Starting phenix.real_space_refine
on Wed Mar  4 00:33:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p49_20247/03_2026/6p49_20247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p49_20247/03_2026/6p49_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_20247/03_2026/6p49_20247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p49_20247/03_2026/6p49_20247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p49_20247/03_2026/6p49_20247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p49_20247/03_2026/6p49_20247.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 3.84, per 1000 atoms: 0.40
  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: 0.72
  Conformation dependent library (CDL) restraints added in 308.8 milliseconds
  

  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: 0.26
  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: 1.24

  Time building geometry restraints manager: 0.99 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.340
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.070
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -6.27 (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
 ARG   0.006   0.001   ARG A 813 
 TYR   0.030   0.003   TYR A 306 
 PHE   0.030   0.003   PHE A 685 
 TRP   0.026   0.003   TRP A 302 
 HIS   0.006   0.002   HIS B 275 

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

*********************** 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  : 0.338 
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: 0.3656 (t)
  outliers start: 34
  outliers final: 10
  residues processed: 222
  average time/residue: 0.1103
  time to fit residues: 33.0352
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  : 0.231 
-------------------------------------------------------------------------------
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 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0070
   chunk 97 optimal weight:    0.0980
   chunk 113 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
** A  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 HIS
** A 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 621 ASN
A 696 ASN
A 730 GLN
A 740 ASN
A 814 ASN
A 825 ASN
B 275 HIS
B 620 ASN
B 621 ASN
B 696 ASN
B 730 GLN
B 740 ASN
B 814 ASN
B 820 GLN
B 830 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5585 r_free = 0.5585 target = 0.278285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.5338 r_free = 0.5338 target = 0.248918 restraints weight = 13001.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.5300 rms_B_bonded: 2.48
r_work: 0.5114 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.5114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5834
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9850  Z= 0.180
  Angle     :  0.829  11.587  13376  Z= 0.430
  Chirality :  0.047   0.199   1480
  Planarity :  0.007   0.067   1630
  Dihedral  :  8.167  48.979   1300
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.14 %
    Favored  : 91.68 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 16.99 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.34 (0.19), residues: 1130
  helix: -3.29 (0.15), residues: 636
  sheet:  None (None), residues: 0
  loop : -3.85 (0.22), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 592 
 TYR   0.021   0.002   TYR B 776 
 PHE   0.016   0.002   PHE A 556 
 TRP   0.019   0.002   TRP A 397 
 HIS   0.004   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9842)
  covalent geometry    : angle       0.82802 (13360)
  SS BOND              : bond        0.00121 (    8)
  SS BOND              : angle       1.45042 (   16)
  hydrogen bonds       : bond        0.07130 (  362)
  hydrogen bonds       : angle       6.98587 ( 1062)

*********************** 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
  191 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 157
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.4140 (OUTLIER) cc_final: 0.2719 (mmtt)
REVERT: A  598 PRO cc_start: 0.7142 (Cg_endo) cc_final: 0.6920 (Cg_exo)
REVERT: A  601 CYS cc_start: 0.6090 (OUTLIER) cc_final: 0.5547 (m)
REVERT: A  634 ILE cc_start: 0.6387 (OUTLIER) cc_final: 0.6115 (pt)
REVERT: B  268 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.7068 (pp)
REVERT: B  601 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6215 (m)
REVERT: B  641 SER cc_start: 0.4156 (OUTLIER) cc_final: 0.3619 (t)
REVERT: B  764 PRO cc_start: 0.7004 (Cg_endo) cc_final: 0.6673 (Cg_exo)
  outliers start: 34
  outliers final: 16
  residues processed: 181
  average time/residue: 0.0886
  time to fit residues: 22.9932
Evaluate side-chains
  144 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 122
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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  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  655 HIS
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  655 HIS
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 111 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0670
   chunk 35 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9980
   chunk 45 optimal weight:    9.9990
   chunk 20 optimal weight:    4.9990
   chunk 79 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
** A 620 ASN ** 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 = 0.5589 r_free = 0.5589 target = 0.278954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.5337 r_free = 0.5337 target = 0.249310 restraints weight = 12997.292|
|-----------------------------------------------------------------------------|
r_work (start): 0.5310 rms_B_bonded: 2.51
r_work: 0.5102 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.5102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5862
moved from start:          0.3389

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= 0.153
  Angle     :  0.752  14.955  13376  Z= 0.382
  Chirality :  0.046   0.205   1480
  Planarity :  0.006   0.067   1630
  Dihedral  :  7.089  41.143   1291
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.85 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.85 (0.20), residues: 1130
  helix: -2.82 (0.16), residues: 654
  sheet:  None (None), residues: 0
  loop : -3.74 (0.23), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 592 
 TYR   0.020   0.002   TYR A 828 
 PHE   0.021   0.002   PHE B 556 
 TRP   0.022   0.002   TRP A 397 
 HIS   0.004   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 9842)
  covalent geometry    : angle       0.75120 (13360)
  SS BOND              : bond        0.00267 (    8)
  SS BOND              : angle       1.16547 (   16)
  hydrogen bonds       : bond        0.06048 (  362)
  hydrogen bonds       : angle       6.21072 ( 1062)

*********************** 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
  168 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
REVERT: A  478 ARG cc_start: 0.6259 (mtt90) cc_final: 0.5775 (mpt-90)
REVERT: A  590 LYS cc_start: 0.4444 (OUTLIER) cc_final: 0.3123 (mmtt)
REVERT: A  598 PRO cc_start: 0.7122 (Cg_endo) cc_final: 0.6909 (Cg_exo)
  outliers start: 31
  outliers final: 17
  residues processed: 158
  average time/residue: 0.0760
  time to fit residues: 17.9996
Evaluate side-chains
  142 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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  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  747 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 91 optimal weight:    4.9990
   chunk 101 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 103 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 620 ASN
A 830 HIS
B  94 GLN
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 726 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5568 r_free = 0.5568 target = 0.277360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5306 r_free = 0.5306 target = 0.246475 restraints weight = 13037.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.5279 rms_B_bonded: 2.77
r_work: 0.5087 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.5087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5905
moved from start:          0.3815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9850  Z= 0.163
  Angle     :  0.737  13.080  13376  Z= 0.377
  Chirality :  0.046   0.183   1480
  Planarity :  0.005   0.057   1630
  Dihedral  :  6.771  39.656   1290
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.67 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 20.46 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.58 (0.20), residues: 1130
  helix: -2.55 (0.17), residues: 656
  sheet:  None (None), residues: 0
  loop : -3.71 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 753 
 TYR   0.023   0.002   TYR B 776 
 PHE   0.028   0.002   PHE A 681 
 TRP   0.018   0.001   TRP A 302 
 HIS   0.005   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 9842)
  covalent geometry    : angle       0.73693 (13360)
  SS BOND              : bond        0.00113 (    8)
  SS BOND              : angle       0.93507 (   16)
  hydrogen bonds       : bond        0.05818 (  362)
  hydrogen bonds       : angle       6.01341 ( 1062)

*********************** 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: 39
    poor density    : 134
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7946 (tp)
REVERT: A  590 LYS cc_start: 0.4567 (OUTLIER) cc_final: 0.3310 (mmtt)
REVERT: A  773 MET cc_start: 0.6639 (mmm) cc_final: 0.6335 (mmm)
REVERT: B  404 LEU cc_start: 0.7402 (mt) cc_final: 0.7003 (pp)
REVERT: B  524 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7962 (tp)
REVERT: B  562 ASN cc_start: 0.7307 (t0) cc_final: 0.7061 (m110)
REVERT: B  725 TRP cc_start: 0.6420 (m100) cc_final: 0.5968 (m100)
REVERT: B  764 PRO cc_start: 0.7119 (Cg_endo) cc_final: 0.6807 (Cg_exo)
  outliers start: 39
  outliers final: 27
  residues processed: 165
  average time/residue: 0.0811
  time to fit residues: 19.8331
Evaluate side-chains
  151 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 121
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  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  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  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  524 LEU
Chi-restraints excluded: chain B residue  527 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  732 ILE
Chi-restraints excluded: chain B residue  747 THR
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 6 optimal weight:    7.9990
   chunk 22 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 80 optimal weight:    1.9990
   chunk 60 optimal weight:    0.1980
   chunk 78 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
** A 710 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 844 HIS
B  94 GLN
B 330 ASN
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5574 r_free = 0.5574 target = 0.278195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5313 r_free = 0.5313 target = 0.247252 restraints weight = 13035.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.5284 rms_B_bonded: 2.76
r_work: 0.5095 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.5095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5894
moved from start:          0.4157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9850  Z= 0.148
  Angle     :  0.720  12.541  13376  Z= 0.366
  Chirality :  0.045   0.182   1480
  Planarity :  0.005   0.064   1630
  Dihedral  :  6.512  38.562   1288
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.38 %
    Favored  : 90.44 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.72 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.32 (0.21), residues: 1130
  helix: -2.30 (0.18), residues: 648
  sheet:  None (None), residues: 0
  loop : -3.64 (0.24), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 753 
 TYR   0.021   0.001   TYR A 306 
 PHE   0.028   0.002   PHE A 125 
 TRP   0.020   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 9842)
  covalent geometry    : angle       0.72018 (13360)
  SS BOND              : bond        0.00125 (    8)
  SS BOND              : angle       0.71311 (   16)
  hydrogen bonds       : bond        0.05549 (  362)
  hydrogen bonds       : angle       5.81141 ( 1062)

*********************** 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
  176 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.4681 (OUTLIER) cc_final: 0.3513 (mmtm)
REVERT: B  464 ILE cc_start: 0.7803 (mm) cc_final: 0.7549 (mm)
REVERT: B  590 LYS cc_start: 0.5343 (OUTLIER) cc_final: 0.4196 (mmtm)
REVERT: B  725 TRP cc_start: 0.6450 (m100) cc_final: 0.6009 (m100)
REVERT: B  764 PRO cc_start: 0.7087 (Cg_endo) cc_final: 0.6802 (Cg_exo)
  outliers start: 41
  outliers final: 29
  residues processed: 168
  average time/residue: 0.0802
  time to fit residues: 20.0536
Evaluate side-chains
  153 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 122
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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  633 LEU
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  334 SER
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  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  611 ILE
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 67 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 57 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0870
   chunk 102 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7960

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

Flipped N/Q/H residues before XYZ refinement:
A 620 ASN
A 710 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 = 0.5579 r_free = 0.5579 target = 0.278234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5319 r_free = 0.5319 target = 0.247535 restraints weight = 13021.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.5293 rms_B_bonded: 2.78
r_work: 0.5106 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.5106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5881
moved from start:          0.4437

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= 0.145
  Angle     :  0.740  18.544  13376  Z= 0.368
  Chirality :  0.046   0.271   1480
  Planarity :  0.005   0.056   1630
  Dihedral  :  6.307  37.639   1287
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 12.63
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.85 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 21.81 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.06 (0.22), residues: 1130
  helix: -2.06 (0.18), residues: 660
  sheet:  None (None), residues: 0
  loop : -3.61 (0.24), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 354 
 TYR   0.024   0.001   TYR B 776 
 PHE   0.026   0.002   PHE B 374 
 TRP   0.019   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9842)
  covalent geometry    : angle       0.74011 (13360)
  SS BOND              : bond        0.00101 (    8)
  SS BOND              : angle       0.70445 (   16)
  hydrogen bonds       : bond        0.05500 (  362)
  hydrogen bonds       : angle       5.69215 ( 1062)

*********************** 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
  173 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 132
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 ARG cc_start: 0.6434 (mtt90) cc_final: 0.6003 (mpt-90)
REVERT: A  590 LYS cc_start: 0.4640 (OUTLIER) cc_final: 0.3610 (mmtm)
REVERT: A  604 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7194 (tp30)
REVERT: B  562 ASN cc_start: 0.7064 (t0) cc_final: 0.6850 (t0)
REVERT: B  590 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.4320 (mmtm)
REVERT: B  725 TRP cc_start: 0.6465 (m100) cc_final: 0.6043 (m100)
REVERT: B  764 PRO cc_start: 0.7114 (Cg_endo) cc_final: 0.6849 (Cg_exo)
  outliers start: 41
  outliers final: 31
  residues processed: 167
  average time/residue: 0.0688
  time to fit residues: 17.9015
Evaluate side-chains
  154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 120
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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  356 CYS
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  604 GLU
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  633 LEU
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  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  410 THR
Chi-restraints excluded: chain B residue  463 TRP
Chi-restraints excluded: chain B residue  527 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9980
   chunk 93 optimal weight:    0.8980
   chunk 2 optimal weight:    4.9990
   chunk 96 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 99 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 7 optimal weight:    7.9990
   chunk 21 optimal weight:    0.0370
   overall best weight:    0.6658

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
A 562 ASN
** 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 = 0.5580 r_free = 0.5580 target = 0.278501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5320 r_free = 0.5320 target = 0.247563 restraints weight = 12989.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.5293 rms_B_bonded: 2.83
r_work: 0.5080 rms_B_bonded: 4.02 restraints_weight: 0.5000
r_work (final): 0.5080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5896
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9850  Z= 0.139
  Angle     :  0.729  15.216  13376  Z= 0.362
  Chirality :  0.046   0.254   1480
  Planarity :  0.005   0.056   1630
  Dihedral  :  6.164  36.497   1287
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.56 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 23.36 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.90 (0.22), residues: 1130
  helix: -1.92 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.56 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 592 
 TYR   0.029   0.001   TYR B 847 
 PHE   0.038   0.002   PHE B 851 
 TRP   0.019   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9842)
  covalent geometry    : angle       0.72893 (13360)
  SS BOND              : bond        0.00097 (    8)
  SS BOND              : angle       0.69368 (   16)
  hydrogen bonds       : bond        0.05319 (  362)
  hydrogen bonds       : angle       5.56896 ( 1062)

*********************** 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
  171 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 131
  time to evaluate  : 0.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 ARG cc_start: 0.6257 (mtt90) cc_final: 0.5908 (mpt-90)
REVERT: A  590 LYS cc_start: 0.5029 (OUTLIER) cc_final: 0.4028 (mmtt)
REVERT: A  604 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7230 (tp30)
REVERT: B  386 MET cc_start: 0.5101 (mmt) cc_final: 0.4837 (mmt)
REVERT: B  590 LYS cc_start: 0.5318 (OUTLIER) cc_final: 0.4404 (mmtm)
REVERT: B  725 TRP cc_start: 0.6340 (m100) cc_final: 0.5930 (m100)
REVERT: B  749 ASP cc_start: 0.6222 (OUTLIER) cc_final: 0.5959 (m-30)
REVERT: B  764 PRO cc_start: 0.6903 (Cg_endo) cc_final: 0.6599 (Cg_exo)
  outliers start: 40
  outliers final: 29
  residues processed: 164
  average time/residue: 0.0713
  time to fit residues: 17.8663
Evaluate side-chains
  154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 121
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
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  570 ILE
Chi-restraints excluded: chain A residue  590 LYS
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  604 GLU
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  633 LEU
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  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  527 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  749 ASP
Chi-restraints excluded: chain B residue  845 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 93 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
** 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 = 0.5564 r_free = 0.5564 target = 0.276618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5300 r_free = 0.5300 target = 0.245368 restraints weight = 13114.382|
|-----------------------------------------------------------------------------|
r_work (start): 0.5269 rms_B_bonded: 2.75
r_work: 0.5069 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.5069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5942
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9850  Z= 0.157
  Angle     :  0.759  14.646  13376  Z= 0.378
  Chirality :  0.046   0.217   1480
  Planarity :  0.005   0.052   1630
  Dihedral  :  6.134  36.818   1286
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 13.25
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  9.56 %
    Favored  : 90.27 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 23.84 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.22), residues: 1130
  helix: -1.87 (0.18), residues: 662
  sheet:  None (None), residues: 0
  loop : -3.49 (0.25), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 753 
 TYR   0.029   0.002   TYR B 822 
 PHE   0.022   0.002   PHE B 681 
 TRP   0.015   0.001   TRP B 397 
 HIS   0.004   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9842)
  covalent geometry    : angle       0.75886 (13360)
  SS BOND              : bond        0.00111 (    8)
  SS BOND              : angle       0.72291 (   16)
  hydrogen bonds       : bond        0.05416 (  362)
  hydrogen bonds       : angle       5.56983 ( 1062)

*********************** 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
  163 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 124
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  590 LYS cc_start: 0.5084 (OUTLIER) cc_final: 0.4103 (mmtt)
REVERT: A  604 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7193 (tp30)
REVERT: B  142 MET cc_start: 0.4442 (tpp) cc_final: 0.4069 (tpp)
REVERT: B  386 MET cc_start: 0.5040 (mmt) cc_final: 0.4788 (mmt)
REVERT: B  524 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8148 (tp)
REVERT: B  590 LYS cc_start: 0.5341 (OUTLIER) cc_final: 0.4479 (mmtm)
REVERT: B  725 TRP cc_start: 0.6416 (m100) cc_final: 0.6046 (m100)
REVERT: B  749 ASP cc_start: 0.6099 (OUTLIER) cc_final: 0.5882 (m-30)
REVERT: B  764 PRO cc_start: 0.7107 (Cg_endo) cc_final: 0.6826 (Cg_exo)
  outliers start: 39
  outliers final: 31
  residues processed: 156
  average time/residue: 0.0706
  time to fit residues: 16.8851
Evaluate side-chains
  154 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 118
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
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  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  604 GLU
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  633 LEU
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  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  527 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  732 ILE
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  749 ASP
Chi-restraints excluded: chain B residue  845 ILE
Chi-restraints excluded: chain B residue  847 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9980
   chunk 81 optimal weight:    4.9990
   chunk 110 optimal weight:    0.1980
   chunk 32 optimal weight:    0.0270
   chunk 57 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 70 optimal weight:    3.9990
   chunk 112 optimal weight:    0.0270
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
A 559 GLN
** B 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 844 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5589 r_free = 0.5589 target = 0.280415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5340 r_free = 0.5340 target = 0.250176 restraints weight = 13011.052|
|-----------------------------------------------------------------------------|
r_work (start): 0.5312 rms_B_bonded: 2.77
r_work: 0.5120 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.5120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5853
moved from start:          0.5149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9850  Z= 0.135
  Angle     :  0.724  14.609  13376  Z= 0.358
  Chirality :  0.045   0.181   1480
  Planarity :  0.005   0.055   1630
  Dihedral  :  5.904  35.180   1286
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.67 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.32 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.51 (0.22), residues: 1130
  helix: -1.58 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -3.41 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 478 
 TYR   0.028   0.001   TYR A 306 
 PHE   0.019   0.001   PHE A 556 
 TRP   0.022   0.001   TRP B 397 
 HIS   0.004   0.001   HIS B 844 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9842)
  covalent geometry    : angle       0.72434 (13360)
  SS BOND              : bond        0.00095 (    8)
  SS BOND              : angle       0.67576 (   16)
  hydrogen bonds       : bond        0.05053 (  362)
  hydrogen bonds       : angle       5.39711 ( 1062)

*********************** 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: 33
    poor density    : 133
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.5015 (mmt) cc_final: 0.4279 (mmt)
REVERT: A  553 MET cc_start: 0.6907 (mmt) cc_final: 0.6207 (mmt)
REVERT: A  590 LYS cc_start: 0.5240 (OUTLIER) cc_final: 0.4465 (mmtt)
REVERT: A  604 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7168 (tp30)
REVERT: B  142 MET cc_start: 0.4295 (tpp) cc_final: 0.3935 (tpp)
REVERT: B  386 MET cc_start: 0.4669 (mmt) cc_final: 0.4345 (mmt)
REVERT: B  524 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8093 (tp)
REVERT: B  553 MET cc_start: 0.6578 (tpt) cc_final: 0.5882 (mmt)
REVERT: B  590 LYS cc_start: 0.5372 (OUTLIER) cc_final: 0.4690 (mmtm)
REVERT: B  725 TRP cc_start: 0.6353 (m100) cc_final: 0.5920 (m100)
REVERT: B  764 PRO cc_start: 0.6961 (Cg_endo) cc_final: 0.6665 (Cg_exo)
REVERT: B  776 TYR cc_start: 0.5163 (t80) cc_final: 0.4888 (t80)
REVERT: B  842 MET cc_start: 0.7760 (mmt) cc_final: 0.7458 (mmt)
  outliers start: 33
  outliers final: 18
  residues processed: 159
  average time/residue: 0.0702
  time to fit residues: 17.4266
Evaluate side-chains
  143 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
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  633 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  471 VAL
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  732 ILE
Chi-restraints excluded: chain B residue  845 ILE
Chi-restraints excluded: chain B residue  848 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 21 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 92 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 72 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 112 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A  94 GLN
A 559 GLN
A 620 ASN
** 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 = 0.5549 r_free = 0.5549 target = 0.274986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.5290 r_free = 0.5290 target = 0.244390 restraints weight = 12821.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.5250 rms_B_bonded: 3.15
r_work: 0.5016 rms_B_bonded: 4.01 restraints_weight: 0.5000
r_work (final): 0.5016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6007
moved from start:          0.5258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9850  Z= 0.192
  Angle     :  0.809  14.238  13376  Z= 0.401
  Chirality :  0.048   0.185   1480
  Planarity :  0.005   0.051   1630
  Dihedral  :  6.113  35.169   1286
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 10.27 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.68 %
    Favored  : 71.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.63 (0.22), residues: 1130
  helix: -1.71 (0.18), residues: 668
  sheet:  None (None), residues: 0
  loop : -3.45 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 478 
 TYR   0.032   0.002   TYR A 306 
 PHE   0.026   0.002   PHE A 681 
 TRP   0.015   0.002   TRP B 397 
 HIS   0.005   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 ( 9842)
  covalent geometry    : angle       0.80950 (13360)
  SS BOND              : bond        0.00124 (    8)
  SS BOND              : angle       0.74453 (   16)
  hydrogen bonds       : bond        0.05566 (  362)
  hydrogen bonds       : angle       5.64652 ( 1062)

********************** 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: 33
    poor density    : 120
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  386 MET cc_start: 0.5226 (mmt) cc_final: 0.4449 (mmt)
REVERT: A  590 LYS cc_start: 0.5223 (OUTLIER) cc_final: 0.4512 (mmtt)
REVERT: A  604 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7180 (tp30)
REVERT: B  142 MET cc_start: 0.4149 (tpp) cc_final: 0.3804 (tpp)
REVERT: B  386 MET cc_start: 0.4744 (mmt) cc_final: 0.4411 (mmt)
REVERT: B  404 LEU cc_start: 0.7697 (mt) cc_final: 0.7013 (pp)
REVERT: B  524 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8042 (tp)
REVERT: B  553 MET cc_start: 0.6790 (tpt) cc_final: 0.6212 (mmt)
REVERT: B  590 LYS cc_start: 0.5395 (OUTLIER) cc_final: 0.4820 (mmtm)
REVERT: B  764 PRO cc_start: 0.7385 (Cg_endo) cc_final: 0.7173 (Cg_exo)
  outliers start: 33
  outliers final: 25
  residues processed: 150
  average time/residue: 0.0641
  time to fit residues: 15.0846
Evaluate side-chains
  144 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
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  604 GLU
Chi-restraints excluded: chain A residue  611 ILE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  768 HIS
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  471 VAL
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  590 LYS
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  609 LEU
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  845 ILE
Chi-restraints excluded: chain B residue  848 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 61 optimal weight:    0.6980
   chunk 113 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0070
   chunk 60 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.6598

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5588 r_free = 0.5588 target = 0.279163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.5320 r_free = 0.5320 target = 0.248670 restraints weight = 12791.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.5283 rms_B_bonded: 2.64
r_work: 0.5090 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.5090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5893
moved from start:          0.5436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9850  Z= 0.142
  Angle     :  0.759  14.406  13376  Z= 0.373
  Chirality :  0.046   0.175   1480
  Planarity :  0.005   0.056   1630
  Dihedral  :  5.952  34.464   1286
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.03 %
    Favored  : 90.97 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 25.87 %
    Favored  : 71.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.40 (0.23), residues: 1130
  helix: -1.51 (0.19), residues: 656
  sheet:  None (None), residues: 0
  loop : -3.34 (0.25), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 400 
 TYR   0.048   0.002   TYR B 828 
 PHE   0.034   0.002   PHE A 851 
 TRP   0.020   0.001   TRP B 397 
 HIS   0.003   0.001   HIS A 824 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9842)
  covalent geometry    : angle       0.75948 (13360)
  SS BOND              : bond        0.00098 (    8)
  SS BOND              : angle       0.69888 (   16)
  hydrogen bonds       : bond        0.05176 (  362)
  hydrogen bonds       : angle       5.51976 ( 1062)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2195.74 seconds
wall clock time: 38 minutes 19.22 seconds (2299.22 seconds total)