Starting phenix.real_space_refine
on Fri Feb  6 06:34:48 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9q0x_72109/02_2026/9q0x_72109_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9q0x_72109/02_2026/9q0x_72109.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9q0x_72109/02_2026/9q0x_72109_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9q0x_72109/02_2026/9q0x_72109_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9q0x_72109/02_2026/9q0x_72109.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9q0x_72109/02_2026/9q0x_72109.map"
  }
  resolution = 3.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     S      66      5.16       5
     C    7378      2.51       5
     N    1942      2.21       5
     O    2053      1.98       5
     H   11005      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 22448
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 12087
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 752, 12087
          Classifications: {'peptide': 752}
          Link IDs: {'PTRANS': 42, 'TRANS': 709}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 10189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 628, 10189
          Classifications: {'peptide': 628}
          Link IDs: {'PTRANS': 35, 'TRANS': 592}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 86
          Unusual residues: {'HEM': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 86
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 86
          Unusual residues: {'HEM': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7611  SG  CYS A 539      48.673  90.918  66.659  1.00141.69           S
  ATOM  17835  SG  CYS B 539      29.585  76.711  39.474  1.00178.59           S

  Time building chain proxies: 4.03, per 1000 atoms: 0.18
  Number of scatterers: 22448
  At special positions: 0
  Unit cell: (81.024, 129.132, 146.856, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S      66     16.00
     O    2053      8.00
     N    1942      7.00
     C    7378      6.00
     H   11005      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  44 " - pdb=" SG  CYS A  72 " 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=4, symmetry=0
  Number of additional bonds: simple=4, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.18
  Conformation dependent library (CDL) restraints added in 833.7 milliseconds
  

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2616

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 13 sheets defined
      62.2% alpha, 8.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 178 through 195
      removed outlier: 3.891A  pdb=" N   ALA A 194 " --> pdb=" O   ASN A 190 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   TRP A 195 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 195 through 211
    Processing helix  chain 'A' and resid 213 through 219
    Processing helix  chain 'A' and resid 220 through 222
      No H-bonds generated for 'chain 'A' and resid 220 through 222'
    Processing helix  chain 'A' and resid 224 through 241
    Processing helix  chain 'A' and resid 265 through 277
      removed outlier: 3.687A  pdb=" N   TYR A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 294
      removed outlier: 3.846A  pdb=" N   GLN A 288 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 297
      No H-bonds generated for 'chain 'A' and resid 295 through 297'
    Processing helix  chain 'A' and resid 301 through 310
      removed outlier: 3.777A  pdb=" N   LYS A 310 " --> pdb=" O   GLU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 337
      removed outlier: 4.561A  pdb=" N   ILE A 325 " --> pdb=" O   ASN A 321 " (cutoff:3.500A)
      removed outlier: 4.412A  pdb=" N   GLY A 326 " --> pdb=" O   THR A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 355
      removed outlier: 3.774A  pdb=" N   TYR A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   PHE A 354 " --> pdb=" O   SER A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 373
      removed outlier: 3.699A  pdb=" N   TYR A 373 " --> pdb=" O   LEU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 382
      removed outlier: 4.076A  pdb=" N   PHE A 380 " --> pdb=" O   VAL A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 404
      removed outlier: 4.095A  pdb=" N   THR A 390 " --> pdb=" O   ASP A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 426
    Processing helix  chain 'A' and resid 429 through 432
    Processing helix  chain 'A' and resid 433 through 446
      removed outlier: 3.514A  pdb=" N   GLU A 437 " --> pdb=" O   GLY A 433 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 495
      removed outlier: 3.517A  pdb=" N   LYS A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   VAL A 468 " --> pdb=" O   ARG A 464 " (cutoff:3.500A)
      Proline residue:  A 472  - end of helix
      removed outlier: 3.752A  pdb=" N   ASN A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 516
    Processing helix  chain 'A' and resid 521 through 535
    Processing helix  chain 'A' and resid 541 through 545
    Processing helix  chain 'A' and resid 558 through 575
      removed outlier: 3.517A  pdb=" N   ASN A 575 " --> pdb=" O   ARG A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 578
      No H-bonds generated for 'chain 'A' and resid 576 through 578'
    Processing helix  chain 'A' and resid 623 through 635
      removed outlier: 3.640A  pdb=" N   THR A 627 " --> pdb=" O   ASN A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 686
      removed outlier: 3.977A  pdb=" N   LYS A 683 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 727
    Processing helix  chain 'A' and resid 733 through 742
    Processing helix  chain 'A' and resid 747 through 750
      removed outlier: 3.514A  pdb=" N   THR A 750 " --> pdb=" O   SER A 747 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 747 through 750'
    Processing helix  chain 'A' and resid 751 through 771
    Processing helix  chain 'A' and resid 777 through 795
    Processing helix  chain 'A' and resid 836 through 842
    Processing helix  chain 'B' and resid 178 through 194
      removed outlier: 3.900A  pdb=" N   ALA B 194 " --> pdb=" O   ASN B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 195 through 211
    Processing helix  chain 'B' and resid 213 through 219
      removed outlier: 3.635A  pdb=" N   ILE B 217 " --> pdb=" O   GLU B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 223
      removed outlier: 4.369A  pdb=" N   GLU B 223 " --> pdb=" O   GLU B 220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 220 through 223'
    Processing helix  chain 'B' and resid 224 through 241
    Processing helix  chain 'B' and resid 265 through 277
    Processing helix  chain 'B' and resid 279 through 294
      removed outlier: 3.662A  pdb=" N   TRP B 283 " --> pdb=" O   GLN B 279 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   GLN B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   VAL B 289 " --> pdb=" O   ARG B 285 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   MET B 293 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 297
      No H-bonds generated for 'chain 'B' and resid 295 through 297'
    Processing helix  chain 'B' and resid 301 through 310
    Processing helix  chain 'B' and resid 314 through 337
      removed outlier: 4.410A  pdb=" N   ILE B 325 " --> pdb=" O   ASN B 321 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   GLY B 326 " --> pdb=" O   THR B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 352
      removed outlier: 3.672A  pdb=" N   GLN B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 373
    Processing helix  chain 'B' and resid 374 through 377
    Processing helix  chain 'B' and resid 384 through 389
      removed outlier: 3.750A  pdb=" N   LEU B 388 " --> pdb=" O   ASP B 384 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   SER B 389 " --> pdb=" O   MET B 385 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 384 through 389'
    Processing helix  chain 'B' and resid 391 through 406
    Processing helix  chain 'B' and resid 407 through 426
    Processing helix  chain 'B' and resid 428 through 430
      No H-bonds generated for 'chain 'B' and resid 428 through 430'
    Processing helix  chain 'B' and resid 431 through 447
      removed outlier: 4.268A  pdb=" N   ILE B 435 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   SER B 436 " --> pdb=" O   TYR B 432 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 495
      removed outlier: 3.632A  pdb=" N   VAL B 468 " --> pdb=" O   ARG B 464 " (cutoff:3.500A)
      Proline residue:  B 472  - end of helix
      removed outlier: 3.951A  pdb=" N   ASN B 475 " --> pdb=" O   LEU B 471 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   GLU B 476 " --> pdb=" O   PRO B 472 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 516
    Processing helix  chain 'B' and resid 521 through 535
    Processing helix  chain 'B' and resid 540 through 548
      removed outlier: 4.212A  pdb=" N   ILE B 543 " --> pdb=" O   ILE B 540 " (cutoff:3.500A)
      removed outlier: 4.701A  pdb=" N   SER B 546 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   MET B 548 " --> pdb=" O   TRP B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 575
    Processing helix  chain 'B' and resid 576 through 578
      No H-bonds generated for 'chain 'B' and resid 576 through 578'
    Processing helix  chain 'B' and resid 621 through 623
      No H-bonds generated for 'chain 'B' and resid 621 through 623'
    Processing helix  chain 'B' and resid 624 through 634
    Processing helix  chain 'B' and resid 665 through 669
      removed outlier: 3.520A  pdb=" N   ILE B 669 " --> pdb=" O   PRO B 666 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 686
      removed outlier: 3.830A  pdb=" N   PHE B 682 " --> pdb=" O   ILE B 679 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   LYS B 683 " --> pdb=" O   PRO B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 717 through 727
      removed outlier: 4.001A  pdb=" N   ILE B 721 " --> pdb=" O   MET B 717 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA B 722 " --> pdb=" O   GLY B 718 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 733 through 742
    Processing helix  chain 'B' and resid 747 through 750
      removed outlier: 3.683A  pdb=" N   THR B 750 " --> pdb=" O   SER B 747 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 747 through 750'
    Processing helix  chain 'B' and resid 751 through 771
    Processing helix  chain 'B' and resid 777 through 795
    Processing helix  chain 'B' and resid 836 through 841
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62
    Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62
      removed outlier: 6.774A  pdb=" N   ARG A 129 " --> pdb=" O   VAL A  21 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   LEU A  23 " --> pdb=" O   ASN A 127 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ASN A 127 " --> pdb=" O   LEU A  23 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ALA A  25 " --> pdb=" O   MET A 125 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   MET A 125 " --> pdb=" O   ALA A  25 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 43
      removed outlier: 3.530A  pdb=" N   LYS A  35 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   THR A  77 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A  43 " --> pdb=" O   LEU A  73 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LEU A  73 " --> pdb=" O   THR A  43 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   VAL A  76 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   SER A  94 " --> pdb=" O   VAL A  76 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU A  78 " --> pdb=" O   ALA A  92 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 550 through 552
      removed outlier: 3.971A  pdb=" N   VAL A 582 " --> pdb=" O   ASN A 713 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 599
    Processing sheet with id=AA6, first strand: chain 'A' and resid 609 through 611
    Processing sheet with id=AA7, first strand: chain 'A' and resid 671 through 673
    Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 707
      removed outlier: 3.638A  pdb=" N   ASP A 701 " --> pdb=" O   ALA A 830 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   ALA A 830 " --> pdb=" O   ASP A 701 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 550 through 552
      removed outlier: 6.682A  pdb=" N   ARG B 551 " --> pdb=" O   VAL B 585 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   VAL B 582 " --> pdb=" O   ASN B 713 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN B 713 " --> pdb=" O   VAL B 582 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 598 through 599
    Processing sheet with id=AB2, first strand: chain 'B' and resid 609 through 611
    Processing sheet with id=AB3, first strand: chain 'B' and resid 671 through 673
    Processing sheet with id=AB4, first strand: chain 'B' and resid 705 through 707
      removed outlier: 3.592A  pdb=" N   ASP B 701 " --> pdb=" O   ALA B 830 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   ALA B 830 " --> pdb=" O   ASP B 701 " (cutoff:3.500A)

    627 hydrogen bonds defined for protein.
    1800 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: 5.05

  Time building geometry restraints manager: 3.15 seconds

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

  Histogram of bond lengths:
        0.84 -     1.08: 10991
        1.08 -     1.33: 2134
        1.33 -     1.57: 9528
        1.57 -     1.81: 113
        1.81 -     2.06: 17
  Bond restraints: 22783
  Sorted by residual:
  bond pdb=" N   GLU B 170 "
       pdb=" CA  GLU B 170 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   VAL A  14 "
       pdb=" CA  VAL A  14 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.84e+00
  bond pdb=" N   GLU B 170 "
       pdb=" H   GLU B 170 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.27e+00
  bond pdb=" N   VAL A  14 "
       pdb=" H   VAL A  14 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.25e+00
  bond pdb=" NA  HEM B1502 "
       pdb="FE   HEM B1502 "
    ideal  model  delta    sigma   weight residual
    2.080  2.011  0.069 7.00e-02 2.04e+02 9.73e-01
  ... (remaining 22778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 40384
        1.59 -     3.18: 595
        3.18 -     4.77: 82
        4.77 -     6.35: 7
        6.35 -     7.94: 11
  Bond angle restraints: 41079
  Sorted by residual:
  angle pdb=" CB  MET B 200 "
        pdb=" CG  MET B 200 "
        pdb=" SD  MET B 200 "
      ideal   model   delta    sigma   weight residual
     112.70  120.55   -7.85 3.00e+00 1.11e-01 6.85e+00
  angle pdb=" CA  MET B 775 "
        pdb=" CB  MET B 775 "
        pdb=" CG  MET B 775 "
      ideal   model   delta    sigma   weight residual
     114.10  119.25   -5.15 2.00e+00 2.50e-01 6.63e+00
  angle pdb=" CB  MET B 291 "
        pdb=" CG  MET B 291 "
        pdb=" SD  MET B 291 "
      ideal   model   delta    sigma   weight residual
     112.70  120.07   -7.37 3.00e+00 1.11e-01 6.03e+00
  angle pdb=" CB  MET A 361 "
        pdb=" CG  MET A 361 "
        pdb=" SD  MET A 361 "
      ideal   model   delta    sigma   weight residual
     112.70  119.87   -7.17 3.00e+00 1.11e-01 5.71e+00
  angle pdb=" CB  MET A 200 "
        pdb=" CG  MET A 200 "
        pdb=" SD  MET A 200 "
      ideal   model   delta    sigma   weight residual
     112.70  119.42   -6.72 3.00e+00 1.11e-01 5.02e+00
  ... (remaining 41074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 9328
       17.66 -    35.32: 913
       35.32 -    52.98: 339
       52.98 -    70.64: 74
       70.64 -    88.30: 28
  Dihedral angle restraints: 10682
    sinusoidal: 5736
      harmonic: 4946
  Sorted by residual:
  dihedral pdb=" CA  HIS A  68 "
           pdb=" C   HIS A  68 "
           pdb=" N   PRO A  69 "
           pdb=" CA  PRO A  69 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.74  -23.26     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  SER A  70 "
           pdb=" C   SER A  70 "
           pdb=" N   ASN A  71 "
           pdb=" CA  ASN A  71 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.73  -21.27     0      5.00e+00 4.00e-02 1.81e+01
  dihedral pdb=" CA  PHE A 443 "
           pdb=" C   PHE A 443 "
           pdb=" N   GLU A 444 "
           pdb=" CA  GLU A 444 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.05   19.95     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 10679 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1091
       0.028 -    0.056: 357
       0.056 -    0.084: 98
       0.084 -    0.112: 82
       0.112 -    0.139: 25
  Chirality restraints: 1653
  Sorted by residual:
  chirality pdb=" CA  ILE B 175 "
            pdb=" N   ILE B 175 "
            pdb=" C   ILE B 175 "
            pdb=" CB  ILE B 175 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.86e-01
  chirality pdb=" CA  VAL A 654 "
            pdb=" N   VAL A 654 "
            pdb=" C   VAL A 654 "
            pdb=" CB  VAL A 654 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  chirality pdb=" CA  ILE B 599 "
            pdb=" N   ILE B 599 "
            pdb=" C   ILE B 599 "
            pdb=" CB  ILE B 599 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.00e-01
  ... (remaining 1650 not shown)

  Planarity restraints: 3354
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 297 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO A 298 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 320 "    0.007 2.00e-02 2.50e+03   1.43e-02 2.04e+00
        pdb=" C   PHE B 320 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   PHE B 320 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ASN B 321 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 204 "    0.007 2.00e-02 2.50e+03   1.41e-02 1.99e+00
        pdb=" C   PHE B 204 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   PHE B 204 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LYS B 205 "    0.008 2.00e-02 2.50e+03
  ... (remaining 3351 not shown)

  Histogram of nonbonded interaction distances:
        1.85 -     2.40: 9368
        2.40 -     2.95: 50371
        2.95 -     3.50: 58565
        3.50 -     4.05: 75108
        4.05 -     4.60: 111062
  Nonbonded interactions: 304474
  Sorted by model distance:
  nonbonded pdb=" H   MET A 347 "
            pdb=" HG2 MET A 347 "
     model   vdw
     1.848 2.270
  nonbonded pdb=" HG1 THR A 368 "
            pdb="HH12 ARG A 372 "
     model   vdw
     1.854 2.100
  nonbonded pdb=" HE1 PHE A 354 "
            pdb=" HD1 PHE A 443 "
     model   vdw
     1.856 2.100
  nonbonded pdb=" HG  SER B 407 "
            pdb="HH21 ARG B 410 "
     model   vdw
     1.880 2.100
  nonbonded pdb=" HH  TYR B 518 "
            pdb=" HE2 HIS B 520 "
     model   vdw
     1.884 2.100
  ... (remaining 304469 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.880
  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:             0.160
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     22.420
  Find NCS groups from input model:        0.070
  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:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
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   0.768  11783  Z= 0.144
  Angle     :  0.576   7.943  16036  Z= 0.278
  Chirality :  0.038   0.139   1653
  Planarity :  0.004   0.048   2058
  Dihedral  : 18.117  88.302   4321
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.81 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 23.17 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.24), residues: 1366
  helix:  1.96 (0.19), residues: 764
  sheet: -1.69 (0.48), residues: 136
  loop : -0.52 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.014   0.001   TYR A 366 
 PHE   0.008   0.001   PHE A 365 
 TRP   0.014   0.001   TRP A 458 
 HIS   0.003   0.001   HIS B 422 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 (11778)
  covalent geometry    : angle       0.57636 (16034)
  SS BOND              : bond        0.00262 (    1)
  SS BOND              : angle       0.39790 (    2)
  hydrogen bonds       : bond        0.15327 (  625)
  hydrogen bonds       : angle       6.33038 ( 1800)
  Misc. bond           : bond        0.38704 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.643 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  610 TYR cc_start: 0.8924 (m-80) cc_final: 0.8584 (m-10)
REVERT: B  187 ASP cc_start: 0.8935 (m-30) cc_final: 0.8606 (t0)
REVERT: B  232 MET cc_start: 0.8709 (ttp) cc_final: 0.8150 (tmm)
REVERT: B  562 MET cc_start: 0.8658 (mtp) cc_final: 0.8253 (mmm)
REVERT: B  618 MET cc_start: 0.9076 (tmm) cc_final: 0.8797 (tmm)
  outliers start: 14
  outliers final: 10
  residues processed: 97
  average time/residue: 0.2007
  time to fit residues: 30.1115
Evaluate side-chains
  93 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 83
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  651 VAL
Chi-restraints excluded: chain B residue  692 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 98 optimal weight:    0.0270
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    4.9990
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    1.0842

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

Flipped N/Q/H residues before XYZ refinement:
B 199 GLN
B 352 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.086193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.060360 restraints weight = 141992.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062457 restraints weight = 60646.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.062816 restraints weight = 37973.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.064114 restraints weight = 29688.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.064263 restraints weight = 24747.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.0609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.321  11783  Z= 0.146
  Angle     :  0.559   9.864  16036  Z= 0.268
  Chirality :  0.037   0.144   1653
  Planarity :  0.004   0.040   2058
  Dihedral  :  7.064  85.233   1570
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.25 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.64 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.20 (0.24), residues: 1366
  helix:  2.06 (0.19), residues: 763
  sheet: -1.54 (0.49), residues: 131
  loop : -0.57 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.015   0.001   TYR A 335 
 PHE   0.012   0.001   PHE A 443 
 TRP   0.018   0.001   TRP A 290 
 HIS   0.003   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (11778)
  covalent geometry    : angle       0.55888 (16034)
  SS BOND              : bond        0.00179 (    1)
  SS BOND              : angle       0.21108 (    2)
  hydrogen bonds       : bond        0.04488 (  625)
  hydrogen bonds       : angle       4.99891 ( 1800)
  Misc. bond           : bond        0.17114 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 PHE cc_start: 0.6440 (OUTLIER) cc_final: 0.6113 (p90)
REVERT: A  391 HIS cc_start: 0.8136 (OUTLIER) cc_final: 0.7883 (t-90)
REVERT: A  439 MET cc_start: 0.8721 (tpt) cc_final: 0.7979 (mtm)
REVERT: B  187 ASP cc_start: 0.8952 (m-30) cc_final: 0.8612 (t0)
REVERT: B  232 MET cc_start: 0.8652 (ttp) cc_final: 0.8079 (tmm)
REVERT: B  293 MET cc_start: 0.9119 (ppp) cc_final: 0.8867 (ppp)
REVERT: B  709 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8429 (t)
  outliers start: 33
  outliers final: 17
  residues processed: 111
  average time/residue: 0.1874
  time to fit residues: 32.4418
Evaluate side-chains
  100 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  709 CYS
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 87 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0010
   chunk 76 optimal weight:    8.9990
   chunk 123 optimal weight:    0.8980
   chunk 102 optimal weight:    8.9990
   chunk 64 optimal weight:    1.9990
   chunk 111 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.1390

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.086061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.060284 restraints weight = 142352.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.062403 restraints weight = 61378.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.062718 restraints weight = 37580.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.063928 restraints weight = 29519.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.064039 restraints weight = 24931.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.0957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.265  11783  Z= 0.144
  Angle     :  0.552   9.934  16036  Z= 0.262
  Chirality :  0.037   0.140   1653
  Planarity :  0.004   0.041   2058
  Dihedral  :  6.871  85.693   1567
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.61 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 21.31 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.24), residues: 1366
  helix:  2.11 (0.19), residues: 763
  sheet: -1.55 (0.48), residues: 131
  loop : -0.61 (0.30), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 335 
 PHE   0.012   0.001   PHE A 443 
 TRP   0.016   0.001   TRP A 290 
 HIS   0.003   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (11778)
  covalent geometry    : angle       0.55200 (16034)
  SS BOND              : bond        0.00211 (    1)
  SS BOND              : angle       0.21643 (    2)
  hydrogen bonds       : bond        0.04109 (  625)
  hydrogen bonds       : angle       4.73693 ( 1800)
  Misc. bond           : bond        0.14668 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  105 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 PHE cc_start: 0.6472 (OUTLIER) cc_final: 0.6156 (p90)
REVERT: A  391 HIS cc_start: 0.8187 (OUTLIER) cc_final: 0.7913 (t-90)
REVERT: A  439 MET cc_start: 0.8735 (tpt) cc_final: 0.8003 (mtm)
REVERT: B  187 ASP cc_start: 0.8971 (m-30) cc_final: 0.8637 (t0)
REVERT: B  232 MET cc_start: 0.8695 (ttp) cc_final: 0.8164 (tmm)
REVERT: B  293 MET cc_start: 0.9028 (ppp) cc_final: 0.8797 (ppp)
REVERT: B  562 MET cc_start: 0.8828 (mmm) cc_final: 0.8158 (mmm)
REVERT: B  709 CYS cc_start: 0.8748 (OUTLIER) cc_final: 0.8393 (t)
  outliers start: 24
  outliers final: 20
  residues processed: 101
  average time/residue: 0.1921
  time to fit residues: 29.8818
Evaluate side-chains
  103 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  709 CYS
Chi-restraints excluded: chain B residue  716 TYR
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 91 optimal weight:    8.9990
   chunk 81 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
A 555 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.084729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.058986 restraints weight = 144095.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.060697 restraints weight = 65128.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.060998 restraints weight = 40619.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.062096 restraints weight = 32178.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.062379 restraints weight = 27331.073|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.206  11783  Z= 0.221
  Angle     :  0.608  15.628  16036  Z= 0.285
  Chirality :  0.038   0.136   1653
  Planarity :  0.004   0.053   2058
  Dihedral  :  6.909  85.507   1567
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.34 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.22 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.24), residues: 1366
  helix:  1.74 (0.19), residues: 773
  sheet: -1.75 (0.48), residues: 131
  loop : -0.85 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 357 
 TYR   0.021   0.001   TYR A 335 
 PHE   0.012   0.001   PHE A 443 
 TRP   0.018   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00526 (11778)
  covalent geometry    : angle       0.60814 (16034)
  SS BOND              : bond        0.00278 (    1)
  SS BOND              : angle       0.29016 (    2)
  hydrogen bonds       : bond        0.04035 (  625)
  hydrogen bonds       : angle       4.76409 ( 1800)
  Misc. bond           : bond        0.12544 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  119 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6390 (p90)
REVERT: A  391 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7941 (t-90)
REVERT: B  187 ASP cc_start: 0.9046 (m-30) cc_final: 0.8701 (t0)
REVERT: B  232 MET cc_start: 0.8771 (ttp) cc_final: 0.8245 (tmm)
REVERT: B  562 MET cc_start: 0.8877 (mmm) cc_final: 0.8227 (mmm)
REVERT: B  653 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7971 (tp30)
REVERT: B  709 CYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8427 (t)
  outliers start: 37
  outliers final: 26
  residues processed: 115
  average time/residue: 0.2034
  time to fit residues: 36.6329
Evaluate side-chains
  110 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.606 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  263 PHE
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  715 TRP
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain A residue  754 ASP
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  224 SER
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  567 GLU
Chi-restraints excluded: chain B residue  584 THR
Chi-restraints excluded: chain B residue  651 VAL
Chi-restraints excluded: chain B residue  653 GLU
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  709 CYS
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 8 optimal weight:    9.9990
   chunk 34 optimal weight:    3.9990
   chunk 111 optimal weight:    0.6980
   chunk 99 optimal weight:   10.0000
   chunk 93 optimal weight:   10.0000
   chunk 100 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 102 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 114 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B 761 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.085561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.059654 restraints weight = 141493.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.061607 restraints weight = 61829.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.061930 restraints weight = 38608.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.062987 restraints weight = 30655.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.063816 restraints weight = 26069.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.229  11783  Z= 0.129
  Angle     :  0.542  10.867  16036  Z= 0.252
  Chirality :  0.037   0.137   1653
  Planarity :  0.004   0.050   2058
  Dihedral  :  6.706  89.637   1563
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.03 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.31 %
    Favored  : 76.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.24), residues: 1366
  helix:  2.03 (0.19), residues: 767
  sheet: -1.72 (0.48), residues: 131
  loop : -0.71 (0.30), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 335 
 PHE   0.011   0.001   PHE A 443 
 TRP   0.018   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (11778)
  covalent geometry    : angle       0.54202 (16034)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.25591 (    2)
  hydrogen bonds       : bond        0.03658 (  625)
  hydrogen bonds       : angle       4.46884 ( 1800)
  Misc. bond           : bond        0.12940 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 81
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 HIS cc_start: 0.8056 (OUTLIER) cc_final: 0.7797 (t-90)
REVERT: B  187 ASP cc_start: 0.8993 (m-30) cc_final: 0.8614 (t0)
REVERT: B  232 MET cc_start: 0.8731 (ttp) cc_final: 0.8240 (tmm)
  outliers start: 30
  outliers final: 23
  residues processed: 106
  average time/residue: 0.2048
  time to fit residues: 33.6376
Evaluate side-chains
  104 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 80
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  631 ILE
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  651 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  716 TYR
Chi-restraints excluded: chain B residue  761 ASN
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 135 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 103 optimal weight:    5.9990
   chunk 70 optimal weight:    0.5980
   chunk 134 optimal weight:    0.7980
   chunk 98 optimal weight:    0.1980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.085857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.060086 restraints weight = 141118.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.061946 restraints weight = 61639.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.062338 restraints weight = 38232.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.063516 restraints weight = 30168.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.063663 restraints weight = 25457.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.231  11783  Z= 0.112
  Angle     :  0.528  10.896  16036  Z= 0.248
  Chirality :  0.037   0.136   1653
  Planarity :  0.004   0.047   2058
  Dihedral  :  6.606  89.632   1563
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.25 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 22.07 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.24), residues: 1366
  helix:  2.15 (0.19), residues: 774
  sheet: -1.80 (0.47), residues: 137
  loop : -0.61 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 335 
 PHE   0.009   0.001   PHE A 443 
 TRP   0.016   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (11778)
  covalent geometry    : angle       0.52847 (16034)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.23496 (    2)
  hydrogen bonds       : bond        0.03526 (  625)
  hydrogen bonds       : angle       4.34140 ( 1800)
  Misc. bond           : bond        0.12905 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  107 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 HIS cc_start: 0.8114 (OUTLIER) cc_final: 0.7861 (t-90)
REVERT: B  187 ASP cc_start: 0.8977 (m-30) cc_final: 0.8608 (t0)
REVERT: B  232 MET cc_start: 0.8717 (ttp) cc_final: 0.8238 (tmm)
  outliers start: 26
  outliers final: 23
  residues processed: 102
  average time/residue: 0.2034
  time to fit residues: 31.2990
Evaluate side-chains
  102 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  710 LEU
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  716 TYR
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 103 optimal weight:    6.9990
   chunk 30 optimal weight:    0.0060
   chunk 53 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 131 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 132 optimal weight:    0.5980
   overall best weight:    1.1200

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.085467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.059443 restraints weight = 142722.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.061445 restraints weight = 66702.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.061616 restraints weight = 39325.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.062696 restraints weight = 31469.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.062919 restraints weight = 26938.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.213  11783  Z= 0.138
  Angle     :  0.530  10.610  16036  Z= 0.250
  Chirality :  0.037   0.135   1653
  Planarity :  0.004   0.046   2058
  Dihedral  :  6.529  88.282   1563
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.69 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 22.07 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.24), residues: 1366
  helix:  2.15 (0.19), residues: 774
  sheet: -1.80 (0.47), residues: 137
  loop : -0.65 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 357 
 TYR   0.018   0.001   TYR A 335 
 PHE   0.010   0.001   PHE A 443 
 TRP   0.016   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (11778)
  covalent geometry    : angle       0.53046 (16034)
  SS BOND              : bond        0.00241 (    1)
  SS BOND              : angle       0.25044 (    2)
  hydrogen bonds       : bond        0.03503 (  625)
  hydrogen bonds       : angle       4.33338 ( 1800)
  Misc. bond           : bond        0.12090 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  109 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  187 ASP cc_start: 0.8980 (m-30) cc_final: 0.8611 (t0)
REVERT: B  232 MET cc_start: 0.8707 (ttp) cc_final: 0.8241 (tmm)
  outliers start: 29
  outliers final: 24
  residues processed: 103
  average time/residue: 0.1919
  time to fit residues: 30.4933
Evaluate side-chains
  106 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain A residue  748 GLU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 THR
Chi-restraints excluded: chain B residue  651 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 111 optimal weight:    3.9990
   chunk 109 optimal weight:    0.8980
   chunk 92 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 47 optimal weight:    0.1980
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.085249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.059695 restraints weight = 140763.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.061275 restraints weight = 67338.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.061365 restraints weight = 42312.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.062553 restraints weight = 33656.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.062986 restraints weight = 27883.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.200  11783  Z= 0.163
  Angle     :  0.556  10.533  16036  Z= 0.261
  Chirality :  0.038   0.135   1653
  Planarity :  0.004   0.049   2058
  Dihedral  :  6.493  83.390   1561
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  5.05 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 22.24 %
    Favored  : 75.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.24), residues: 1366
  helix:  2.11 (0.19), residues: 774
  sheet: -1.83 (0.46), residues: 137
  loop : -0.69 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 357 
 TYR   0.019   0.001   TYR A 335 
 PHE   0.007   0.001   PHE A 443 
 TRP   0.016   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (11778)
  covalent geometry    : angle       0.55611 (16034)
  SS BOND              : bond        0.00260 (    1)
  SS BOND              : angle       0.28581 (    2)
  hydrogen bonds       : bond        0.03535 (  625)
  hydrogen bonds       : angle       4.37267 ( 1800)
  Misc. bond           : bond        0.11388 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  114 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 84
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  637 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8435 (pp30)
REVERT: B  187 ASP cc_start: 0.9026 (m-30) cc_final: 0.8649 (t0)
REVERT: B  232 MET cc_start: 0.8749 (ttp) cc_final: 0.8268 (tmm)
  outliers start: 30
  outliers final: 23
  residues processed: 109
  average time/residue: 0.1946
  time to fit residues: 32.5619
Evaluate side-chains
  107 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 83
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  294 LEU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 THR
Chi-restraints excluded: chain B residue  651 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 83 optimal weight:    8.9990
   chunk 47 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 88 optimal weight:    7.9990
   chunk 114 optimal weight:    2.9990
   chunk 86 optimal weight:    4.9990
   chunk 106 optimal weight:    7.9990
   chunk 102 optimal weight:    5.9990
   chunk 18 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 97 optimal weight:    3.9990
   overall best weight:    2.3388

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.083916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.057802 restraints weight = 143076.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.059590 restraints weight = 67762.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.059685 restraints weight = 41420.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.060596 restraints weight = 33756.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.061519 restraints weight = 28820.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.180  11783  Z= 0.256
  Angle     :  0.647  16.642  16036  Z= 0.305
  Chirality :  0.039   0.135   1653
  Planarity :  0.005   0.061   2058
  Dihedral  :  6.724  77.755   1561
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  6.00 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 22.41 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.24), residues: 1366
  helix:  1.68 (0.19), residues: 773
  sheet: -1.95 (0.45), residues: 140
  loop : -0.95 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 357 
 TYR   0.024   0.001   TYR A 335 
 PHE   0.011   0.002   PHE A 319 
 TRP   0.015   0.001   TRP A 290 
 HIS   0.006   0.001   HIS A 788 

Details of bonding type rmsd
  covalent geometry    : bond        0.00618 (11778)
  covalent geometry    : angle       0.64696 (16034)
  SS BOND              : bond        0.00350 (    1)
  SS BOND              : angle       0.43026 (    2)
  hydrogen bonds       : bond        0.04028 (  625)
  hydrogen bonds       : angle       4.67933 ( 1800)
  Misc. bond           : bond        0.10698 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 82
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  637 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8475 (pp30)
REVERT: B  187 ASP cc_start: 0.9071 (m-30) cc_final: 0.8665 (t0)
REVERT: B  232 MET cc_start: 0.8921 (ttp) cc_final: 0.8351 (tmm)
  outliers start: 31
  outliers final: 27
  residues processed: 108
  average time/residue: 0.2155
  time to fit residues: 34.3280
Evaluate side-chains
  110 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  239 GLU
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  710 LEU
Chi-restraints excluded: chain A residue  715 TRP
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  200 MET
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  328 MET
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  557 THR
Chi-restraints excluded: chain B residue  651 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 27 optimal weight:    0.0770
   chunk 76 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 126 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9980
   chunk 135 optimal weight:    5.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    0.6938

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.085528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.059022 restraints weight = 141250.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.061099 restraints weight = 64914.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.061137 restraints weight = 39825.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.062524 restraints weight = 32760.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.062870 restraints weight = 26959.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.2447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.223  11783  Z= 0.113
  Angle     :  0.556  11.575  16036  Z= 0.259
  Chirality :  0.038   0.139   1653
  Planarity :  0.004   0.059   2058
  Dihedral  :  6.438  76.272   1561
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  3.88 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 23.08 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.06 (0.24), residues: 1366
  helix:  2.02 (0.19), residues: 773
  sheet: -1.87 (0.45), residues: 146
  loop : -0.69 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 656 
 TYR   0.016   0.001   TYR A 335 
 PHE   0.008   0.001   PHE B 222 
 TRP   0.022   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (11778)
  covalent geometry    : angle       0.55652 (16034)
  SS BOND              : bond        0.00260 (    1)
  SS BOND              : angle       0.26245 (    2)
  hydrogen bonds       : bond        0.03499 (  625)
  hydrogen bonds       : angle       4.33283 ( 1800)
  Misc. bond           : bond        0.12093 (    4)

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

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

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2732 Ramachandran restraints generated.
    1366 Oldfield, 0 Emsley, 1366 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  844 is missing expected H atoms. Skipping.
Residue LEU  846 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.598 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  637 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8478 (pp30)
REVERT: B  187 ASP cc_start: 0.9027 (m-30) cc_final: 0.8612 (t0)
REVERT: B  232 MET cc_start: 0.8811 (ttp) cc_final: 0.8341 (tmm)
REVERT: B  700 MET cc_start: 0.8099 (ttp) cc_final: 0.7772 (tpp)
  outliers start: 23
  outliers final: 20
  residues processed: 100
  average time/residue: 0.2012
  time to fit residues: 30.7551
Evaluate side-chains
  102 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   90 HIS
Chi-restraints excluded: chain A residue  106 GLN
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  132 CYS
Chi-restraints excluded: chain A residue  188 VAL
Chi-restraints excluded: chain A residue  279 GLN
Chi-restraints excluded: chain A residue  366 TYR
Chi-restraints excluded: chain A residue  391 HIS
Chi-restraints excluded: chain A residue  398 PHE
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  584 THR
Chi-restraints excluded: chain A residue  605 ILE
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  716 TYR
Chi-restraints excluded: chain B residue  239 GLU
Chi-restraints excluded: chain B residue  272 LEU
Chi-restraints excluded: chain B residue  414 GLU
Chi-restraints excluded: chain B residue  550 VAL
Chi-restraints excluded: chain B residue  692 VAL
Chi-restraints excluded: chain B residue  768 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 137
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 136 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 110 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   chunk 39 optimal weight:    1.9990
   chunk 101 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 57 optimal weight:    0.0170
   chunk 13 optimal weight:    1.9990
   chunk 129 optimal weight:    0.1980
   overall best weight:    0.5620

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.085762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.059572 restraints weight = 141630.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.061618 restraints weight = 64252.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.061771 restraints weight = 39705.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.063211 restraints weight = 32047.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 61)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.063504 restraints weight = 26081.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.221  11783  Z= 0.108
  Angle     :  0.546  11.258  16036  Z= 0.252
  Chirality :  0.037   0.137   1653
  Planarity :  0.004   0.047   2058
  Dihedral  :  6.229  77.052   1561
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.25 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 23.08 %
    Favored  : 75.06 %
  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 are not related in a simple way.
  whole:  1.26 (0.24), residues: 1366
  helix:  2.20 (0.19), residues: 774
  sheet: -1.81 (0.45), residues: 146
  loop : -0.63 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 357 
 TYR   0.016   0.001   TYR A 335 
 PHE   0.008   0.001   PHE A 365 
 TRP   0.018   0.001   TRP A 290 
 HIS   0.004   0.001   HIS A 417 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (11778)
  covalent geometry    : angle       0.54589 (16034)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.19706 (    2)
  hydrogen bonds       : bond        0.03293 (  625)
  hydrogen bonds       : angle       4.20534 ( 1800)
  Misc. bond           : bond        0.11859 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3846.19 seconds
wall clock time: 66 minutes 14.91 seconds (3974.91 seconds total)