Starting phenix.real_space_refine
on Wed Sep 17 16:21:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wtm_37836/09_2025/8wtm_37836.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wtm_37836/09_2025/8wtm_37836.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wtm_37836/09_2025/8wtm_37836.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wtm_37836/09_2025/8wtm_37836.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wtm_37836/09_2025/8wtm_37836.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wtm_37836/09_2025/8wtm_37836.cif"
  }
  resolution = 2.65
  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=  -0.001 sd=   0.111
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6298      2.51       5
     N    1622      2.21       5
     O    1718      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9680
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 614, 4825
          Classifications: {'peptide': 614}
          Link IDs: {'PTRANS': 23, 'TRANS': 590}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {'JAA': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.77, per 1000 atoms: 0.39
  Number of scatterers: 9680
  At special positions: 0
  Unit cell: (80.51, 100.43, 136.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1718      8.00
     N    1622      7.00
     C    6298      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 646 " - pdb=" SG  CYS A 687 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 646 " - pdb=" SG  CYS B 687 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 286.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      60.3% alpha, 7.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 130 through 139
    Processing helix  chain 'A' and resid 181 through 194
    Processing helix  chain 'A' and resid 199 through 214
    Processing helix  chain 'A' and resid 233 through 246
      removed outlier: 3.670A  pdb=" N   ARG A 239 " --> pdb=" O   GLY A 235 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP A 245 " --> pdb=" O   SER A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 279
      removed outlier: 3.793A  pdb=" N   VAL A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 298
      removed outlier: 3.543A  pdb=" N   SER A 297 " --> pdb=" O   ARG A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 318 through 325
      removed outlier: 3.838A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 347
    Processing helix  chain 'A' and resid 354 through 365
      removed outlier: 3.584A  pdb=" N   LYS A 363 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 369
      removed outlier: 3.867A  pdb=" N   LYS A 369 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 366 through 369'
    Processing helix  chain 'A' and resid 387 through 399
      removed outlier: 3.549A  pdb=" N   SER A 393 " --> pdb=" O   LYS A 389 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 397 " --> pdb=" O   SER A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 445
      removed outlier: 3.607A  pdb=" N   ILE A 432 " --> pdb=" O   PHE A 428 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ARG A 445 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 468
    Processing helix  chain 'A' and resid 474 through 495
      removed outlier: 3.577A  pdb=" N   GLN A 479 " --> pdb=" O   PRO A 475 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE A 493 " --> pdb=" O   MET A 489 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 499 through 506
      removed outlier: 3.729A  pdb=" N   GLU A 506 " --> pdb=" O   VAL A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 514
      removed outlier: 3.502A  pdb=" N   ARG A 512 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 532
      removed outlier: 3.504A  pdb=" N   VAL A 525 " --> pdb=" O   ARG A 521 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR A 532 " --> pdb=" O   HIS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 552
      removed outlier: 4.742A  pdb=" N   TRP A 549 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ALA A 550 " --> pdb=" O   THR A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 582
    Processing helix  chain 'A' and resid 587 through 605
    Processing helix  chain 'A' and resid 611 through 615
    Processing helix  chain 'A' and resid 619 through 624
      removed outlier: 3.556A  pdb=" N   HIS A 623 " --> pdb=" O   TRP A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 640
    Processing helix  chain 'A' and resid 649 through 655
      removed outlier: 3.679A  pdb=" N   LEU A 653 " --> pdb=" O   GLY A 650 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE A 654 " --> pdb=" O   VAL A 651 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASP A 655 " --> pdb=" O   GLN A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 679
      removed outlier: 3.754A  pdb=" N   ARG A 669 " --> pdb=" O   GLY A 665 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP A 672 " --> pdb=" O   LEU A 668 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER A 673 " --> pdb=" O   ARG A 669 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL A 674 " --> pdb=" O   LEU A 670 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 675 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   SER A 677 " --> pdb=" O   SER A 673 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE A 678 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 699
    Processing helix  chain 'A' and resid 704 through 733
      removed outlier: 3.717A  pdb=" N   SER A 731 " --> pdb=" O   LEU A 727 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LYS A 732 " --> pdb=" O   LEU A 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 139
    Processing helix  chain 'B' and resid 181 through 194
    Processing helix  chain 'B' and resid 199 through 214
    Processing helix  chain 'B' and resid 233 through 246
      removed outlier: 3.670A  pdb=" N   ARG B 239 " --> pdb=" O   GLY B 235 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP B 245 " --> pdb=" O   SER B 241 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 279
      removed outlier: 3.793A  pdb=" N   VAL B 271 " --> pdb=" O   ALA B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 298
      removed outlier: 3.542A  pdb=" N   SER B 297 " --> pdb=" O   ARG B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 317
      No H-bonds generated for 'chain 'B' and resid 315 through 317'
    Processing helix  chain 'B' and resid 318 through 325
      removed outlier: 3.838A  pdb=" N   GLY B 325 " --> pdb=" O   SER B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 347
    Processing helix  chain 'B' and resid 354 through 365
      removed outlier: 3.584A  pdb=" N   LYS B 363 " --> pdb=" O   GLU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 366 through 369
      removed outlier: 3.867A  pdb=" N   LYS B 369 " --> pdb=" O   GLU B 366 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 366 through 369'
    Processing helix  chain 'B' and resid 387 through 399
      removed outlier: 3.549A  pdb=" N   SER B 393 " --> pdb=" O   LYS B 389 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER B 397 " --> pdb=" O   SER B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 427 through 445
      removed outlier: 3.607A  pdb=" N   ILE B 432 " --> pdb=" O   PHE B 428 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   ARG B 445 " --> pdb=" O   LEU B 441 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 468
    Processing helix  chain 'B' and resid 474 through 495
      removed outlier: 3.578A  pdb=" N   GLN B 479 " --> pdb=" O   PRO B 475 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE B 493 " --> pdb=" O   MET B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 498
      No H-bonds generated for 'chain 'B' and resid 496 through 498'
    Processing helix  chain 'B' and resid 499 through 506
      removed outlier: 3.729A  pdb=" N   GLU B 506 " --> pdb=" O   VAL B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 514
      removed outlier: 3.502A  pdb=" N   ARG B 512 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 532
      removed outlier: 3.504A  pdb=" N   VAL B 525 " --> pdb=" O   ARG B 521 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR B 532 " --> pdb=" O   HIS B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 552
      removed outlier: 4.742A  pdb=" N   TRP B 549 " --> pdb=" O   VAL B 545 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   ALA B 550 " --> pdb=" O   THR B 546 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 582
    Processing helix  chain 'B' and resid 587 through 605
    Processing helix  chain 'B' and resid 611 through 615
    Processing helix  chain 'B' and resid 619 through 624
      removed outlier: 3.555A  pdb=" N   HIS B 623 " --> pdb=" O   TRP B 619 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 628 through 640
    Processing helix  chain 'B' and resid 649 through 655
      removed outlier: 3.678A  pdb=" N   LEU B 653 " --> pdb=" O   GLY B 650 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   PHE B 654 " --> pdb=" O   VAL B 651 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASP B 655 " --> pdb=" O   GLN B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 663 through 679
      removed outlier: 3.754A  pdb=" N   ARG B 669 " --> pdb=" O   GLY B 665 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP B 672 " --> pdb=" O   LEU B 668 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER B 673 " --> pdb=" O   ARG B 669 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   VAL B 674 " --> pdb=" O   LEU B 670 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER B 675 " --> pdb=" O   LEU B 671 " (cutoff:3.500A)
      removed outlier: 4.455A  pdb=" N   SER B 677 " --> pdb=" O   SER B 673 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ILE B 678 " --> pdb=" O   VAL B 674 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 699
    Processing helix  chain 'B' and resid 704 through 733
      removed outlier: 3.717A  pdb=" N   SER B 731 " --> pdb=" O   LEU B 727 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LYS B 732 " --> pdb=" O   LEU B 728 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 116
      removed outlier: 6.627A  pdb=" N   ASP A 109 " --> pdb=" O   THR A  79 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR A  79 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   ILE A 111 " --> pdb=" O   ASN A  77 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LEU A  78 " --> pdb=" O   LYS A 148 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   LYS A 148 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 170
      removed outlier: 6.103A  pdb=" N   ALA A 168 " --> pdb=" O   PHE A 254 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LEU A 121 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   LEU A 302 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER A 313 " --> pdb=" O   LEU A 302 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   PHE A 304 " --> pdb=" O   VAL A 311 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 108 through 116
      removed outlier: 6.627A  pdb=" N   ASP B 109 " --> pdb=" O   THR B  79 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   THR B  79 " --> pdb=" O   ASP B 109 " (cutoff:3.500A)
      removed outlier: 5.364A  pdb=" N   ILE B 111 " --> pdb=" O   ASN B  77 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   LEU B  78 " --> pdb=" O   LYS B 148 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   LYS B 148 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 170
      removed outlier: 6.102A  pdb=" N   ALA B 168 " --> pdb=" O   PHE B 254 " (cutoff:3.500A)
      removed outlier: 6.273A  pdb=" N   LEU B 121 " --> pdb=" O   MET B 286 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   LEU B 302 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER B 313 " --> pdb=" O   LEU B 302 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   PHE B 304 " --> pdb=" O   VAL B 311 " (cutoff:3.500A)

    494 hydrogen bonds defined for protein.
    1452 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: 1.52

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.17 -     1.29: 1500
        1.29 -     1.42: 2626
        1.42 -     1.55: 5670
        1.55 -     1.68: 18
        1.68 -     1.81: 74
  Bond restraints: 9888
  Sorted by residual:
  bond pdb=" C04 JAA A 802 "
       pdb=" C05 JAA A 802 "
    ideal  model  delta    sigma   weight residual
    1.534  1.346  0.188 2.00e-02 2.50e+03 8.81e+01
  bond pdb=" C04 JAA A 801 "
       pdb=" C05 JAA A 801 "
    ideal  model  delta    sigma   weight residual
    1.534  1.346  0.188 2.00e-02 2.50e+03 8.80e+01
  bond pdb=" C07 JAA A 802 "
       pdb=" C08 JAA A 802 "
    ideal  model  delta    sigma   weight residual
    1.514  1.342  0.172 2.00e-02 2.50e+03 7.38e+01
  bond pdb=" C07 JAA A 801 "
       pdb=" C08 JAA A 801 "
    ideal  model  delta    sigma   weight residual
    1.514  1.343  0.171 2.00e-02 2.50e+03 7.34e+01
  bond pdb=" C05 JAA A 802 "
       pdb=" C08 JAA A 802 "
    ideal  model  delta    sigma   weight residual
    1.515  1.684 -0.169 2.00e-02 2.50e+03 7.16e+01
  ... (remaining 9883 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.28: 12980
        2.28 -     4.57: 315
        4.57 -     6.85: 59
        6.85 -     9.13: 14
        9.13 -    11.42: 2
  Bond angle restraints: 13370
  Sorted by residual:
  angle pdb=" C   GLN A 172 "
        pdb=" N   ASP A 173 "
        pdb=" CA  ASP A 173 "
      ideal   model   delta    sigma   weight residual
     121.54  129.56   -8.02 1.91e+00 2.74e-01 1.76e+01
  angle pdb=" C   GLN B 172 "
        pdb=" N   ASP B 173 "
        pdb=" CA  ASP B 173 "
      ideal   model   delta    sigma   weight residual
     121.54  129.52   -7.98 1.91e+00 2.74e-01 1.75e+01
  angle pdb=" C   LYS A 105 "
        pdb=" N   THR A 106 "
        pdb=" CA  THR A 106 "
      ideal   model   delta    sigma   weight residual
     121.54  129.15   -7.61 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" C   LYS B 105 "
        pdb=" N   THR B 106 "
        pdb=" CA  THR B 106 "
      ideal   model   delta    sigma   weight residual
     121.54  129.15   -7.61 1.91e+00 2.74e-01 1.59e+01
  angle pdb=" CA  THR B 106 "
        pdb=" CB  THR B 106 "
        pdb=" CG2 THR B 106 "
      ideal   model   delta    sigma   weight residual
     110.50  117.01   -6.51 1.70e+00 3.46e-01 1.47e+01
  ... (remaining 13365 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 5355
       17.88 -    35.75: 442
       35.75 -    53.63: 65
       53.63 -    71.50: 14
       71.50 -    89.38: 8
  Dihedral angle restraints: 5884
    sinusoidal: 2364
      harmonic: 3520
  Sorted by residual:
  dihedral pdb=" CA  GLN B 172 "
           pdb=" C   GLN B 172 "
           pdb=" N   ASP B 173 "
           pdb=" CA  ASP B 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.31   31.69     0      5.00e+00 4.00e-02 4.02e+01
  dihedral pdb=" CA  GLN A 172 "
           pdb=" C   GLN A 172 "
           pdb=" N   ASP A 173 "
           pdb=" CA  ASP A 173 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.32   31.68     0      5.00e+00 4.00e-02 4.02e+01
  dihedral pdb=" CB  CYS A 646 "
           pdb=" SG  CYS A 646 "
           pdb=" SG  CYS A 687 "
           pdb=" CB  CYS A 687 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  139.00  -46.00     1      1.00e+01 1.00e-02 2.93e+01
  ... (remaining 5881 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1221
       0.064 -    0.129: 281
       0.129 -    0.193: 38
       0.193 -    0.257: 2
       0.257 -    0.321: 2
  Chirality restraints: 1544
  Sorted by residual:
  chirality pdb=" C05 JAA A 801 "
            pdb=" C04 JAA A 801 "
            pdb=" C08 JAA A 801 "
            pdb=" C09 JAA A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.82   -0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb=" C05 JAA A 802 "
            pdb=" C04 JAA A 802 "
            pdb=" C08 JAA A 802 "
            pdb=" C09 JAA A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50    2.82   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" CA  THR A 106 "
            pdb=" N   THR A 106 "
            pdb=" C   THR A 106 "
            pdb=" CB  THR A 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1541 not shown)

  Planarity restraints: 1668
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B  67 "    0.043 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO B  68 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B  68 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B  68 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  67 "   -0.043 5.00e-02 4.00e+02   6.55e-02 6.87e+00
        pdb=" N   PRO A  68 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 507 "   -0.013 2.00e-02 2.50e+03   2.60e-02 6.76e+00
        pdb=" C   ARG A 507 "    0.045 2.00e-02 2.50e+03
        pdb=" O   ARG A 507 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   TYR A 508 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1665 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 2394
        2.78 -     3.31: 8329
        3.31 -     3.84: 15597
        3.84 -     4.37: 19914
        4.37 -     4.90: 32759
  Nonbonded interactions: 78993
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 163 "
            pdb=" OG  SER A 167 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   LEU B 163 "
            pdb=" OG  SER B 167 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" OH  TYR A 494 "
            pdb=" OH  TYR A 592 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" OH  TYR B 494 "
            pdb=" OH  TYR B 592 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   ILE A 277 "
            pdb=" OG  SER A 280 "
     model   vdw
     2.331 3.040
  ... (remaining 78988 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 67 through 733)
  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:             1.640
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.060
  Process input model:                     11.290
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
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      :  0.008   0.188   9890  Z= 0.368
  Angle     :  0.915  11.417  13374  Z= 0.489
  Chirality :  0.055   0.321   1544
  Planarity :  0.007   0.066   1668
  Dihedral  : 13.621  89.378   3610
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.11 %
    Favored  : 94.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.76 (0.17), residues: 1212
  helix: -4.00 (0.09), residues: 670
  sheet:  0.28 (0.59), residues: 66
  loop : -2.06 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 507 
 TYR   0.011   0.003   TYR A 630 
 PHE   0.015   0.002   PHE A  75 
 TRP   0.009   0.002   TRP B 621 
 HIS   0.007   0.002   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00820 ( 9888)
  covalent geometry    : angle       0.91524 (13370)
  SS BOND              : bond        0.00324 (    2)
  SS BOND              : angle       1.24976 (    4)
  hydrogen bonds       : bond        0.29568 (  494)
  hydrogen bonds       : angle       9.18213 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 158
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  187 MET cc_start: 0.8276 (tpt) cc_final: 0.8068 (mmm)
REVERT: A  237 ARG cc_start: 0.7696 (mtm-85) cc_final: 0.7469 (mtp180)
REVERT: A  269 MET cc_start: 0.7112 (tpt) cc_final: 0.6584 (tpt)
REVERT: A  272 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7275 (mtpp)
REVERT: A  307 ARG cc_start: 0.7817 (ptp-170) cc_final: 0.7478 (ptp90)
REVERT: A  342 ASP cc_start: 0.7400 (t0) cc_final: 0.7101 (t0)
REVERT: A  511 MET cc_start: 0.7817 (mtm) cc_final: 0.7174 (mmt)
REVERT: A  528 HIS cc_start: 0.8249 (t-90) cc_final: 0.8011 (t-170)
REVERT: A  598 ILE cc_start: 0.8408 (mt) cc_final: 0.8147 (tp)
REVERT: B  187 MET cc_start: 0.8279 (tpt) cc_final: 0.8076 (mmm)
REVERT: B  237 ARG cc_start: 0.7664 (mtm-85) cc_final: 0.7443 (mtp180)
REVERT: B  269 MET cc_start: 0.7104 (tpt) cc_final: 0.6675 (tpt)
REVERT: B  272 LYS cc_start: 0.7673 (ttpt) cc_final: 0.7296 (mtpp)
REVERT: B  307 ARG cc_start: 0.7809 (ptp-170) cc_final: 0.7466 (ptp90)
REVERT: B  342 ASP cc_start: 0.7380 (t0) cc_final: 0.7115 (t0)
REVERT: B  511 MET cc_start: 0.7813 (mtm) cc_final: 0.7184 (mmt)
REVERT: B  528 HIS cc_start: 0.8240 (t-90) cc_final: 0.8002 (t-170)
REVERT: B  589 MET cc_start: 0.8589 (tpt) cc_final: 0.8289 (tpt)
REVERT: B  598 ILE cc_start: 0.8414 (mt) cc_final: 0.8158 (tp)
  outliers start: 2
  outliers final: 2
  residues processed: 160
  average time/residue: 0.7429
  time to fit residues: 125.4139
Evaluate side-chains
  122 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 120
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain B residue  182 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 108 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 113 optimal weight:    0.0870
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.9980
   chunk 117 optimal weight:   10.0000
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 248 HIS
A 611 ASN
A 617 GLN
B  81 ASN
B 248 HIS
B 611 ASN
B 617 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.174842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.105009 restraints weight = 9269.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 1.72
r_work: 0.2931 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.42 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8453
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9890  Z= 0.119
  Angle     :  0.558   6.061  13374  Z= 0.298
  Chirality :  0.040   0.136   1544
  Planarity :  0.005   0.073   1668
  Dihedral  :  6.277  66.087   1366
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.17 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.87 (0.22), residues: 1212
  helix: -1.07 (0.17), residues: 702
  sheet:  0.88 (0.53), residues: 82
  loop : -1.74 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 301 
 TYR   0.013   0.002   TYR A 494 
 PHE   0.012   0.001   PHE B 562 
 TRP   0.007   0.001   TRP B 572 
 HIS   0.003   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9888)
  covalent geometry    : angle       0.55784 (13370)
  SS BOND              : bond        0.00004 (    2)
  SS BOND              : angle       1.16144 (    4)
  hydrogen bonds       : bond        0.04649 (  494)
  hydrogen bonds       : angle       4.17290 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7105 (tm-30)
REVERT: A  237 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.7451 (mtp180)
REVERT: A  272 LYS cc_start: 0.7627 (ttpt) cc_final: 0.7202 (mtpp)
REVERT: A  307 ARG cc_start: 0.8018 (ptp-170) cc_final: 0.7807 (ptp-170)
REVERT: A  338 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.6211 (tm-30)
REVERT: A  444 ARG cc_start: 0.7813 (ttm170) cc_final: 0.7503 (ttm-80)
REVERT: A  511 MET cc_start: 0.8717 (mtm) cc_final: 0.7991 (mmt)
REVERT: A  528 HIS cc_start: 0.8526 (t-90) cc_final: 0.8324 (t-170)
REVERT: A  598 ILE cc_start: 0.8431 (mt) cc_final: 0.8194 (tp)
REVERT: A  680 MET cc_start: 0.5953 (mtp) cc_final: 0.5556 (ptt)
REVERT: B  114 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7083 (tm-30)
REVERT: B  237 ARG cc_start: 0.7666 (mtm-85) cc_final: 0.7446 (mtp180)
REVERT: B  272 LYS cc_start: 0.7599 (ttpt) cc_final: 0.7175 (mtpp)
REVERT: B  307 ARG cc_start: 0.8007 (ptp-170) cc_final: 0.7794 (ptp-170)
REVERT: B  338 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6185 (tm-30)
REVERT: B  444 ARG cc_start: 0.7799 (ttm170) cc_final: 0.7488 (ttm-80)
REVERT: B  511 MET cc_start: 0.8735 (mtm) cc_final: 0.8001 (mmt)
REVERT: B  598 ILE cc_start: 0.8430 (mt) cc_final: 0.8198 (tp)
  outliers start: 13
  outliers final: 1
  residues processed: 142
  average time/residue: 0.6168
  time to fit residues: 93.3579
Evaluate side-chains
  113 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 110
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain B residue  338 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 112 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 110 optimal weight:    2.9990
   chunk 40 optimal weight:    3.9990
   chunk 117 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 120 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 617 GLN
B  81 ASN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.171186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.104591 restraints weight = 9332.100|
|-----------------------------------------------------------------------------|
r_work (start): 0.3075 rms_B_bonded: 1.92
r_work: 0.2859 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2725 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   9890  Z= 0.212
  Angle     :  0.635   8.311  13374  Z= 0.328
  Chirality :  0.046   0.155   1544
  Planarity :  0.005   0.067   1668
  Dihedral  :  6.184  62.843   1364
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 12.78 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.23), residues: 1212
  helix:  0.21 (0.19), residues: 698
  sheet:  0.47 (0.55), residues: 66
  loop : -1.61 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 301 
 TYR   0.018   0.002   TYR A 601 
 PHE   0.016   0.002   PHE A 562 
 TRP   0.007   0.001   TRP B 621 
 HIS   0.005   0.002   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 9888)
  covalent geometry    : angle       0.63455 (13370)
  SS BOND              : bond        0.00099 (    2)
  SS BOND              : angle       0.75384 (    4)
  hydrogen bonds       : bond        0.05873 (  494)
  hydrogen bonds       : angle       3.97783 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.400 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7162 (tm-30)
REVERT: A  173 ASP cc_start: 0.6918 (m-30) cc_final: 0.6478 (t0)
REVERT: A  218 ASN cc_start: 0.7233 (p0) cc_final: 0.6569 (p0)
REVERT: A  236 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7371 (mt-10)
REVERT: A  237 ARG cc_start: 0.7836 (mtm-85) cc_final: 0.7598 (mtp-110)
REVERT: A  272 LYS cc_start: 0.7655 (ttpt) cc_final: 0.7218 (mtpp)
REVERT: A  307 ARG cc_start: 0.8010 (ptp-170) cc_final: 0.7797 (ptp-170)
REVERT: A  428 PHE cc_start: 0.8035 (t80) cc_final: 0.7804 (t80)
REVERT: A  511 MET cc_start: 0.8854 (mtm) cc_final: 0.8099 (mmt)
REVERT: A  528 HIS cc_start: 0.8605 (t-90) cc_final: 0.8357 (t-170)
REVERT: A  598 ILE cc_start: 0.8575 (mt) cc_final: 0.8303 (tp)
REVERT: B  114 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7114 (tm-30)
REVERT: B  173 ASP cc_start: 0.6912 (m-30) cc_final: 0.6473 (t0)
REVERT: B  218 ASN cc_start: 0.7232 (p0) cc_final: 0.6592 (p0)
REVERT: B  236 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7390 (mt-10)
REVERT: B  237 ARG cc_start: 0.7851 (mtm-85) cc_final: 0.7615 (mtp-110)
REVERT: B  272 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7202 (mtpp)
REVERT: B  307 ARG cc_start: 0.7994 (ptp-170) cc_final: 0.7782 (ptp-170)
REVERT: B  342 ASP cc_start: 0.7297 (t0) cc_final: 0.6976 (t0)
REVERT: B  428 PHE cc_start: 0.8034 (t80) cc_final: 0.7803 (t80)
REVERT: B  511 MET cc_start: 0.8866 (mtm) cc_final: 0.8107 (mmt)
REVERT: B  598 ILE cc_start: 0.8571 (mt) cc_final: 0.8299 (tp)
  outliers start: 37
  outliers final: 18
  residues processed: 146
  average time/residue: 0.6786
  time to fit residues: 105.1626
Evaluate side-chains
  142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  260 SER
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  328 ASN
Chi-restraints excluded: chain B residue  502 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 1 optimal weight:    9.9990
   chunk 12 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    0.5980
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 617 GLN
B  81 ASN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.172282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.102274 restraints weight = 9304.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.2982 rms_B_bonded: 2.36
r_work: 0.2804 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2665 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.2030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9890  Z= 0.159
  Angle     :  0.581   9.716  13374  Z= 0.299
  Chirality :  0.044   0.142   1544
  Planarity :  0.004   0.054   1668
  Dihedral  :  5.885  55.197   1364
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 13.64 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.24), residues: 1212
  helix:  0.89 (0.20), residues: 688
  sheet:  0.62 (0.53), residues: 94
  loop : -1.39 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 301 
 TYR   0.012   0.002   TYR A 630 
 PHE   0.012   0.001   PHE A 562 
 TRP   0.006   0.001   TRP B 621 
 HIS   0.004   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 9888)
  covalent geometry    : angle       0.58047 (13370)
  SS BOND              : bond        0.00088 (    2)
  SS BOND              : angle       0.75767 (    4)
  hydrogen bonds       : bond        0.04844 (  494)
  hydrogen bonds       : angle       3.75176 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 122
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7032 (tm-30)
REVERT: A  236 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7304 (mp0)
REVERT: A  237 ARG cc_start: 0.7814 (mtm-85) cc_final: 0.7591 (mtp-110)
REVERT: A  260 SER cc_start: 0.8291 (OUTLIER) cc_final: 0.8072 (p)
REVERT: A  272 LYS cc_start: 0.7693 (ttpt) cc_final: 0.7263 (mtpp)
REVERT: A  307 ARG cc_start: 0.7981 (ptp-170) cc_final: 0.7754 (ptp-170)
REVERT: A  428 PHE cc_start: 0.8028 (t80) cc_final: 0.7800 (t80)
REVERT: A  511 MET cc_start: 0.8813 (mtm) cc_final: 0.8096 (mmt)
REVERT: A  528 HIS cc_start: 0.8588 (t-90) cc_final: 0.8387 (t-170)
REVERT: A  598 ILE cc_start: 0.8553 (mt) cc_final: 0.8309 (tp)
REVERT: A  680 MET cc_start: 0.6057 (mtp) cc_final: 0.5630 (ptt)
REVERT: B  114 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7071 (tm-30)
REVERT: B  236 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7307 (mp0)
REVERT: B  237 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7604 (mtp-110)
REVERT: B  260 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8067 (p)
REVERT: B  272 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7251 (mtpp)
REVERT: B  307 ARG cc_start: 0.7962 (ptp-170) cc_final: 0.7734 (ptp-170)
REVERT: B  428 PHE cc_start: 0.8025 (t80) cc_final: 0.7795 (t80)
REVERT: B  511 MET cc_start: 0.8819 (mtm) cc_final: 0.8102 (mmt)
REVERT: B  598 ILE cc_start: 0.8549 (mt) cc_final: 0.8308 (tp)
REVERT: B  680 MET cc_start: 0.6059 (mtp) cc_final: 0.5637 (ptt)
  outliers start: 47
  outliers final: 18
  residues processed: 157
  average time/residue: 0.5980
  time to fit residues: 100.2235
Evaluate side-chains
  136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  260 SER
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  502 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 120 optimal weight:    0.9990
   chunk 95 optimal weight:    0.5980
   chunk 87 optimal weight:    9.9990
   chunk 91 optimal weight:    0.0370
   chunk 94 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 84 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.0862

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 617 GLN
B  81 ASN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.173184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.101663 restraints weight = 9347.690|
|-----------------------------------------------------------------------------|
r_work (start): 0.2976 rms_B_bonded: 2.16
r_work: 0.2835 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2697 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9890  Z= 0.130
  Angle     :  0.554  10.584  13374  Z= 0.284
  Chirality :  0.042   0.133   1544
  Planarity :  0.004   0.044   1668
  Dihedral  :  5.561  45.273   1364
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.20 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.25), residues: 1212
  helix:  1.29 (0.20), residues: 690
  sheet:  0.75 (0.52), residues: 94
  loop : -1.31 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 649 
 TYR   0.014   0.002   TYR A 494 
 PHE   0.010   0.001   PHE B 562 
 TRP   0.005   0.001   TRP B 572 
 HIS   0.003   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9888)
  covalent geometry    : angle       0.55376 (13370)
  SS BOND              : bond        0.00074 (    2)
  SS BOND              : angle       1.26540 (    4)
  hydrogen bonds       : bond        0.04306 (  494)
  hydrogen bonds       : angle       3.59594 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 124
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.7754 (tm-30) cc_final: 0.6928 (tm-30)
REVERT: A  171 MET cc_start: 0.8501 (mtp) cc_final: 0.7880 (mmm)
REVERT: A  237 ARG cc_start: 0.7769 (mtm-85) cc_final: 0.7552 (mtp-110)
REVERT: A  260 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.8053 (p)
REVERT: A  272 LYS cc_start: 0.7529 (ttpt) cc_final: 0.7206 (mtpp)
REVERT: A  307 ARG cc_start: 0.7940 (ptp-170) cc_final: 0.7687 (ptp-170)
REVERT: A  511 MET cc_start: 0.8734 (mtm) cc_final: 0.7992 (mmt)
REVERT: A  554 GLU cc_start: 0.8480 (tp30) cc_final: 0.8267 (mm-30)
REVERT: A  598 ILE cc_start: 0.8514 (mt) cc_final: 0.8278 (tp)
REVERT: A  680 MET cc_start: 0.6038 (mtp) cc_final: 0.5639 (ptt)
REVERT: B  114 GLU cc_start: 0.7841 (tm-30) cc_final: 0.6991 (tm-30)
REVERT: B  171 MET cc_start: 0.8482 (mtp) cc_final: 0.7872 (mmm)
REVERT: B  237 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7574 (mtp-110)
REVERT: B  272 LYS cc_start: 0.7513 (ttpt) cc_final: 0.7188 (mtpp)
REVERT: B  307 ARG cc_start: 0.7930 (ptp-170) cc_final: 0.7678 (ptp-170)
REVERT: B  511 MET cc_start: 0.8751 (mtm) cc_final: 0.7998 (mmt)
REVERT: B  598 ILE cc_start: 0.8513 (mt) cc_final: 0.8281 (tp)
REVERT: B  642 ASP cc_start: 0.6981 (m-30) cc_final: 0.6761 (t0)
REVERT: B  680 MET cc_start: 0.6033 (mtp) cc_final: 0.5635 (ptt)
  outliers start: 41
  outliers final: 22
  residues processed: 154
  average time/residue: 0.6090
  time to fit residues: 99.9801
Evaluate side-chains
  133 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0470
   chunk 30 optimal weight:    0.2980
   chunk 109 optimal weight:    3.9990
   overall best weight:    1.8684

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 528 HIS
A 617 GLN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.171168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.099722 restraints weight = 9334.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.2960 rms_B_bonded: 2.19
r_work: 0.2816 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2679 rms_B_bonded: 3.72 restraints_weight: 0.2500
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   9890  Z= 0.185
  Angle     :  0.617  11.593  13374  Z= 0.312
  Chirality :  0.045   0.148   1544
  Planarity :  0.004   0.040   1668
  Dihedral  :  5.607  34.992   1364
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 14.30 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.25), residues: 1212
  helix:  1.25 (0.20), residues: 692
  sheet:  0.71 (0.52), residues: 94
  loop : -1.32 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 649 
 TYR   0.017   0.002   TYR A 494 
 PHE   0.013   0.002   PHE A 562 
 TRP   0.006   0.001   TRP A 621 
 HIS   0.004   0.001   HIS A 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 9888)
  covalent geometry    : angle       0.61732 (13370)
  SS BOND              : bond        0.00073 (    2)
  SS BOND              : angle       0.86571 (    4)
  hydrogen bonds       : bond        0.05108 (  494)
  hydrogen bonds       : angle       3.70105 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 119
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7830 (tm-30) cc_final: 0.6960 (tm-30)
REVERT: A  218 ASN cc_start: 0.7298 (p0) cc_final: 0.6798 (p0)
REVERT: A  237 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.7548 (mtp180)
REVERT: A  260 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.8104 (p)
REVERT: A  272 LYS cc_start: 0.7648 (ttpt) cc_final: 0.7311 (mtpp)
REVERT: A  307 ARG cc_start: 0.7967 (ptp-170) cc_final: 0.7731 (ptp-170)
REVERT: A  342 ASP cc_start: 0.7340 (t0) cc_final: 0.7059 (t0)
REVERT: A  511 MET cc_start: 0.8798 (mtm) cc_final: 0.8047 (mmt)
REVERT: A  598 ILE cc_start: 0.8572 (mt) cc_final: 0.8301 (tp)
REVERT: A  680 MET cc_start: 0.6009 (mtp) cc_final: 0.5592 (ptt)
REVERT: B  114 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7035 (tm-30)
REVERT: B  218 ASN cc_start: 0.7294 (p0) cc_final: 0.6796 (p0)
REVERT: B  237 ARG cc_start: 0.7786 (mtm-85) cc_final: 0.7578 (mtp180)
REVERT: B  272 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7306 (mtpp)
REVERT: B  307 ARG cc_start: 0.7960 (ptp-170) cc_final: 0.7723 (ptp-170)
REVERT: B  342 ASP cc_start: 0.7345 (t0) cc_final: 0.7043 (t0)
REVERT: B  511 MET cc_start: 0.8810 (mtm) cc_final: 0.8059 (mmt)
REVERT: B  598 ILE cc_start: 0.8563 (mt) cc_final: 0.8295 (tp)
REVERT: B  642 ASP cc_start: 0.6985 (m-30) cc_final: 0.6772 (t0)
REVERT: B  680 MET cc_start: 0.6002 (mtp) cc_final: 0.5594 (ptt)
  outliers start: 40
  outliers final: 24
  residues processed: 146
  average time/residue: 0.5944
  time to fit residues: 92.7794
Evaluate side-chains
  142 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0870
   chunk 93 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 5 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 95 optimal weight:    1.9990
   chunk 71 optimal weight:    0.1980
   overall best weight:    0.9762

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
A 617 GLN
B  81 ASN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.173712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.105640 restraints weight = 9269.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.07
r_work: 0.2874 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8489
moved from start:          0.2418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9890  Z= 0.122
  Angle     :  0.563  12.579  13374  Z= 0.283
  Chirality :  0.042   0.132   1544
  Planarity :  0.004   0.035   1668
  Dihedral  :  5.332  29.739   1364
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 16.19 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.25), residues: 1212
  helix:  1.51 (0.20), residues: 696
  sheet:  0.76 (0.51), residues: 94
  loop : -1.21 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 301 
 TYR   0.013   0.001   TYR A 494 
 PHE   0.010   0.001   PHE B  75 
 TRP   0.006   0.001   TRP A 572 
 HIS   0.003   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9888)
  covalent geometry    : angle       0.56299 (13370)
  SS BOND              : bond        0.00046 (    2)
  SS BOND              : angle       0.77420 (    4)
  hydrogen bonds       : bond        0.04054 (  494)
  hydrogen bonds       : angle       3.51439 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.377 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.7827 (tm-30) cc_final: 0.6973 (tm-30)
REVERT: A  171 MET cc_start: 0.8503 (mtp) cc_final: 0.7930 (mmm)
REVERT: A  236 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7061 (mp0)
REVERT: A  237 ARG cc_start: 0.7768 (mtm-85) cc_final: 0.7562 (mtp-110)
REVERT: A  272 LYS cc_start: 0.7552 (ttpt) cc_final: 0.7127 (mtpp)
REVERT: A  307 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7697 (ptp-170)
REVERT: A  511 MET cc_start: 0.8695 (mtm) cc_final: 0.7931 (mmt)
REVERT: A  598 ILE cc_start: 0.8505 (mt) cc_final: 0.8290 (tp)
REVERT: A  680 MET cc_start: 0.6052 (mtp) cc_final: 0.5685 (ptt)
REVERT: B  114 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7039 (tm-30)
REVERT: B  171 MET cc_start: 0.8539 (mtp) cc_final: 0.7909 (mmm)
REVERT: B  236 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7066 (mp0)
REVERT: B  237 ARG cc_start: 0.7782 (mtm-85) cc_final: 0.7578 (mtp-110)
REVERT: B  272 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7127 (mtpp)
REVERT: B  307 ARG cc_start: 0.7942 (ptp-170) cc_final: 0.7683 (ptp-170)
REVERT: B  511 MET cc_start: 0.8710 (mtm) cc_final: 0.7947 (mmt)
REVERT: B  598 ILE cc_start: 0.8494 (mt) cc_final: 0.8286 (tp)
REVERT: B  642 ASP cc_start: 0.6938 (m-30) cc_final: 0.6723 (t0)
REVERT: B  680 MET cc_start: 0.5948 (mtp) cc_final: 0.5626 (ptt)
  outliers start: 29
  outliers final: 19
  residues processed: 141
  average time/residue: 0.6144
  time to fit residues: 92.5797
Evaluate side-chains
  138 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  289 HIS
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 78 optimal weight:    8.9990
   chunk 120 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 19 optimal weight:    7.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 528 HIS
A 617 GLN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.170525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.099159 restraints weight = 9316.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.18
r_work: 0.2804 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2667 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9890  Z= 0.208
  Angle     :  0.642  13.832  13374  Z= 0.322
  Chirality :  0.046   0.155   1544
  Planarity :  0.004   0.037   1668
  Dihedral  :  5.518  30.360   1364
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 16.38 %
    Favored  : 80.49 %
  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 aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1212
  helix:  1.25 (0.20), residues: 698
  sheet:  0.70 (0.51), residues: 94
  loop : -1.26 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 649 
 TYR   0.019   0.002   TYR A 494 
 PHE   0.014   0.002   PHE B 562 
 TRP   0.006   0.001   TRP B 621 
 HIS   0.004   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 ( 9888)
  covalent geometry    : angle       0.64190 (13370)
  SS BOND              : bond        0.00035 (    2)
  SS BOND              : angle       0.70012 (    4)
  hydrogen bonds       : bond        0.05328 (  494)
  hydrogen bonds       : angle       3.70794 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7846 (tm-30) cc_final: 0.6959 (tm-30)
REVERT: A  141 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6827 (mtt180)
REVERT: A  218 ASN cc_start: 0.7281 (p0) cc_final: 0.6714 (p0)
REVERT: A  272 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7233 (mtpp)
REVERT: A  307 ARG cc_start: 0.7958 (ptp-170) cc_final: 0.7716 (ptp-170)
REVERT: A  342 ASP cc_start: 0.7360 (t0) cc_final: 0.7054 (t0)
REVERT: A  389 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8239 (mmtm)
REVERT: A  511 MET cc_start: 0.8805 (mtm) cc_final: 0.7961 (mmt)
REVERT: A  598 ILE cc_start: 0.8571 (mt) cc_final: 0.8286 (tp)
REVERT: A  680 MET cc_start: 0.5945 (mtp) cc_final: 0.5561 (ptt)
REVERT: B  114 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7029 (tm-30)
REVERT: B  218 ASN cc_start: 0.7284 (p0) cc_final: 0.6719 (p0)
REVERT: B  272 LYS cc_start: 0.7644 (ttpt) cc_final: 0.7237 (mtpp)
REVERT: B  307 ARG cc_start: 0.7953 (ptp-170) cc_final: 0.7713 (ptp-170)
REVERT: B  342 ASP cc_start: 0.7361 (t0) cc_final: 0.7054 (t0)
REVERT: B  389 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8240 (mmtm)
REVERT: B  511 MET cc_start: 0.8814 (mtm) cc_final: 0.7972 (mmt)
REVERT: B  598 ILE cc_start: 0.8568 (mt) cc_final: 0.8288 (tp)
REVERT: B  642 ASP cc_start: 0.7013 (m-30) cc_final: 0.6789 (t0)
REVERT: B  680 MET cc_start: 0.5904 (mtp) cc_final: 0.5530 (ptt)
  outliers start: 33
  outliers final: 21
  residues processed: 148
  average time/residue: 0.6689
  time to fit residues: 105.1685
Evaluate side-chains
  140 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  502 VAL
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 105 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0270
   chunk 102 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 95 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 93 optimal weight:    0.2980
   overall best weight:    1.2644

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

Flipped N/Q/H residues before XYZ refinement:
A 528 HIS
A 617 GLN
B  81 ASN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.172391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.102557 restraints weight = 9216.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3001 rms_B_bonded: 2.23
r_work: 0.2837 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9890  Z= 0.142
  Angle     :  0.584  13.045  13374  Z= 0.294
  Chirality :  0.043   0.138   1544
  Planarity :  0.004   0.036   1668
  Dihedral  :  5.376  29.741   1364
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.11 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 16.86 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.25), residues: 1212
  helix:  1.43 (0.20), residues: 696
  sheet:  0.75 (0.51), residues: 94
  loop : -1.13 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 649 
 TYR   0.016   0.002   TYR A 494 
 PHE   0.011   0.001   PHE A 562 
 TRP   0.005   0.001   TRP A 549 
 HIS   0.003   0.001   HIS B 587 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9888)
  covalent geometry    : angle       0.58404 (13370)
  SS BOND              : bond        0.00033 (    2)
  SS BOND              : angle       0.76804 (    4)
  hydrogen bonds       : bond        0.04420 (  494)
  hydrogen bonds       : angle       3.57739 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 120
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.7837 (tm-30) cc_final: 0.6941 (tm-30)
REVERT: A  141 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6775 (mtt180)
REVERT: A  171 MET cc_start: 0.8485 (mtp) cc_final: 0.7895 (mmm)
REVERT: A  218 ASN cc_start: 0.7258 (p0) cc_final: 0.6590 (p0)
REVERT: A  236 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.6998 (mp0)
REVERT: A  272 LYS cc_start: 0.7532 (ttpt) cc_final: 0.7132 (mtpp)
REVERT: A  307 ARG cc_start: 0.7947 (ptp-170) cc_final: 0.7705 (ptp-170)
REVERT: A  389 LYS cc_start: 0.8513 (mmtt) cc_final: 0.8230 (mmtm)
REVERT: A  511 MET cc_start: 0.8757 (mtm) cc_final: 0.8035 (mmt)
REVERT: A  598 ILE cc_start: 0.8522 (mt) cc_final: 0.8281 (tp)
REVERT: A  680 MET cc_start: 0.5838 (mtp) cc_final: 0.5502 (ptt)
REVERT: B  114 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7006 (tm-30)
REVERT: B  171 MET cc_start: 0.8502 (mtp) cc_final: 0.7920 (mmm)
REVERT: B  218 ASN cc_start: 0.7260 (p0) cc_final: 0.6590 (p0)
REVERT: B  236 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7000 (mp0)
REVERT: B  272 LYS cc_start: 0.7588 (ttpt) cc_final: 0.7187 (mtpp)
REVERT: B  307 ARG cc_start: 0.7930 (ptp-170) cc_final: 0.7686 (ptp-170)
REVERT: B  389 LYS cc_start: 0.8524 (mmtt) cc_final: 0.8243 (mmtm)
REVERT: B  511 MET cc_start: 0.8771 (mtm) cc_final: 0.8050 (mmt)
REVERT: B  598 ILE cc_start: 0.8517 (mt) cc_final: 0.8280 (tp)
REVERT: B  642 ASP cc_start: 0.7024 (m-30) cc_final: 0.6814 (t0)
REVERT: B  680 MET cc_start: 0.5747 (mtp) cc_final: 0.5461 (ptt)
  outliers start: 27
  outliers final: 20
  residues processed: 140
  average time/residue: 0.6551
  time to fit residues: 97.4457
Evaluate side-chains
  139 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  289 HIS
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 71 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 1 optimal weight:    8.9990
   chunk 55 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 92 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A  81 ASN
A 528 HIS
A 617 GLN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.170355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.102830 restraints weight = 9281.042|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.24
r_work: 0.2826 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9890  Z= 0.205
  Angle     :  0.644  13.476  13374  Z= 0.323
  Chirality :  0.046   0.153   1544
  Planarity :  0.004   0.037   1668
  Dihedral  :  5.531  31.144   1364
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.23 %
    Favored  : 80.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), residues: 1212
  helix:  1.24 (0.20), residues: 698
  sheet:  0.70 (0.51), residues: 94
  loop : -1.21 (0.32), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 649 
 TYR   0.018   0.002   TYR A 494 
 PHE   0.014   0.002   PHE A 562 
 TRP   0.006   0.001   TRP A 549 
 HIS   0.004   0.001   HIS A 248 

Details of bonding type rmsd
  covalent geometry    : bond        0.00512 ( 9888)
  covalent geometry    : angle       0.64407 (13370)
  SS BOND              : bond        0.00039 (    2)
  SS BOND              : angle       0.69926 (    4)
  hydrogen bonds       : bond        0.05277 (  494)
  hydrogen bonds       : angle       3.70636 ( 1452)

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 116
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7012 (tm-30)
REVERT: A  141 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6849 (mtt180)
REVERT: A  272 LYS cc_start: 0.7665 (ttpt) cc_final: 0.7348 (mtpp)
REVERT: A  342 ASP cc_start: 0.7416 (t0) cc_final: 0.7116 (t0)
REVERT: A  511 MET cc_start: 0.8828 (mtm) cc_final: 0.7988 (mmt)
REVERT: A  598 ILE cc_start: 0.8566 (mt) cc_final: 0.8282 (tp)
REVERT: A  680 MET cc_start: 0.5897 (mtp) cc_final: 0.5507 (ptt)
REVERT: B  114 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7040 (tm-30)
REVERT: B  272 LYS cc_start: 0.7678 (ttpt) cc_final: 0.7274 (mtpp)
REVERT: B  307 ARG cc_start: 0.7959 (ptp-170) cc_final: 0.7722 (ptp-170)
REVERT: B  342 ASP cc_start: 0.7400 (t0) cc_final: 0.7070 (t0)
REVERT: B  511 MET cc_start: 0.8839 (mtm) cc_final: 0.8001 (mmt)
REVERT: B  598 ILE cc_start: 0.8562 (mt) cc_final: 0.8282 (tp)
REVERT: B  642 ASP cc_start: 0.7019 (m-30) cc_final: 0.6792 (t0)
REVERT: B  680 MET cc_start: 0.5898 (mtp) cc_final: 0.5523 (ptt)
  outliers start: 27
  outliers final: 21
  residues processed: 135
  average time/residue: 0.6512
  time to fit residues: 93.5383
Evaluate side-chains
  136 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  141 ARG
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  182 VAL
Chi-restraints excluded: chain A residue  236 GLU
Chi-restraints excluded: chain A residue  321 SER
Chi-restraints excluded: chain A residue  454 LEU
Chi-restraints excluded: chain A residue  718 LEU
Chi-restraints excluded: chain B residue  114 GLU
Chi-restraints excluded: chain B residue  115 THR
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  147 LEU
Chi-restraints excluded: chain B residue  150 THR
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  182 VAL
Chi-restraints excluded: chain B residue  236 GLU
Chi-restraints excluded: chain B residue  321 SER
Chi-restraints excluded: chain B residue  454 LEU
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  718 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 122
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    0.4980
   chunk 113 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 98 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 87 optimal weight:   10.0000
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 528 HIS
A 617 GLN
B  81 ASN
B 218 ASN
B 528 HIS
B 617 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.173282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.105719 restraints weight = 9285.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.33
r_work: 0.2840 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9890  Z= 0.123
  Angle     :  0.574  14.015  13374  Z= 0.288
  Chirality :  0.042   0.132   1544
  Planarity :  0.004   0.036   1668
  Dihedral  :  5.286  29.285   1364
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 17.61 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.25), residues: 1212
  helix:  1.58 (0.20), residues: 690
  sheet:  0.76 (0.51), residues: 94
  loop : -0.99 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 649 
 TYR   0.014   0.002   TYR A 494 
 PHE   0.010   0.001   PHE A  75 
 TRP   0.005   0.001   TRP A 572 
 HIS   0.003   0.001   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9888)
  covalent geometry    : angle       0.57370 (13370)
  SS BOND              : bond        0.00011 (    2)
  SS BOND              : angle       0.77402 (    4)
  hydrogen bonds       : bond        0.04079 (  494)
  hydrogen bonds       : angle       3.51201 ( 1452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4564.14 seconds
wall clock time: 78 minutes 13.58 seconds (4693.58 seconds total)