Starting phenix.real_space_refine
on Sun Jul 27 17:58:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p49_20247/07_2025/6p49_20247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p49_20247/07_2025/6p49_20247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p49_20247/07_2025/6p49_20247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p49_20247/07_2025/6p49_20247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p49_20247/07_2025/6p49_20247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p49_20247/07_2025/6p49_20247.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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      2      9.91       5
     S      66      5.16       5
     C    6352      2.51       5
     N    1520      2.21       5
     O    1636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9576
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4787
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 583, 4787
          Classifications: {'peptide': 583}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 556}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.35, per 1000 atoms: 0.98
  Number of scatterers: 9576
  At special positions: 0
  Unit cell: (84.72, 111.195, 106.959, 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      2     19.99
     S      66     16.00
     O    1636      8.00
     N    1520      7.00
     C    6352      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=2.05
    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=2.01
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 601 " distance=1.84
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=2.05
    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=2.01
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 601 " distance=1.84

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.95
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2212

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 2 sheets defined
      55.4% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 100
      removed outlier: 3.724A  pdb=" N   ALA A 100 " --> pdb=" O   ARG A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 135 through 139
      removed outlier: 3.724A  pdb=" N   TYR A 138 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
      removed outlier: 3.573A  pdb=" N   TYR A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 240
    Processing helix  chain 'A' and resid 267 through 271
    Processing helix  chain 'A' and resid 284 through 292
      removed outlier: 4.026A  pdb=" N   ILE A 288 " --> pdb=" O   PRO A 284 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS A 290 " --> pdb=" O   ASP A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 327
      removed outlier: 3.618A  pdb=" N   TRP A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   GLY A 304 " --> pdb=" O   PHE A 300 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   ALA A 313 " --> pdb=" O   MET A 309 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   CYS A 320 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TYR A 323 " --> pdb=" O   ALA A 319 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLY A 324 " --> pdb=" O   CYS A 320 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASP A 327 " --> pdb=" O   TYR A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 378 through 408
      removed outlier: 3.871A  pdb=" N   VAL A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A 385 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   GLU A 395 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 461
    Processing helix  chain 'A' and resid 462 through 480
      removed outlier: 3.767A  pdb=" N   LEU A 466 " --> pdb=" O   PHE A 462 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE A 474 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A 475 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   VAL A 476 " --> pdb=" O   ILE A 472 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR A 477 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 486
      removed outlier: 3.558A  pdb=" N   SER A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 529
      removed outlier: 3.824A  pdb=" N   SER A 514 " --> pdb=" O   SER A 510 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR A 526 " --> pdb=" O   MET A 522 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 527 " --> pdb=" O   ILE A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 531 through 537
    Processing helix  chain 'A' and resid 547 through 563
      removed outlier: 3.937A  pdb=" N   MET A 553 " --> pdb=" O   ASN A 549 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   PHE A 556 " --> pdb=" O   THR A 552 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU A 557 " --> pdb=" O   MET A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.619A  pdb=" N   LEU A 588 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 614
      removed outlier: 4.377A  pdb=" N   GLN A 608 " --> pdb=" O   GLU A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 627
    Processing helix  chain 'A' and resid 637 through 642
      removed outlier: 3.835A  pdb=" N   GLY A 642 " --> pdb=" O   LYS A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 676
      removed outlier: 4.478A  pdb=" N   MET A 671 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 4.064A  pdb=" N   ILE A 700 " --> pdb=" O   ASN A 696 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   ALA A 704 " --> pdb=" O   ILE A 700 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 707 " --> pdb=" O   ASP A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 747
      removed outlier: 4.171A  pdb=" N   LEU A 735 " --> pdb=" O   GLY A 731 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 759
      removed outlier: 3.617A  pdb=" N   TYR A 756 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR A 757 " --> pdb=" O   ARG A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 839
      removed outlier: 3.587A  pdb=" N   TRP A 829 " --> pdb=" O   ASN A 825 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA A 837 " --> pdb=" O   ALA A 833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 845
    Processing helix  chain 'A' and resid 845 through 853
    Processing helix  chain 'B' and resid 94 through 100
      removed outlier: 3.724A  pdb=" N   ALA B 100 " --> pdb=" O   ARG B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 135 through 139
      removed outlier: 3.724A  pdb=" N   TYR B 138 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 218
      removed outlier: 3.573A  pdb=" N   TYR B 214 " --> pdb=" O   SER B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 235 through 240
    Processing helix  chain 'B' and resid 267 through 271
    Processing helix  chain 'B' and resid 284 through 292
      removed outlier: 4.026A  pdb=" N   ILE B 288 " --> pdb=" O   PRO B 284 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS B 290 " --> pdb=" O   ASP B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 327
      removed outlier: 3.617A  pdb=" N   TRP B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLY B 304 " --> pdb=" O   PHE B 300 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   LEU B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA B 313 " --> pdb=" O   MET B 309 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   CYS B 320 " --> pdb=" O   VAL B 316 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE B 321 " --> pdb=" O   GLY B 317 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TYR B 323 " --> pdb=" O   ALA B 319 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY B 324 " --> pdb=" O   CYS B 320 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASP B 327 " --> pdb=" O   TYR B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 369
    Processing helix  chain 'B' and resid 378 through 408
      removed outlier: 3.871A  pdb=" N   VAL B 384 " --> pdb=" O   LEU B 380 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE B 385 " --> pdb=" O   ILE B 381 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   GLU B 395 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 461
    Processing helix  chain 'B' and resid 462 through 480
      removed outlier: 3.767A  pdb=" N   LEU B 466 " --> pdb=" O   PHE B 462 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ILE B 474 " --> pdb=" O   SER B 470 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   ILE B 475 " --> pdb=" O   VAL B 471 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   VAL B 476 " --> pdb=" O   ILE B 472 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR B 477 " --> pdb=" O   GLY B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 486
      removed outlier: 3.558A  pdb=" N   SER B 486 " --> pdb=" O   PHE B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 529
      removed outlier: 3.824A  pdb=" N   SER B 514 " --> pdb=" O   SER B 510 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   THR B 526 " --> pdb=" O   MET B 522 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE B 527 " --> pdb=" O   ILE B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 531 through 537
    Processing helix  chain 'B' and resid 547 through 563
      removed outlier: 3.937A  pdb=" N   MET B 553 " --> pdb=" O   ASN B 549 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   PHE B 556 " --> pdb=" O   THR B 552 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   LEU B 557 " --> pdb=" O   MET B 553 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.619A  pdb=" N   LEU B 588 " --> pdb=" O   VAL B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 614
      removed outlier: 4.377A  pdb=" N   GLN B 608 " --> pdb=" O   GLU B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 622 through 627
    Processing helix  chain 'B' and resid 637 through 642
      removed outlier: 3.834A  pdb=" N   GLY B 642 " --> pdb=" O   LYS B 638 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 676
      removed outlier: 4.479A  pdb=" N   MET B 671 " --> pdb=" O   GLU B 667 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 4.063A  pdb=" N   ILE B 700 " --> pdb=" O   ASN B 696 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ALA B 704 " --> pdb=" O   ILE B 700 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU B 707 " --> pdb=" O   ASP B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 747
      removed outlier: 4.171A  pdb=" N   LEU B 735 " --> pdb=" O   GLY B 731 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 734 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 759
      removed outlier: 3.617A  pdb=" N   TYR B 756 " --> pdb=" O   PRO B 752 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   TYR B 757 " --> pdb=" O   ARG B 753 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 839
      removed outlier: 3.586A  pdb=" N   TRP B 829 " --> pdb=" O   ASN B 825 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ALA B 837 " --> pdb=" O   ALA B 833 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 840 through 845
    Processing helix  chain 'B' and resid 845 through 853
    Processing sheet with id=AA1, first strand: chain 'A' and resid 782 through 783
      removed outlier: 3.770A  pdb=" N   SER A 782 " --> pdb=" O   TYR A 809 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 782 through 783
      removed outlier: 3.770A  pdb=" N   SER B 782 " --> pdb=" O   TYR B 809 " (cutoff:3.500A)

    362 hydrogen bonds defined for protein.
    1062 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: 2.54

  Time building geometry restraints manager: 2.91 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: 2795
        1.34 -     1.46: 2362
        1.46 -     1.58: 4581
        1.58 -     1.70: 0
        1.70 -     1.81: 104
  Bond restraints: 9842
  Sorted by residual:
  bond pdb=" C   THR B 504 "
       pdb=" N   PRO B 505 "
    ideal  model  delta    sigma   weight residual
    1.334  1.401 -0.067 2.34e-02 1.83e+03 8.22e+00
  bond pdb=" C   THR A 504 "
       pdb=" N   PRO A 505 "
    ideal  model  delta    sigma   weight residual
    1.334  1.400 -0.066 2.34e-02 1.83e+03 8.03e+00
  bond pdb=" C   PRO A 763 "
       pdb=" N   PRO A 764 "
    ideal  model  delta    sigma   weight residual
    1.333  1.361 -0.028 1.01e-02 9.80e+03 7.68e+00
  bond pdb=" C   PRO B 763 "
       pdb=" N   PRO B 764 "
    ideal  model  delta    sigma   weight residual
    1.333  1.361 -0.028 1.01e-02 9.80e+03 7.56e+00
  bond pdb=" N   PRO A 686 "
       pdb=" CD  PRO A 686 "
    ideal  model  delta    sigma   weight residual
    1.473  1.511 -0.038 1.40e-02 5.10e+03 7.31e+00
  ... (remaining 9837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.04: 12702
        3.04 -     6.09: 519
        6.09 -     9.13: 107
        9.13 -    12.18: 18
       12.18 -    15.22: 14
  Bond angle restraints: 13360
  Sorted by residual:
  angle pdb=" N   VAL B 682 "
        pdb=" CA  VAL B 682 "
        pdb=" C   VAL B 682 "
      ideal   model   delta    sigma   weight residual
     106.21  120.75  -14.54 1.07e+00 8.73e-01 1.85e+02
  angle pdb=" N   VAL A 682 "
        pdb=" CA  VAL A 682 "
        pdb=" C   VAL A 682 "
      ideal   model   delta    sigma   weight residual
     106.21  120.74  -14.53 1.07e+00 8.73e-01 1.84e+02
  angle pdb=" N   GLN B 720 "
        pdb=" CA  GLN B 720 "
        pdb=" C   GLN B 720 "
      ideal   model   delta    sigma   weight residual
     111.14  124.92  -13.78 1.08e+00 8.57e-01 1.63e+02
  angle pdb=" N   GLN A 720 "
        pdb=" CA  GLN A 720 "
        pdb=" C   GLN A 720 "
      ideal   model   delta    sigma   weight residual
     111.14  124.88  -13.74 1.08e+00 8.57e-01 1.62e+02
  angle pdb=" N   ARG A 478 "
        pdb=" CA  ARG A 478 "
        pdb=" C   ARG A 478 "
      ideal   model   delta    sigma   weight residual
     113.43   98.21   15.22 1.26e+00 6.30e-01 1.46e+02
  ... (remaining 13355 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.97: 4989
       17.97 -    35.95: 607
       35.95 -    53.92: 122
       53.92 -    71.89: 22
       71.89 -    89.87: 12
  Dihedral angle restraints: 5752
    sinusoidal: 2312
      harmonic: 3440
  Sorted by residual:
  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 -163.44   77.44     1      1.00e+01 1.00e-02 7.51e+01
  dihedral pdb=" CB  CYS B 596 "
           pdb=" SG  CYS B 596 "
           pdb=" SG  CYS B 601 "
           pdb=" CB  CYS B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.38   77.38     1      1.00e+01 1.00e-02 7.50e+01
  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 -149.79   63.79     1      1.00e+01 1.00e-02 5.36e+01
  ... (remaining 5749 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1339
       0.122 -    0.243: 114
       0.243 -    0.364: 17
       0.364 -    0.486: 8
       0.486 -    0.607: 2
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CB  VAL B 640 "
            pdb=" CA  VAL B 640 "
            pdb=" CG1 VAL B 640 "
            pdb=" CG2 VAL B 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.02   -0.61 2.00e-01 2.50e+01 9.21e+00
  chirality pdb=" CB  VAL A 640 "
            pdb=" CA  VAL A 640 "
            pdb=" CG1 VAL A 640 "
            pdb=" CG2 VAL A 640 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.02   -0.61 2.00e-01 2.50e+01 9.15e+00
  chirality pdb=" CA  ASP B 749 "
            pdb=" N   ASP B 749 "
            pdb=" C   ASP B 749 "
            pdb=" CB  ASP B 749 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.21e+00
  ... (remaining 1477 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 719 "   -0.025 2.00e-02 2.50e+03   4.97e-02 2.47e+01
        pdb=" C   ALA A 719 "    0.086 2.00e-02 2.50e+03
        pdb=" O   ALA A 719 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   GLN A 720 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 719 "   -0.025 2.00e-02 2.50e+03   4.95e-02 2.45e+01
        pdb=" C   ALA B 719 "    0.086 2.00e-02 2.50e+03
        pdb=" O   ALA B 719 "   -0.033 2.00e-02 2.50e+03
        pdb=" N   GLN B 720 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 688 "    0.066 5.00e-02 4.00e+02   1.01e-01 1.62e+01
        pdb=" N   PRO B 689 "   -0.174 5.00e-02 4.00e+02
        pdb=" CA  PRO B 689 "    0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO B 689 "    0.056 5.00e-02 4.00e+02
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 610
        2.71 -     3.26: 9308
        3.26 -     3.81: 15541
        3.81 -     4.35: 19408
        4.35 -     4.90: 30570
  Nonbonded interactions: 75437
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 628 "
            pdb=" O   TRP B 629 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   PRO A 628 "
            pdb=" O   TRP A 629 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" CD1 TRP A 359 "
            pdb=" N   ARG A 360 "
     model   vdw
     2.191 3.340
  nonbonded pdb=" CD1 TRP B 359 "
            pdb=" N   ARG B 360 "
     model   vdw
     2.191 3.340
  nonbonded pdb=" OH  TYR A 847 "
            pdb=" OH  TYR B 847 "
     model   vdw
     2.221 3.040
  ... (remaining 75432 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             27.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     28.280
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  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:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5705
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      :  0.007   0.189   9850  Z= 0.377
  Angle     :  1.585  39.996  13376  Z= 0.963
  Chirality :  0.082   0.607   1480
  Planarity :  0.010   0.101   1630
  Dihedral  : 16.183  89.867   3516
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 18.26
  Ramachandran Plot:
    Outliers :  0.71 %
    Allowed  :  6.90 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 10.23 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.27 (0.17), residues: 1130
  helix: -4.42 (0.10), residues: 654
  sheet:  None (None), residues: 0
  loop : -3.58 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 302 
 HIS   0.006   0.002   HIS B 275 
 PHE   0.030   0.003   PHE A 685 
 TYR   0.030   0.003   TYR A 306 
 ARG   0.006   0.001   ARG A 813 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.33047 (  362)
  hydrogen bonds       : angle      12.18805 ( 1062)
  SS BOND              : bond        0.09553 (    8)
  SS BOND              : angle      14.84253 (   16)
  covalent geometry    : bond        0.00697 ( 9842)
  covalent geometry    : angle       1.50071 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 193
  time to evaluate  : 1.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  553 MET cc_start: 0.5982 (mmm) cc_final: 0.5635 (mmt)
REVERT: A  590 LYS cc_start: 0.4027 (OUTLIER) cc_final: 0.2743 (mmtt)
REVERT: A  725 TRP cc_start: 0.6509 (m100) cc_final: 0.6083 (m100)
REVERT: B  142 MET cc_start: 0.3547 (tpt) cc_final: 0.3199 (tpp)
REVERT: B  553 MET cc_start: 0.5506 (mmm) cc_final: 0.5264 (mmt)
REVERT: B  641 SER cc_start: 0.4003 (OUTLIER) cc_final: 0.3650 (t)
  outliers start: 34
  outliers final: 10
  residues processed: 222
  average time/residue: 0.2821
  time to fit residues: 83.9786
Evaluate side-chains
  138 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  268 LEU
Chi-restraints excluded: chain A residue  337 VAL
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  702 VAL
Chi-restraints excluded: chain B residue  233 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  702 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 90 optimal weight:    7.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 67 optimal weight:    0.5980
   chunk 105 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 275 HIS
** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 696 ASN
A 730 GLN
A 740 ASN
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 275 HIS
B 620 ASN
B 621 ASN
B 696 ASN
B 730 GLN
B 740 ASN
B 814 ASN
B 830 HIS

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5588 r_free = 0.5588 target = 0.278530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5344 r_free = 0.5344 target = 0.249700 restraints weight = 13116.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.5309 rms_B_bonded: 2.44
r_work: 0.5116 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.5116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5851
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9850  Z= 0.178
  Angle     :  0.837  12.048  13376  Z= 0.432
  Chirality :  0.047   0.198   1480
  Planarity :  0.007   0.066   1630
  Dihedral  :  8.145  49.382   1300
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 13.51
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.23 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.37 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.33 (0.19), residues: 1130
  helix: -3.28 (0.15), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.84 (0.22), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 397 
 HIS   0.003   0.001   HIS A 824 
 PHE   0.016   0.002   PHE A 556 
 TYR   0.022   0.002   TYR B 776 
 ARG   0.007   0.001   ARG B 592 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06678 (  362)
  hydrogen bonds       : angle       6.95451 ( 1062)
  SS BOND              : bond        0.00471 (    8)
  SS BOND              : angle       1.43716 (   16)
  covalent geometry    : bond        0.00375 ( 9842)
  covalent geometry    : angle       0.83569 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 160
  time to evaluate  : 1.032 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.4145 (OUTLIER) cc_final: 0.2725 (mmtt)
REVERT: A  598 PRO cc_start: 0.7139 (Cg_endo) cc_final: 0.6918 (Cg_exo)
REVERT: A  601 CYS cc_start: 0.6233 (OUTLIER) cc_final: 0.5679 (m)
REVERT: A  634 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.6308 (pt)
REVERT: B  268 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7026 (pp)
REVERT: B  601 CYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6261 (m)
REVERT: B  641 SER cc_start: 0.4245 (OUTLIER) cc_final: 0.3748 (t)
REVERT: B  764 PRO cc_start: 0.6960 (Cg_endo) cc_final: 0.6628 (Cg_exo)
  outliers start: 32
  outliers final: 15
  residues processed: 183
  average time/residue: 0.2099
  time to fit residues: 54.2323
Evaluate side-chains
  145 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  601 CYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  714 MET
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  520 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  601 CYS
Chi-restraints excluded: chain B residue  641 SER
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 85 optimal weight:    6.9990
   chunk 70 optimal weight:    2.9990
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    0.4980
   chunk 58 optimal weight:   20.0000
   chunk 44 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 7 optimal weight:    9.9990
   chunk 71 optimal weight:    0.6980
   chunk 72 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 608 GLN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 830 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5580 r_free = 0.5580 target = 0.278357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.5216 r_free = 0.5216 target = 0.242499 restraints weight = 13087.859|
|-----------------------------------------------------------------------------|
r_work (start): 0.5235 rms_B_bonded: 2.79
r_work: 0.5097 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.5097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5857
moved from start:          0.3344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9850  Z= 0.154
  Angle     :  0.747  15.474  13376  Z= 0.381
  Chirality :  0.045   0.198   1480
  Planarity :  0.006   0.067   1630
  Dihedral  :  7.174  41.357   1291
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.76 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 18.82 %
    Favored  : 77.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.87 (0.20), residues: 1130
  helix: -2.89 (0.16), residues: 654
  sheet:  None (None), residues: 0
  loop : -3.67 (0.23), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 397 
 HIS   0.011   0.001   HIS A 818 
 PHE   0.022   0.002   PHE B 556 
 TYR   0.025   0.002   TYR A 528 
 ARG   0.006   0.000   ARG A 753 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06180 (  362)
  hydrogen bonds       : angle       6.23952 ( 1062)
  SS BOND              : bond        0.00279 (    8)
  SS BOND              : angle       1.24676 (   16)
  covalent geometry    : bond        0.00316 ( 9842)
  covalent geometry    : angle       0.74612 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 138
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 ARG cc_start: 0.6052 (mtt90) cc_final: 0.5721 (mpt-90)
REVERT: A  528 TYR cc_start: 0.6470 (m-80) cc_final: 0.6074 (m-80)
REVERT: A  590 LYS cc_start: 0.4418 (OUTLIER) cc_final: 0.3047 (mmtt)
REVERT: A  598 PRO cc_start: 0.7152 (Cg_endo) cc_final: 0.6937 (Cg_exo)
REVERT: A  634 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5894 (pt)
  outliers start: 34
  outliers final: 18
  residues processed: 163
  average time/residue: 0.2050
  time to fit residues: 49.5039
Evaluate side-chains
  147 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 1.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 107 optimal weight:    0.4980
   chunk 19 optimal weight:    0.6980
   chunk 109 optimal weight:    5.9990
   chunk 113 optimal weight:    0.7980
   chunk 6 optimal weight:    9.9990
   chunk 89 optimal weight:    0.4980
   chunk 62 optimal weight:    0.0980
   chunk 25 optimal weight:    6.9990
   chunk 84 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 608 GLN
** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  94 GLN
B 330 ASN
** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5603 r_free = 0.5603 target = 0.281672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.5350 r_free = 0.5350 target = 0.252986 restraints weight = 12925.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.5334 rms_B_bonded: 2.53
r_work: 0.5135 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.5135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5818
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9850  Z= 0.140
  Angle     :  0.710  13.155  13376  Z= 0.361
  Chirality :  0.045   0.177   1480
  Planarity :  0.005   0.060   1630
  Dihedral  :  6.655  39.315   1290
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.41 %
    Favored  : 91.42 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.98 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.48 (0.21), residues: 1130
  helix: -2.47 (0.17), residues: 656
  sheet:  None (None), residues: 0
  loop : -3.67 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 397 
 HIS   0.003   0.001   HIS A 824 
 PHE   0.024   0.001   PHE A 681 
 TYR   0.020   0.001   TYR B 776 
 ARG   0.004   0.000   ARG B 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05625 (  362)
  hydrogen bonds       : angle       5.89969 ( 1062)
  SS BOND              : bond        0.00179 (    8)
  SS BOND              : angle       0.89503 (   16)
  covalent geometry    : bond        0.00294 ( 9842)
  covalent geometry    : angle       0.70966 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 139
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7939 (tp)
REVERT: A  590 LYS cc_start: 0.4601 (OUTLIER) cc_final: 0.3379 (mmtm)
REVERT: A  634 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5916 (pt)
REVERT: B  404 LEU cc_start: 0.7470 (mt) cc_final: 0.7046 (pp)
REVERT: B  524 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7974 (tp)
REVERT: B  562 ASN cc_start: 0.7481 (t0) cc_final: 0.7040 (m110)
REVERT: B  725 TRP cc_start: 0.6197 (m100) cc_final: 0.5633 (m100)
REVERT: B  764 PRO cc_start: 0.7124 (Cg_endo) cc_final: 0.6820 (Cg_exo)
  outliers start: 34
  outliers final: 23
  residues processed: 164
  average time/residue: 0.2073
  time to fit residues: 49.7732
Evaluate side-chains
  150 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 1.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  410 THR
Chi-restraints excluded: chain A residue  463 TRP
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  634 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 31 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 21 optimal weight:   10.0000
   chunk 41 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9980
   chunk 99 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
A 608 GLN
B  94 GLN
B 559 GLN
** B 562 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5582 r_free = 0.5582 target = 0.278600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5322 r_free = 0.5322 target = 0.247837 restraints weight = 12865.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.5298 rms_B_bonded: 2.74
r_work: 0.5092 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.5092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5898
moved from start:          0.4141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9850  Z= 0.154
  Angle     :  0.711  12.151  13376  Z= 0.363
  Chirality :  0.045   0.183   1480
  Planarity :  0.005   0.060   1630
  Dihedral  :  6.490  38.047   1290
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.91 %
    Favored  : 89.91 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 20.17 %
    Favored  : 75.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.27 (0.21), residues: 1130
  helix: -2.26 (0.18), residues: 654
  sheet:  None (None), residues: 0
  loop : -3.64 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 397 
 HIS   0.005   0.001   HIS A 824 
 PHE   0.023   0.002   PHE A 681 
 TYR   0.022   0.002   TYR A 306 
 ARG   0.003   0.000   ARG A 753 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05584 (  362)
  hydrogen bonds       : angle       5.77462 ( 1062)
  SS BOND              : bond        0.00142 (    8)
  SS BOND              : angle       0.75332 (   16)
  covalent geometry    : bond        0.00328 ( 9842)
  covalent geometry    : angle       0.71078 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 133
  time to evaluate  : 2.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.4643 (OUTLIER) cc_final: 0.3512 (mmtm)
REVERT: B  562 ASN cc_start: 0.7336 (t0) cc_final: 0.5992 (t0)
REVERT: B  590 LYS cc_start: 0.5319 (OUTLIER) cc_final: 0.4230 (mmtm)
REVERT: B  725 TRP cc_start: 0.6418 (m100) cc_final: 0.5970 (m100)
REVERT: B  764 PRO cc_start: 0.6992 (Cg_endo) cc_final: 0.6667 (Cg_exo)
  outliers start: 44
  outliers final: 29
  residues processed: 167
  average time/residue: 0.2218
  time to fit residues: 55.3710
Evaluate side-chains
  154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  463 TRP
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 98 optimal weight:    5.9990
   chunk 43 optimal weight:    0.5980
   chunk 75 optimal weight:    0.9980
   chunk 110 optimal weight:    5.9990
   chunk 0 optimal weight:   20.0000
   chunk 67 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0020
   chunk 69 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 91 optimal weight:    0.0270
   overall best weight:    0.4646

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
A 608 GLN
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5604 r_free = 0.5604 target = 0.280992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5356 r_free = 0.5356 target = 0.251056 restraints weight = 12940.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.5331 rms_B_bonded: 2.78
r_work: 0.5131 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.5131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5823
moved from start:          0.4455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9850  Z= 0.135
  Angle     :  0.702  12.047  13376  Z= 0.354
  Chirality :  0.045   0.176   1480
  Planarity :  0.005   0.063   1630
  Dihedral  :  6.167  37.257   1287
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.50 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.62 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.22), residues: 1130
  helix: -2.02 (0.18), residues: 656
  sheet:  None (None), residues: 0
  loop : -3.57 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 397 
 HIS   0.002   0.000   HIS A 824 
 PHE   0.026   0.002   PHE B 374 
 TYR   0.023   0.001   TYR B 776 
 ARG   0.004   0.000   ARG B 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05323 (  362)
  hydrogen bonds       : angle       5.58233 ( 1062)
  SS BOND              : bond        0.00109 (    8)
  SS BOND              : angle       0.60109 (   16)
  covalent geometry    : bond        0.00274 ( 9842)
  covalent geometry    : angle       0.70206 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 141
  time to evaluate  : 2.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.4929 (OUTLIER) cc_final: 0.3897 (mmtm)
REVERT: A  604 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7065 (tp30)
REVERT: A  729 MET cc_start: 0.6233 (ttp) cc_final: 0.5986 (ttp)
REVERT: B  142 MET cc_start: 0.3981 (tpp) cc_final: 0.3601 (tpp)
REVERT: B  590 LYS cc_start: 0.5313 (OUTLIER) cc_final: 0.4378 (mmtm)
REVERT: B  725 TRP cc_start: 0.6177 (m100) cc_final: 0.5749 (m100)
REVERT: B  764 PRO cc_start: 0.6923 (Cg_endo) cc_final: 0.6614 (Cg_exo)
REVERT: B  773 MET cc_start: 0.5841 (mmm) cc_final: 0.4565 (mmt)
  outliers start: 34
  outliers final: 25
  residues processed: 167
  average time/residue: 0.2870
  time to fit residues: 71.5997
Evaluate side-chains
  157 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 1.863 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  654 TYR
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0270
   chunk 62 optimal weight:    0.2980
   chunk 96 optimal weight:    0.0570
   chunk 101 optimal weight:    0.6980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.3756

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
A 608 GLN
A 726 GLN
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5614 r_free = 0.5614 target = 0.283167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5371 r_free = 0.5371 target = 0.253384 restraints weight = 13016.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.5340 rms_B_bonded: 2.76
r_work: 0.5130 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.5130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5821
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9850  Z= 0.130
  Angle     :  0.713  11.781  13376  Z= 0.355
  Chirality :  0.044   0.177   1480
  Planarity :  0.005   0.065   1630
  Dihedral  :  5.987  36.056   1287
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.65 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 22.59 %
    Favored  : 73.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.76 (0.22), residues: 1130
  helix: -1.80 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.51 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 397 
 HIS   0.002   0.001   HIS A 824 
 PHE   0.041   0.002   PHE B 851 
 TYR   0.032   0.001   TYR B 847 
 ARG   0.003   0.000   ARG B 542 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05153 (  362)
  hydrogen bonds       : angle       5.41571 ( 1062)
  SS BOND              : bond        0.00077 (    8)
  SS BOND              : angle       0.58416 (   16)
  covalent geometry    : bond        0.00269 ( 9842)
  covalent geometry    : angle       0.71283 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 133
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.5111 (OUTLIER) cc_final: 0.4160 (mmtm)
REVERT: A  750 MET cc_start: 0.7461 (tpt) cc_final: 0.7107 (tpp)
REVERT: B  142 MET cc_start: 0.4149 (tpp) cc_final: 0.3778 (tpp)
REVERT: B  386 MET cc_start: 0.5133 (mmt) cc_final: 0.4879 (mmt)
REVERT: B  404 LEU cc_start: 0.7694 (mt) cc_final: 0.7094 (pp)
REVERT: B  524 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7853 (tp)
REVERT: B  590 LYS cc_start: 0.5224 (OUTLIER) cc_final: 0.4434 (mmtm)
REVERT: B  725 TRP cc_start: 0.6115 (m100) cc_final: 0.5677 (m100)
REVERT: B  750 MET cc_start: 0.6914 (tpt) cc_final: 0.6690 (tpt)
REVERT: B  764 PRO cc_start: 0.6805 (Cg_endo) cc_final: 0.6516 (Cg_exo)
  outliers start: 39
  outliers final: 26
  residues processed: 164
  average time/residue: 0.2121
  time to fit residues: 52.7584
Evaluate side-chains
  152 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 1.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  570 ILE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  654 TYR
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  845 ILE
Chi-restraints excluded: chain B residue  847 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0040
   chunk 55 optimal weight:    0.9990
   chunk 104 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 58 optimal weight:   20.0000
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.4992

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5610 r_free = 0.5610 target = 0.282756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5368 r_free = 0.5368 target = 0.252845 restraints weight = 13133.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.5347 rms_B_bonded: 2.79
r_work: 0.5140 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.5140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5814
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9850  Z= 0.132
  Angle     :  0.702  11.608  13376  Z= 0.352
  Chirality :  0.044   0.173   1480
  Planarity :  0.005   0.066   1630
  Dihedral  :  5.840  36.369   1286
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.58 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.36 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.56 (0.22), residues: 1130
  helix: -1.60 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.49 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 397 
 HIS   0.002   0.001   HIS A 824 
 PHE   0.023   0.002   PHE B 681 
 TYR   0.028   0.001   TYR A 847 
 ARG   0.005   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05108 (  362)
  hydrogen bonds       : angle       5.37078 ( 1062)
  SS BOND              : bond        0.00070 (    8)
  SS BOND              : angle       0.57672 (   16)
  covalent geometry    : bond        0.00277 ( 9842)
  covalent geometry    : angle       0.70234 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 130
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7349 (mm-40)
REVERT: A  386 MET cc_start: 0.4989 (mmt) cc_final: 0.4275 (mmt)
REVERT: A  590 LYS cc_start: 0.5127 (OUTLIER) cc_final: 0.4225 (mmtt)
REVERT: B  142 MET cc_start: 0.4368 (tpp) cc_final: 0.3956 (tpp)
REVERT: B  386 MET cc_start: 0.5084 (mmt) cc_final: 0.4826 (mmt)
REVERT: B  404 LEU cc_start: 0.7603 (mt) cc_final: 0.7036 (pp)
REVERT: B  524 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7649 (tp)
REVERT: B  590 LYS cc_start: 0.5587 (OUTLIER) cc_final: 0.4820 (mmtm)
REVERT: B  725 TRP cc_start: 0.6188 (m100) cc_final: 0.5680 (m100)
REVERT: B  764 PRO cc_start: 0.6992 (Cg_endo) cc_final: 0.6692 (Cg_exo)
REVERT: B  842 MET cc_start: 0.7690 (mmt) cc_final: 0.7280 (mmt)
  outliers start: 34
  outliers final: 26
  residues processed: 156
  average time/residue: 0.2188
  time to fit residues: 51.9890
Evaluate side-chains
  148 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 1.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  331 CYS
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  654 TYR
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0870
   chunk 12 optimal weight:    0.7980
   chunk 115 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 105 optimal weight:    0.8980
   chunk 57 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 108 optimal weight:    0.0010
   overall best weight:    0.5564

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

Flipped N/Q/H residues before XYZ refinement:
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 844 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5614 r_free = 0.5614 target = 0.283625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5374 r_free = 0.5374 target = 0.253752 restraints weight = 12905.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.5351 rms_B_bonded: 2.72
r_work: 0.5140 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.5140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5814
moved from start:          0.5134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9850  Z= 0.134
  Angle     :  0.716  13.682  13376  Z= 0.354
  Chirality :  0.044   0.175   1480
  Planarity :  0.005   0.065   1630
  Dihedral  :  5.759  35.128   1286
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.73 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 24.13 %
    Favored  : 72.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.23), residues: 1130
  helix: -1.46 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.46 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 397 
 HIS   0.005   0.001   HIS A 824 
 PHE   0.038   0.002   PHE A 851 
 TYR   0.025   0.001   TYR B 822 
 ARG   0.005   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05006 (  362)
  hydrogen bonds       : angle       5.31281 ( 1062)
  SS BOND              : bond        0.00077 (    8)
  SS BOND              : angle       0.60911 (   16)
  covalent geometry    : bond        0.00283 ( 9842)
  covalent geometry    : angle       0.71618 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 135
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7363 (mm-40)
REVERT: A  386 MET cc_start: 0.5007 (mmt) cc_final: 0.4313 (mmt)
REVERT: A  553 MET cc_start: 0.6713 (mmt) cc_final: 0.6073 (mmt)
REVERT: A  590 LYS cc_start: 0.5213 (OUTLIER) cc_final: 0.4398 (mmtt)
REVERT: A  698 LEU cc_start: 0.6603 (mm) cc_final: 0.6345 (mt)
REVERT: B  142 MET cc_start: 0.4475 (tpp) cc_final: 0.4119 (tpp)
REVERT: B  386 MET cc_start: 0.5090 (mmt) cc_final: 0.4814 (mmt)
REVERT: B  404 LEU cc_start: 0.7552 (mt) cc_final: 0.6974 (pp)
REVERT: B  590 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5071 (mmtt)
REVERT: B  725 TRP cc_start: 0.6183 (m100) cc_final: 0.5712 (m100)
REVERT: B  750 MET cc_start: 0.7047 (tpt) cc_final: 0.6761 (tpt)
REVERT: B  764 PRO cc_start: 0.6988 (Cg_endo) cc_final: 0.6695 (Cg_exo)
REVERT: B  842 MET cc_start: 0.7705 (mmt) cc_final: 0.7302 (mmt)
  outliers start: 31
  outliers final: 27
  residues processed: 161
  average time/residue: 0.1780
  time to fit residues: 43.0322
Evaluate side-chains
  152 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 123
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  654 TYR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  654 TYR
Chi-restraints excluded: chain B residue  707 LEU
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 73 optimal weight:    0.0980
   chunk 54 optimal weight:    1.9990
   chunk 110 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 99 optimal weight:    0.5980
   chunk 78 optimal weight:    0.7980
   chunk 104 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 623 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5615 r_free = 0.5615 target = 0.282802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5360 r_free = 0.5360 target = 0.252818 restraints weight = 12653.322|
|-----------------------------------------------------------------------------|
r_work (start): 0.5329 rms_B_bonded: 2.74
r_work: 0.5127 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.5127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5812
moved from start:          0.5278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9850  Z= 0.137
  Angle     :  0.708  11.283  13376  Z= 0.354
  Chirality :  0.045   0.172   1480
  Planarity :  0.005   0.066   1630
  Dihedral  :  5.731  34.305   1286
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 24.32 %
    Favored  : 73.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.33 (0.23), residues: 1130
  helix: -1.39 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.44 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 844 
 PHE   0.020   0.002   PHE B 681 
 TYR   0.024   0.001   TYR B 828 
 ARG   0.004   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04981 (  362)
  hydrogen bonds       : angle       5.29759 ( 1062)
  SS BOND              : bond        0.00064 (    8)
  SS BOND              : angle       0.55500 (   16)
  covalent geometry    : bond        0.00290 ( 9842)
  covalent geometry    : angle       0.70844 (13360)

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

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

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2260 Ramachandran restraints generated.
    1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.865 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 GLN cc_start: 0.7599 (mm-40) cc_final: 0.7359 (mm-40)
REVERT: A  386 MET cc_start: 0.5011 (mmt) cc_final: 0.4331 (mmt)
REVERT: A  404 LEU cc_start: 0.7613 (mt) cc_final: 0.7121 (pp)
REVERT: A  553 MET cc_start: 0.6897 (mmt) cc_final: 0.6215 (mmt)
REVERT: A  590 LYS cc_start: 0.5546 (OUTLIER) cc_final: 0.4724 (mmtt)
REVERT: A  698 LEU cc_start: 0.6706 (mm) cc_final: 0.6448 (mt)
REVERT: A  773 MET cc_start: 0.5285 (mmt) cc_final: 0.4282 (mmt)
REVERT: B  142 MET cc_start: 0.4489 (tpp) cc_final: 0.4113 (tpp)
REVERT: B  386 MET cc_start: 0.5072 (mmt) cc_final: 0.4786 (mmt)
REVERT: B  404 LEU cc_start: 0.7580 (mt) cc_final: 0.6973 (pp)
REVERT: B  590 LYS cc_start: 0.5878 (OUTLIER) cc_final: 0.5338 (mmtt)
REVERT: B  725 TRP cc_start: 0.6236 (m100) cc_final: 0.5743 (m100)
REVERT: B  750 MET cc_start: 0.6959 (tpt) cc_final: 0.6649 (tpt)
REVERT: B  764 PRO cc_start: 0.6898 (Cg_endo) cc_final: 0.6610 (Cg_exo)
REVERT: B  842 MET cc_start: 0.7681 (mmt) cc_final: 0.7304 (mmt)
  outliers start: 27
  outliers final: 24
  residues processed: 148
  average time/residue: 0.1667
  time to fit residues: 38.0502
Evaluate side-chains
  145 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 1.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ILE
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  356 CYS
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  382 PHE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  845 ILE
Chi-restraints excluded: chain A residue  848 SER
Chi-restraints excluded: chain B residue  288 ILE
Chi-restraints excluded: chain B residue  334 SER
Chi-restraints excluded: chain B residue  356 CYS
Chi-restraints excluded: chain B residue  382 PHE
Chi-restraints excluded: chain B residue  535 ILE
Chi-restraints excluded: chain B residue  570 ILE
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
Chi-restraints excluded: chain B residue  654 TYR
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0770
   chunk 14 optimal weight:    0.0870
   chunk 96 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 101 optimal weight:    0.5980
   chunk 109 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0030
   overall best weight:    0.3126

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

Flipped N/Q/H residues before XYZ refinement:
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 623 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 = 0.5643 r_free = 0.5643 target = 0.285892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5394 r_free = 0.5394 target = 0.257284 restraints weight = 12578.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.5365 rms_B_bonded: 2.51
r_work: 0.5165 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.5165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5759
moved from start:          0.5499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9850  Z= 0.129
  Angle     :  0.712  15.032  13376  Z= 0.350
  Chirality :  0.044   0.173   1480
  Planarity :  0.005   0.066   1630
  Dihedral  :  5.609  33.796   1286
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.76 %
    Favored  : 91.24 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 24.32 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.23), residues: 1130
  helix: -1.24 (0.19), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.40 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 397 
 HIS   0.005   0.001   HIS B 844 
 PHE   0.026   0.001   PHE A 556 
 TYR   0.043   0.001   TYR A 822 
 ARG   0.002   0.000   ARG A 478 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04827 (  362)
  hydrogen bonds       : angle       5.17083 ( 1062)
  SS BOND              : bond        0.00056 (    8)
  SS BOND              : angle       0.53937 (   16)
  covalent geometry    : bond        0.00268 ( 9842)
  covalent geometry    : angle       0.71248 (13360)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5234.78 seconds
wall clock time: 95 minutes 54.17 seconds (5754.17 seconds total)