cc_start: 0.9312 (pt) cc_final: 0.9075 (pt)
REVERT: A  534 MET cc_start: 0.6840 (mmm) cc_final: 0.6300 (mtt)
REVERT: A  559 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8289 (tp-100)
REVERT: A  672 ILE cc_start: 0.9134 (mm) cc_final: 0.8762 (mm)
REVERT: A  729 MET cc_start: 0.8658 (mpp) cc_final: 0.8196 (mpp)
REVERT: A  742 MET cc_start: 0.9365 (mmp) cc_final: 0.9136 (mmm)
REVERT: A  808 ARG cc_start: 0.8907 (tpp80) cc_final: 0.8482 (tpp80)
REVERT: A  850 LYS cc_start: 0.9325 (mmtm) cc_final: 0.8879 (mmmm)
REVERT: B  273 TRP cc_start: 0.8641 (t-100) cc_final: 0.8329 (t-100)
REVERT: B  300 PHE cc_start: 0.9095 (m-80) cc_final: 0.8875 (m-10)
REVERT: B  309 MET cc_start: 0.7970 (pmm) cc_final: 0.7468 (pmm)
REVERT: B  385 PHE cc_start: 0.8697 (t80) cc_final: 0.8463 (t80)
REVERT: B  398 LYS cc_start: 0.9469 (tppt) cc_final: 0.9173 (tptp)
REVERT: B  559 GLN cc_start: 0.8696 (tp-100) cc_final: 0.8325 (tp-100)
REVERT: B  672 ILE cc_start: 0.9238 (mm) cc_final: 0.8991 (mm)
REVERT: B  729 MET cc_start: 0.8734 (mpp) cc_final: 0.8359 (mpp)
REVERT: B  742 MET cc_start: 0.9381 (mmp) cc_final: 0.9074 (mmm)
REVERT: B  808 ARG cc_start: 0.8876 (tpp80) cc_final: 0.8269 (tpp80)
REVERT: B  850 LYS cc_start: 0.9121 (mmtm) cc_final: 0.8490 (tptp)
  outliers start: 2
  outliers final: 0
  residues processed: 269
  average time/residue: 0.1021
  time to fit residues: 40.3663
Evaluate side-chains
  216 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 68 optimal weight:    7.9990
   chunk 136 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 9 optimal weight:    0.0060
   chunk 95 optimal weight:    6.9990
   chunk 81 optimal weight:    3.9990
   chunk 11 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 5 optimal weight:   30.0000
   chunk 92 optimal weight:   20.0000
   chunk 86 optimal weight:    5.9990
   overall best weight:    4.6004

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 655 HIS
** B 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.107846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.076910 restraints weight = 44405.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.079591 restraints weight = 28813.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.081452 restraints weight = 21466.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.082834 restraints weight = 17436.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.083535 restraints weight = 15038.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.3310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  11870  Z= 0.206
  Angle     :  0.707   8.269  16112  Z= 0.378
  Chirality :  0.047   0.278   1772
  Planarity :  0.005   0.069   2000
  Dihedral  :  4.647  18.148   1562
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 19.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  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: -0.55 (0.22), residues: 1386
  helix:  0.19 (0.17), residues: 844
  sheet: -1.48 (0.74), residues: 52
  loop : -1.04 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 712 
 TYR   0.031   0.002   TYR B 305 
 PHE   0.028   0.002   PHE B 838 
 TRP   0.019   0.002   TRP A 408 
 HIS   0.006   0.001   HIS B 824 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00436 /  0.21 (11860)
  covalent geometry    : angle       0.70462 /  0.38 (16092)
  SS BOND              : bond        0.00519 /  0.30 (   10)
  SS BOND              : angle       1.72276 /  1.06 (   20)
  hydrogen bonds       : bond        0.04036 /  2.60 (  628)
  hydrogen bonds       : angle       5.00059 /  3.39 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 0.454 
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  225 MET cc_start: 0.8645 (pmm) cc_final: 0.8405 (pmm)
REVERT: A  385 PHE cc_start: 0.8669 (t80) cc_final: 0.8302 (t80)
REVERT: A  386 MET cc_start: 0.9002 (tpt) cc_final: 0.8679 (mmm)
REVERT: A  397 TRP cc_start: 0.7756 (t-100) cc_final: 0.7220 (t-100)
REVERT: A  523 ILE cc_start: 0.9318 (pt) cc_final: 0.9063 (pt)
REVERT: A  559 GLN cc_start: 0.8635 (tp-100) cc_final: 0.8293 (tp-100)
REVERT: A  672 ILE cc_start: 0.9221 (mm) cc_final: 0.8940 (mm)
REVERT: A  718 LYS cc_start: 0.9332 (ptpp) cc_final: 0.9102 (tmtt)
REVERT: A  729 MET cc_start: 0.8844 (mpp) cc_final: 0.8442 (mpp)
REVERT: A  742 MET cc_start: 0.9391 (mmp) cc_final: 0.9167 (mmm)
REVERT: A  850 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9118 (mmmm)
REVERT: B  298 ILE cc_start: 0.8615 (pt) cc_final: 0.8399 (pt)
REVERT: B  305 TYR cc_start: 0.7419 (p90) cc_final: 0.7126 (p90)
REVERT: B  385 PHE cc_start: 0.8722 (t80) cc_final: 0.8439 (t80)
REVERT: B  386 MET cc_start: 0.8182 (mmp) cc_final: 0.7970 (mmp)
REVERT: B  397 TRP cc_start: 0.7691 (t-100) cc_final: 0.7302 (t-100)
REVERT: B  534 MET cc_start: 0.6723 (mmm) cc_final: 0.6339 (ttt)
REVERT: B  546 ASP cc_start: 0.8441 (t0) cc_final: 0.8085 (t70)
REVERT: B  558 PHE cc_start: 0.9374 (m-80) cc_final: 0.9161 (m-80)
REVERT: B  559 GLN cc_start: 0.8583 (tp-100) cc_final: 0.8251 (tp-100)
REVERT: B  608 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9098 (tm-30)
REVERT: B  671 MET cc_start: 0.8491 (ppp) cc_final: 0.7764 (tpp)
REVERT: B  699 GLU cc_start: 0.8923 (tp30) cc_final: 0.8600 (tp30)
REVERT: B  729 MET cc_start: 0.8848 (mpp) cc_final: 0.8343 (mpp)
REVERT: B  742 MET cc_start: 0.9419 (mmp) cc_final: 0.9174 (mmm)
REVERT: B  808 ARG cc_start: 0.8911 (tpp80) cc_final: 0.8587 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 263
  average time/residue: 0.0995
  time to fit residues: 38.9048
Evaluate side-chains
  209 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 101 optimal weight:   40.0000
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 1 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 48 optimal weight:    8.9990
   chunk 136 optimal weight:    9.9990
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:   20.0000
   overall best weight:    2.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 129 HIS
A 655 HIS
A 674 GLN
B 129 HIS
B 143 HIS
B 720 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.109203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.078019 restraints weight = 43166.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.080648 restraints weight = 28234.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.082525 restraints weight = 21177.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.083723 restraints weight = 17321.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.084690 restraints weight = 15182.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11870  Z= 0.157
  Angle     :  0.683   8.970  16112  Z= 0.361
  Chirality :  0.046   0.232   1772
  Planarity :  0.005   0.088   2000
  Dihedral  :  4.541  22.458   1562
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  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: -0.39 (0.23), residues: 1386
  helix:  0.31 (0.18), residues: 844
  sheet: -1.40 (0.78), residues: 52
  loop : -0.96 (0.29), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 639 
 TYR   0.031   0.001   TYR B 847 
 PHE   0.059   0.002   PHE A 838 
 TRP   0.015   0.002   TRP A 333 
 HIS   0.004   0.001   HIS B 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.16 (11860)
  covalent geometry    : angle       0.68059 /  0.36 (16092)
  SS BOND              : bond        0.00401 /  0.19 (   10)
  SS BOND              : angle       1.81756 /  1.14 (   20)
  hydrogen bonds       : bond        0.03847 /  2.48 (  628)
  hydrogen bonds       : angle       4.89766 /  3.31 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ILE cc_start: 0.8622 (pt) cc_final: 0.8348 (pt)
REVERT: A  385 PHE cc_start: 0.8656 (t80) cc_final: 0.8287 (t80)
REVERT: A  386 MET cc_start: 0.8953 (tpt) cc_final: 0.8703 (mmm)
REVERT: A  397 TRP cc_start: 0.7696 (t-100) cc_final: 0.6952 (t-100)
REVERT: A  546 ASP cc_start: 0.8518 (t0) cc_final: 0.8176 (t70)
REVERT: A  559 GLN cc_start: 0.8627 (tp-100) cc_final: 0.8224 (tp-100)
REVERT: A  671 MET cc_start: 0.8527 (ppp) cc_final: 0.7581 (tpp)
REVERT: A  729 MET cc_start: 0.8808 (mpp) cc_final: 0.8318 (mpp)
REVERT: A  730 GLN cc_start: 0.8729 (pm20) cc_final: 0.8508 (pm20)
REVERT: A  850 LYS cc_start: 0.9328 (mmtp) cc_final: 0.8882 (mmmm)
REVERT: B  298 ILE cc_start: 0.8548 (pt) cc_final: 0.8311 (pt)
REVERT: B  305 TYR cc_start: 0.7406 (p90) cc_final: 0.7152 (p90)
REVERT: B  385 PHE cc_start: 0.8733 (t80) cc_final: 0.8455 (t80)
REVERT: B  397 TRP cc_start: 0.7712 (t-100) cc_final: 0.7239 (t-100)
REVERT: B  523 ILE cc_start: 0.9319 (pt) cc_final: 0.9085 (pt)
REVERT: B  534 MET cc_start: 0.6735 (mmm) cc_final: 0.6350 (ttt)
REVERT: B  559 GLN cc_start: 0.8636 (tp-100) cc_final: 0.8258 (tp-100)
REVERT: B  608 GLN cc_start: 0.9318 (tm-30) cc_final: 0.9085 (tm-30)
REVERT: B  671 MET cc_start: 0.8459 (ppp) cc_final: 0.7642 (tpt)
REVERT: B  729 MET cc_start: 0.8656 (mpp) cc_final: 0.8148 (mpp)
REVERT: B  742 MET cc_start: 0.9391 (mmp) cc_final: 0.9161 (mmm)
REVERT: B  808 ARG cc_start: 0.8931 (tpp80) cc_final: 0.8587 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.0933
  time to fit residues: 36.3710
Evaluate side-chains
  212 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 48 optimal weight:    7.9990
   chunk 94 optimal weight:    0.7980
   chunk 4 optimal weight:   20.0000
   chunk 70 optimal weight:   50.0000
   chunk 83 optimal weight:    8.9990
   chunk 100 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0170
   chunk 99 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.5422

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 674 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 = 0.4381 r_free = 0.4381 target = 0.111025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.079494 restraints weight = 42562.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.082299 restraints weight = 27912.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.084357 restraints weight = 20855.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.085661 restraints weight = 16881.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.086693 restraints weight = 14631.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.3412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11870  Z= 0.132
  Angle     :  0.693   9.269  16112  Z= 0.359
  Chirality :  0.045   0.211   1772
  Planarity :  0.005   0.069   2000
  Dihedral  :  4.421  21.455   1562
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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: -0.39 (0.23), residues: 1386
  helix:  0.37 (0.18), residues: 852
  sheet: -1.35 (0.77), residues: 52
  loop : -1.13 (0.29), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 712 
 TYR   0.027   0.001   TYR B 847 
 PHE   0.049   0.002   PHE A 838 
 TRP   0.026   0.002   TRP A 408 
 HIS   0.008   0.001   HIS B 143 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 (11860)
  covalent geometry    : angle       0.69112 /  0.36 (16092)
  SS BOND              : bond        0.00317 /  0.13 (   10)
  SS BOND              : angle       1.67134 /  1.04 (   20)
  hydrogen bonds       : bond        0.03717 /  2.41 (  628)
  hydrogen bonds       : angle       4.78713 /  3.25 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  385 PHE cc_start: 0.8636 (t80) cc_final: 0.8402 (t80)
REVERT: A  397 TRP cc_start: 0.8013 (t-100) cc_final: 0.6991 (t-100)
REVERT: A  546 ASP cc_start: 0.8511 (t0) cc_final: 0.8176 (t70)
REVERT: A  559 GLN cc_start: 0.8756 (tp-100) cc_final: 0.8323 (tp-100)
REVERT: A  664 LEU cc_start: 0.9145 (pp) cc_final: 0.8943 (pp)
REVERT: A  671 MET cc_start: 0.8448 (ppp) cc_final: 0.7430 (tpt)
REVERT: A  729 MET cc_start: 0.8755 (mpp) cc_final: 0.8272 (mpp)
REVERT: A  730 GLN cc_start: 0.8686 (pm20) cc_final: 0.8463 (pm20)
REVERT: A  742 MET cc_start: 0.9357 (mmp) cc_final: 0.9076 (mmm)
REVERT: A  850 LYS cc_start: 0.9306 (mmtp) cc_final: 0.8879 (mmmm)
REVERT: B  273 TRP cc_start: 0.8739 (t-100) cc_final: 0.8422 (t-100)
REVERT: B  397 TRP cc_start: 0.7795 (t-100) cc_final: 0.7294 (t-100)
REVERT: B  534 MET cc_start: 0.6744 (mmm) cc_final: 0.6382 (ttt)
REVERT: B  559 GLN cc_start: 0.8754 (tp-100) cc_final: 0.8329 (tp-100)
REVERT: B  573 PHE cc_start: 0.7737 (m-80) cc_final: 0.7266 (m-80)
REVERT: B  664 LEU cc_start: 0.9154 (pp) cc_final: 0.8943 (pp)
REVERT: B  671 MET cc_start: 0.8476 (ppp) cc_final: 0.7686 (tpt)
REVERT: B  699 GLU cc_start: 0.8657 (tp30) cc_final: 0.8293 (tp30)
REVERT: B  729 MET cc_start: 0.8650 (mpp) cc_final: 0.8143 (mpp)
REVERT: B  742 MET cc_start: 0.9401 (mmp) cc_final: 0.9131 (mmm)
REVERT: B  808 ARG cc_start: 0.8939 (tpp80) cc_final: 0.8645 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.0935
  time to fit residues: 37.5227
Evaluate side-chains
  214 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 105 optimal weight:    8.9990
   chunk 111 optimal weight:    1.9990
   chunk 86 optimal weight:    5.9990
   chunk 72 optimal weight:    9.9990
   chunk 64 optimal weight:    4.9990
   chunk 113 optimal weight:    0.4980
   chunk 43 optimal weight:    0.5980
   chunk 100 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 63 optimal weight:    8.9990
   overall best weight:    2.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 824 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.110640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.078836 restraints weight = 42525.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.081588 restraints weight = 27948.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.083588 restraints weight = 20996.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.084971 restraints weight = 17096.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.085796 restraints weight = 14772.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11870  Z= 0.147
  Angle     :  0.712   8.992  16112  Z= 0.376
  Chirality :  0.046   0.203   1772
  Planarity :  0.005   0.062   2000
  Dihedral  :  4.402  20.754   1562
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  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: -0.40 (0.22), residues: 1386
  helix:  0.44 (0.18), residues: 850
  sheet: -2.06 (0.61), residues: 72
  loop : -1.12 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 712 
 TYR   0.032   0.001   TYR B 305 
 PHE   0.050   0.002   PHE A 838 
 TRP   0.021   0.002   TRP A 333 
 HIS   0.008   0.001   HIS B 655 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00318 /  0.15 (11860)
  covalent geometry    : angle       0.71022 /  0.38 (16092)
  SS BOND              : bond        0.00301 /  0.12 (   10)
  SS BOND              : angle       1.60691 /  1.00 (   20)
  hydrogen bonds       : bond        0.03839 /  2.49 (  628)
  hydrogen bonds       : angle       4.84826 /  3.30 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.473 
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  323 TYR cc_start: 0.9201 (t80) cc_final: 0.8925 (t80)
REVERT: A  397 TRP cc_start: 0.7781 (t-100) cc_final: 0.6547 (t-100)
REVERT: A  559 GLN cc_start: 0.8703 (tp-100) cc_final: 0.8310 (tp-100)
REVERT: A  672 ILE cc_start: 0.9130 (mm) cc_final: 0.8785 (mm)
REVERT: A  729 MET cc_start: 0.8760 (mpp) cc_final: 0.8313 (mpp)
REVERT: A  742 MET cc_start: 0.9357 (mmp) cc_final: 0.9085 (mmm)
REVERT: A  808 ARG cc_start: 0.8954 (tpp80) cc_final: 0.8622 (mmt90)
REVERT: A  850 LYS cc_start: 0.9305 (mmtp) cc_final: 0.8843 (mmmm)
REVERT: B  273 TRP cc_start: 0.8734 (t-100) cc_final: 0.8060 (t-100)
REVERT: B  298 ILE cc_start: 0.8738 (pt) cc_final: 0.8460 (pt)
REVERT: B  305 TYR cc_start: 0.7462 (p90) cc_final: 0.7079 (p90)
REVERT: B  397 TRP cc_start: 0.7935 (t-100) cc_final: 0.7042 (t-100)
REVERT: B  534 MET cc_start: 0.6710 (mmm) cc_final: 0.6329 (ttt)
REVERT: B  559 GLN cc_start: 0.8695 (tp-100) cc_final: 0.8285 (tp-100)
REVERT: B  672 ILE cc_start: 0.9129 (mm) cc_final: 0.8693 (mm)
REVERT: B  693 LEU cc_start: 0.9483 (mm) cc_final: 0.9253 (mm)
REVERT: B  699 GLU cc_start: 0.8701 (tp30) cc_final: 0.8436 (tp30)
REVERT: B  729 MET cc_start: 0.8586 (mpp) cc_final: 0.8062 (mpp)
REVERT: B  742 MET cc_start: 0.9397 (mmp) cc_final: 0.9165 (mmm)
REVERT: B  808 ARG cc_start: 0.8931 (tpp80) cc_final: 0.8640 (tpp80)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.0943
  time to fit residues: 37.1998
Evaluate side-chains
  218 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 101 optimal weight:   50.0000
   chunk 49 optimal weight:    8.9990
   chunk 85 optimal weight:    9.9990
   chunk 1 optimal weight:   20.0000
   chunk 42 optimal weight:    0.3980
   chunk 93 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 17 optimal weight:    7.9990
   chunk 139 optimal weight:    4.9990
   chunk 69 optimal weight:    0.4980
   chunk 34 optimal weight:    7.9990
   overall best weight:    3.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 655 HIS
B 674 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.107220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.076389 restraints weight = 43116.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.078947 restraints weight = 28365.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.080783 restraints weight = 21326.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.082076 restraints weight = 17410.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.082980 restraints weight = 15036.815|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7292
moved from start:          0.3874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11870  Z= 0.178
  Angle     :  0.736   9.289  16112  Z= 0.392
  Chirality :  0.047   0.315   1772
  Planarity :  0.005   0.066   2000
  Dihedral  :  4.596  21.256   1562
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.77 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.46 (0.22), residues: 1386
  helix:  0.35 (0.18), residues: 842
  sheet: -2.07 (0.60), residues: 72
  loop : -1.03 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 636 
 TYR   0.038   0.002   TYR B 305 
 PHE   0.051   0.002   PHE A 838 
 TRP   0.018   0.002   TRP A 333 
 HIS   0.007   0.001   HIS B 655 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.18 (11860)
  covalent geometry    : angle       0.73400 /  0.39 (16092)
  SS BOND              : bond        0.00341 /  0.14 (   10)
  SS BOND              : angle       1.73170 /  1.06 (   20)
  hydrogen bonds       : bond        0.04025 /  2.61 (  628)
  hydrogen bonds       : angle       4.95220 /  3.36 ( 1866)

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

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

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2772 Ramachandran restraints generated.
    1386 Oldfield, 0 Emsley, 1386 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  323 TYR cc_start: 0.9226 (t80) cc_final: 0.8931 (t80)
REVERT: A  385 PHE cc_start: 0.8659 (t80) cc_final: 0.8421 (t80)
REVERT: A  397 TRP cc_start: 0.7693 (t-100) cc_final: 0.6819 (t-100)
REVERT: A  559 GLN cc_start: 0.8716 (tp-100) cc_final: 0.8355 (tp-100)
REVERT: A  729 MET cc_start: 0.8721 (mpp) cc_final: 0.8326 (mpp)
REVERT: A  839 ILE cc_start: 0.9117 (pt) cc_final: 0.8669 (pt)
REVERT: A  842 MET cc_start: 0.9279 (mpp) cc_final: 0.8819 (mpp)
REVERT: B  305 TYR cc_start: 0.7565 (p90) cc_final: 0.7216 (p90)
REVERT: B  397 TRP cc_start: 0.7739 (t-100) cc_final: 0.7180 (t-100)
REVERT: B  523 ILE cc_start: 0.9302 (pt) cc_final: 0.9068 (pt)
REVERT: B  534 MET cc_start: 0.6816 (mmm) cc_final: 0.6418 (ttt)
REVERT: B  559 GLN cc_start: 0.8694 (tp-100) cc_final: 0.8311 (tp-100)
REVERT: B  671 MET cc_start: 0.8493 (ppp) cc_final: 0.7673 (tpp)
REVERT: B  742 MET cc_start: 0.9397 (mmp) cc_final: 0.9168 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.0905
  time to fit residues: 35.8151
Evaluate side-chains
  219 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 219
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0970
   chunk 49 optimal weight:    8.9990
   chunk 101 optimal weight:    1.9990
   chunk 56 optimal weight:    6.9990
   chunk 7 optimal weight:    5.9990
   chunk 74 optimal weight:    0.7980
   chunk 129 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:   20.0000
   chunk 60 optimal weight:    1.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 674 GLN
B 674 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.111836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.079731 restraints weight = 42752.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.082688 restraints weight = 27765.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.084728 restraints weight = 20604.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.086198 restraints weight = 16743.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.087085 restraints weight = 14420.061|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7214
moved from start:          0.3779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11870  Z= 0.135
  Angle     :  0.725   9.366  16112  Z= 0.377
  Chirality :  0.046   0.247   1772
  Planarity :  0.005   0.063   2000
  Dihedral  :  4.411  20.708   1562
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  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: -0.36 (0.22), residues: 1386
  helix:  0.44 (0.17), residues: 850
  sheet: -1.33 (0.70), residues: 52
  loop : -1.22 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 712 
 TYR   0.031   0.001   TYR B 305 
 PHE   0.044   0.002   PHE A 838 
 TRP   0.023   0.002   TRP A 273 
 HIS   0.008   0.001   HIS B 655 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.13 (11860)
  covalent geometry    : angle       0.72303 /  0.38 (16092)
  SS BOND              : bond        0.00303 /  0.13 (   10)
  SS BOND              : angle       1.57948 /  0.97 (   20)
  hydrogen bonds       : bond        0.03836 /  2.48 (  628)
  hydrogen bonds       : angle       4.74322 /  3.22 ( 1866)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2473.00 seconds
wall clock time: 43 minutes 36.27 seconds (2616.27 seconds total)