Starting phenix.real_space_refine
on Fri Aug 22 16:01:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bzx_30262/08_2025/7bzx_30262.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bzx_30262/08_2025/7bzx_30262.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bzx_30262/08_2025/7bzx_30262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bzx_30262/08_2025/7bzx_30262.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bzx_30262/08_2025/7bzx_30262.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bzx_30262/08_2025/7bzx_30262.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.026
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: 3
    Type Number    sf(0)   Gaussians
     C    3346      2.51       5
     N    1154      2.21       5
     O    1152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5652
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 2850
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 2850
          Classifications: {'peptide': 582}
          Incomplete info: {'truncation_to_alanine': 466}
          Link IDs: {'PCIS': 3, 'PTRANS': 26, 'TRANS': 552}
          Chain breaks: 2
          Unresolved chain link angles: 29
          Unresolved non-hydrogen bonds: 1634
          Unresolved non-hydrogen angles: 2099
          Unresolved non-hydrogen dihedrals: 1341
          Unresolved non-hydrogen chiralities: 168
          Planarities with less than four sites: {'ASP:plan': 38, 'ASN:plan1': 21, 'TYR:plan': 17, 'HIS:plan': 17, 'GLU:plan': 26, 'GLN:plan1': 16, 'ARG:plan': 27, 'PHE:plan': 22, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 834
    Chain: "A"
      Number of atoms: 2802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 2802
          Classifications: {'peptide': 572}
          Incomplete info: {'truncation_to_alanine': 459}
          Link IDs: {'PCIS': 3, 'PTRANS': 23, 'TRANS': 545}
          Chain breaks: 2
          Unresolved chain link angles: 26
          Unresolved non-hydrogen bonds: 1618
          Unresolved non-hydrogen angles: 2078
          Unresolved non-hydrogen dihedrals: 1327
          Unresolved non-hydrogen chiralities: 166
          Planarities with less than four sites: {'ASP:plan': 38, 'ASN:plan1': 21, 'TYR:plan': 17, 'HIS:plan': 17, 'GLU:plan': 26, 'GLN:plan1': 16, 'ARG:plan': 27, 'PHE:plan': 22, 'TRP:plan': 2}
          Unresolved non-hydrogen planarities: 834
  Time building chain proxies: 1.61, per 1000 atoms: 0.28
  Number of scatterers: 5652
  At special positions: 0
  Unit cell: (87.55, 93.73, 82.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1152      8.00
     N    1154      7.00
     C    3346      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 468.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2076

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 6 sheets defined
      49.6% alpha, 12.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 74 through 80
    Processing helix  chain 'B' and resid 82 through 89
    Processing helix  chain 'B' and resid 93 through 111
      removed outlier: 3.656A  pdb=" N   LYS B 111 " --> pdb=" O   PHE B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 133
      removed outlier: 5.013A  pdb=" N   GLU B 124 " --> pdb=" O   LEU B 120 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   LEU B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 154
    Processing helix  chain 'B' and resid 155 through 156
      No H-bonds generated for 'chain 'B' and resid 155 through 156'
    Processing helix  chain 'B' and resid 157 through 164
      Proline residue:  B 162  - end of helix
    Processing helix  chain 'B' and resid 191 through 206
    Processing helix  chain 'B' and resid 218 through 222
    Processing helix  chain 'B' and resid 223 through 237
    Processing helix  chain 'B' and resid 336 through 346
    Processing helix  chain 'B' and resid 368 through 374
    Processing helix  chain 'B' and resid 374 through 379
    Processing helix  chain 'B' and resid 393 through 398
    Processing helix  chain 'B' and resid 400 through 416
      removed outlier: 3.614A  pdb=" N   GLU B 414 " --> pdb=" O   VAL B 410 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   VAL B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 439
    Processing helix  chain 'B' and resid 449 through 463
    Processing helix  chain 'B' and resid 473 through 477
    Processing helix  chain 'B' and resid 479 through 485
    Processing helix  chain 'B' and resid 487 through 491
    Processing helix  chain 'B' and resid 507 through 511
      removed outlier: 4.015A  pdb=" N   THR B 510 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 515 through 520
    Processing helix  chain 'B' and resid 521 through 523
      No H-bonds generated for 'chain 'B' and resid 521 through 523'
    Processing helix  chain 'B' and resid 533 through 547
    Processing helix  chain 'B' and resid 566 through 570
    Processing helix  chain 'B' and resid 595 through 605
    Processing helix  chain 'B' and resid 605 through 610
    Processing helix  chain 'B' and resid 627 through 636
    Processing helix  chain 'B' and resid 651 through 663
    Processing helix  chain 'B' and resid 664 through 667
    Processing helix  chain 'B' and resid 686 through 694
    Processing helix  chain 'B' and resid 697 through 708
    Processing helix  chain 'A' and resid 74 through 79
    Processing helix  chain 'A' and resid 82 through 88
    Processing helix  chain 'A' and resid 91 through 111
      removed outlier: 4.106A  pdb=" N   LYS A  95 " --> pdb=" O   VAL A  91 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   GLN A  96 " --> pdb=" O   LYS A  92 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LYS A 111 " --> pdb=" O   PHE A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 133
      removed outlier: 4.971A  pdb=" N   GLU A 124 " --> pdb=" O   LEU A 120 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   LEU A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 154
    Processing helix  chain 'A' and resid 155 through 156
      No H-bonds generated for 'chain 'A' and resid 155 through 156'
    Processing helix  chain 'A' and resid 157 through 164
      Proline residue:  A 162  - end of helix
    Processing helix  chain 'A' and resid 191 through 206
    Processing helix  chain 'A' and resid 218 through 222
    Processing helix  chain 'A' and resid 223 through 237
    Processing helix  chain 'A' and resid 336 through 348
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 368 through 374
    Processing helix  chain 'A' and resid 374 through 379
    Processing helix  chain 'A' and resid 393 through 398
    Processing helix  chain 'A' and resid 400 through 416
      removed outlier: 3.727A  pdb=" N   GLU A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 439
    Processing helix  chain 'A' and resid 449 through 463
    Processing helix  chain 'A' and resid 473 through 477
    Processing helix  chain 'A' and resid 479 through 485
    Processing helix  chain 'A' and resid 487 through 491
    Processing helix  chain 'A' and resid 515 through 520
    Processing helix  chain 'A' and resid 521 through 523
      No H-bonds generated for 'chain 'A' and resid 521 through 523'
    Processing helix  chain 'A' and resid 533 through 547
    Processing helix  chain 'A' and resid 595 through 605
    Processing helix  chain 'A' and resid 605 through 610
    Processing helix  chain 'A' and resid 627 through 636
    Processing helix  chain 'A' and resid 651 through 663
    Processing helix  chain 'A' and resid 686 through 694
    Processing helix  chain 'A' and resid 697 through 707
    Processing sheet with id=AA1, first strand: chain 'B' and resid 139 through 142
      removed outlier: 5.734A  pdb=" N   LYS B 139 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 7.203A  pdb=" N   VAL B 215 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU B 141 " --> pdb=" O   VAL B 215 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   GLY B 217 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   VAL B 212 " --> pdb=" O   ILE B 241 " (cutoff:3.500A)
      removed outlier: 7.815A  pdb=" N   ILE B 243 " --> pdb=" O   VAL B 212 " (cutoff:3.500A)
      removed outlier: 6.540A  pdb=" N   ALA B 214 " --> pdb=" O   ILE B 243 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ASN B 245 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   ILE B 216 " --> pdb=" O   ASN B 245 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   MET B 240 " --> pdb=" O   VAL B 356 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   ILE B 358 " --> pdb=" O   MET B 240 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL B 242 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   VAL B 360 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   LEU B 244 " --> pdb=" O   VAL B 360 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR B 327 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 7.379A  pdb=" N   HIS B 359 " --> pdb=" O   TYR B 327 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE B 329 " --> pdb=" O   HIS B 359 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   VAL B 361 " --> pdb=" O   ILE B 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 443 through 445
      removed outlier: 6.380A  pdb=" N   VAL B 420 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ALA B 470 " --> pdb=" O   VAL B 420 " (cutoff:3.500A)
      removed outlier: 5.800A  pdb=" N   ILE B 422 " --> pdb=" O   ALA B 470 " (cutoff:3.500A)
      removed outlier: 8.179A  pdb=" N   TYR B 472 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ILE B 527 " --> pdb=" O   CYS B 553 " (cutoff:3.500A)
      removed outlier: 7.737A  pdb=" N   ARG B 555 " --> pdb=" O   ILE B 527 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   MET B 529 " --> pdb=" O   ARG B 555 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 581 through 584
      removed outlier: 6.096A  pdb=" N   VAL B 617 " --> pdb=" O   LEU B 583 " (cutoff:3.500A)
      removed outlier: 6.918A  pdb=" N   LEU B 641 " --> pdb=" O   ARG B 673 " (cutoff:3.500A)
      removed outlier: 7.665A  pdb=" N   MET B 675 " --> pdb=" O   LEU B 641 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   THR B 643 " --> pdb=" O   MET B 675 " (cutoff:3.500A)
      removed outlier: 8.123A  pdb=" N   LEU B 677 " --> pdb=" O   THR B 643 " (cutoff:3.500A)
      removed outlier: 7.901A  pdb=" N   GLU B 645 " --> pdb=" O   LEU B 677 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 139 through 142
      removed outlier: 5.763A  pdb=" N   LYS A 139 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   VAL A 215 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   LEU A 141 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 8.128A  pdb=" N   GLY A 217 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   VAL A 212 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ILE A 243 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   ALA A 214 " --> pdb=" O   ILE A 243 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   ASN A 245 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE A 216 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL A 242 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   VAL A 360 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 5.940A  pdb=" N   LEU A 244 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   TYR A 327 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   HIS A 359 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
      removed outlier: 6.118A  pdb=" N   ILE A 329 " --> pdb=" O   HIS A 359 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   VAL A 361 " --> pdb=" O   ILE A 329 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 443 through 445
      removed outlier: 6.298A  pdb=" N   VAL A 420 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ALA A 470 " --> pdb=" O   VAL A 420 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   ILE A 422 " --> pdb=" O   ALA A 470 " (cutoff:3.500A)
      removed outlier: 8.181A  pdb=" N   TYR A 472 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
      removed outlier: 7.281A  pdb=" N   ALA A 497 " --> pdb=" O   PRO A 467 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   CYS A 469 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ASP A 499 " --> pdb=" O   CYS A 469 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   ILE A 471 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE A 527 " --> pdb=" O   CYS A 553 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   ARG A 555 " --> pdb=" O   ILE A 527 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   MET A 529 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 581 through 584
      removed outlier: 6.045A  pdb=" N   VAL A 617 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 5.869A  pdb=" N   ALA A 590 " --> pdb=" O   ILE A 642 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   VAL A 644 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   LEU A 592 " --> pdb=" O   VAL A 644 " (cutoff:3.500A)
      removed outlier: 8.333A  pdb=" N   GLU A 646 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
      removed outlier: 6.970A  pdb=" N   LEU A 641 " --> pdb=" O   ARG A 673 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   MET A 675 " --> pdb=" O   LEU A 641 " (cutoff:3.500A)
      removed outlier: 6.285A  pdb=" N   THR A 643 " --> pdb=" O   MET A 675 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   LEU A 677 " --> pdb=" O   THR A 643 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   GLU A 645 " --> pdb=" O   LEU A 677 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1014 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: 0.87

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.19 -     1.26: 1151
        1.26 -     1.34: 901
        1.34 -     1.41: 276
        1.41 -     1.48: 1196
        1.48 -     1.56: 2122
  Bond restraints: 5646
  Sorted by residual:
  bond pdb=" N   PRO B 524 "
       pdb=" CA  PRO B 524 "
    ideal  model  delta    sigma   weight residual
    1.467  1.399  0.068 1.17e-02 7.31e+03 3.41e+01
  bond pdb=" CA  THR A 256 "
       pdb=" C   THR A 256 "
    ideal  model  delta    sigma   weight residual
    1.522  1.470  0.052 9.30e-03 1.16e+04 3.17e+01
  bond pdb=" N   PRO A 557 "
       pdb=" CA  PRO A 557 "
    ideal  model  delta    sigma   weight residual
    1.465  1.404  0.061 1.10e-02 8.26e+03 3.08e+01
  bond pdb=" N   PRO A 467 "
       pdb=" CA  PRO A 467 "
    ideal  model  delta    sigma   weight residual
    1.467  1.402  0.065 1.19e-02 7.06e+03 2.97e+01
  bond pdb=" N   ALA A 618 "
       pdb=" CA  ALA A 618 "
    ideal  model  delta    sigma   weight residual
    1.456  1.391  0.065 1.21e-02 6.83e+03 2.92e+01
  ... (remaining 5641 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.62: 6057
        2.62 -     5.25: 1615
        5.25 -     7.87: 132
        7.87 -    10.49: 16
       10.49 -    13.11: 6
  Bond angle restraints: 7826
  Sorted by residual:
  angle pdb=" C   LYS B 393 "
        pdb=" N   THR B 394 "
        pdb=" CA  THR B 394 "
      ideal   model   delta    sigma   weight residual
     120.54  132.72  -12.18 1.35e+00 5.49e-01 8.14e+01
  angle pdb=" N   PRO B 567 "
        pdb=" CA  PRO B 567 "
        pdb=" C   PRO B 567 "
      ideal   model   delta    sigma   weight residual
     110.70  119.92   -9.22 1.22e+00 6.72e-01 5.72e+01
  angle pdb=" N   GLY A 653 "
        pdb=" CA  GLY A 653 "
        pdb=" C   GLY A 653 "
      ideal   model   delta    sigma   weight residual
     112.50  104.47    8.03 1.16e+00 7.43e-01 4.79e+01
  angle pdb=" C   GLY B 145 "
        pdb=" N   HIS B 146 "
        pdb=" CA  HIS B 146 "
      ideal   model   delta    sigma   weight residual
     120.31  130.48  -10.17 1.52e+00 4.33e-01 4.48e+01
  angle pdb=" C   ASN B 247 "
        pdb=" CA  ASN B 247 "
        pdb=" CB  ASN B 247 "
      ideal   model   delta    sigma   weight residual
     110.79   99.71   11.08 1.66e+00 3.63e-01 4.45e+01
  ... (remaining 7821 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.51: 2703
        6.51 -    13.02: 375
       13.02 -    19.53: 107
       19.53 -    26.04: 30
       26.04 -    32.55: 9
  Dihedral angle restraints: 3224
    sinusoidal: 0
      harmonic: 3224
  Sorted by residual:
  dihedral pdb=" C   THR B 112 "
           pdb=" N   THR B 112 "
           pdb=" CA  THR B 112 "
           pdb=" CB  THR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -142.58   20.58     0      2.50e+00 1.60e-01 6.78e+01
  dihedral pdb=" CA  GLY B 429 "
           pdb=" C   GLY B 429 "
           pdb=" N   THR B 430 "
           pdb=" CA  THR B 430 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.45   32.55     0      5.00e+00 4.00e-02 4.24e+01
  dihedral pdb=" N   THR B 112 "
           pdb=" C   THR B 112 "
           pdb=" CA  THR B 112 "
           pdb=" CB  THR B 112 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  138.49  -15.09     0      2.50e+00 1.60e-01 3.64e+01
  ... (remaining 3221 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.137: 825
       0.137 -    0.273: 188
       0.273 -    0.410: 21
       0.410 -    0.547: 1
       0.547 -    0.683: 3
  Chirality restraints: 1038
  Sorted by residual:
  chirality pdb=" CA  THR B 112 "
            pdb=" N   THR B 112 "
            pdb=" C   THR B 112 "
            pdb=" CB  THR B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    1.84    0.68 2.00e-01 2.50e+01 1.17e+01
  chirality pdb=" CA  ASP A 507 "
            pdb=" N   ASP A 507 "
            pdb=" C   ASP A 507 "
            pdb=" CB  ASP A 507 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.90    0.61 2.00e-01 2.50e+01 9.21e+00
  chirality pdb=" CA  PRO B 253 "
            pdb=" N   PRO B 253 "
            pdb=" C   PRO B 253 "
            pdb=" CB  PRO B 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.16    0.56 2.00e-01 2.50e+01 7.72e+00
  ... (remaining 1035 not shown)

  Planarity restraints: 1148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 173 "    0.022 2.00e-02 2.50e+03   4.33e-02 1.87e+01
        pdb=" C   PHE A 173 "   -0.075 2.00e-02 2.50e+03
        pdb=" O   PHE A 173 "    0.028 2.00e-02 2.50e+03
        pdb=" N   THR A 174 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 253 "    0.019 2.00e-02 2.50e+03   3.84e-02 1.48e+01
        pdb=" C   PRO A 253 "   -0.066 2.00e-02 2.50e+03
        pdb=" O   PRO A 253 "    0.025 2.00e-02 2.50e+03
        pdb=" N   THR A 254 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 640 "   -0.015 2.00e-02 2.50e+03   3.10e-02 9.58e+00
        pdb=" C   VAL B 640 "    0.054 2.00e-02 2.50e+03
        pdb=" O   VAL B 640 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU B 641 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1145 not shown)

  Histogram of nonbonded interaction distances:
        2.49 -     2.97: 3416
        2.97 -     3.45: 6817
        3.45 -     3.93: 8153
        3.93 -     4.42: 10762
        4.42 -     4.90: 14735
  Nonbonded interactions: 43883
  Sorted by model distance:
  nonbonded pdb=" N   GLU B  93 "
            pdb=" N   LEU B  94 "
     model   vdw
     2.485 2.560
  nonbonded pdb=" N   LYS B 248 "
            pdb=" N   GLN B 249 "
     model   vdw
     2.532 2.560
  nonbonded pdb=" N   ILE A 471 "
            pdb=" O   ILE A 471 "
     model   vdw
     2.534 2.496
  nonbonded pdb=" N   ASP B 507 "
            pdb=" N   GLY B 508 "
     model   vdw
     2.541 2.560
  nonbonded pdb=" N   THR A 254 "
            pdb=" O   THR A 254 "
     model   vdw
     2.555 2.496
  ... (remaining 43878 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 73 through 258 or resid 320 through 708))
}

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:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.810
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.000
  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:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2515
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      :  0.019   0.068   5646  Z= 1.459
  Angle     :  2.216  13.114   7826  Z= 1.609
  Chirality :  0.118   0.683   1038
  Planarity :  0.009   0.043   1148
  Dihedral  :  8.559  32.555   1148
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  1.31 %
    Allowed  :  6.57 %
    Favored  : 92.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.87 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.90 (0.21), residues: 1142
  helix: -1.44 (0.20), residues: 505
  sheet: -2.51 (0.44), residues: 111
  loop : -2.20 (0.23), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.01895 ( 5646)
  covalent geometry    : angle       2.21616 ( 7826)
  hydrogen bonds       : bond        0.15563 (  356)
  hydrogen bonds       : angle       8.16099 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.186 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0281
  time to fit residues: 2.0401
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:   30.0000
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    8.9990
   chunk 100 optimal weight:    0.1980
   overall best weight:    2.8386

-------------------------------------------------------------------------------
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 = 0.5208 r_free = 0.5208 target = 0.156486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.127512 restraints weight = 32209.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4849 r_free = 0.4849 target = 0.129691 restraints weight = 26350.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4876 r_free = 0.4876 target = 0.131477 restraints weight = 22225.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4893 r_free = 0.4893 target = 0.132525 restraints weight = 19498.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.133584 restraints weight = 17685.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.4608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3943
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5646  Z= 0.166
  Angle     :  0.563   5.213   7826  Z= 0.342
  Chirality :  0.045   0.140   1038
  Planarity :  0.003   0.012   1148
  Dihedral  :  5.263  27.854   1148
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.99 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.10 (0.24), residues: 1142
  helix:  0.46 (0.22), residues: 520
  sheet: -1.89 (0.41), residues: 159
  loop : -1.61 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 5646)
  covalent geometry    : angle       0.56343 ( 7826)
  hydrogen bonds       : bond        0.03482 (  356)
  hydrogen bonds       : angle       5.34393 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.230 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0290
  time to fit residues: 2.0756
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:   20.0000
   chunk 94 optimal weight:   30.0000
   chunk 30 optimal weight:   30.0000
   chunk 35 optimal weight:    9.9990
   chunk 109 optimal weight:   20.0000
   chunk 65 optimal weight:    0.5980
   chunk 38 optimal weight:   30.0000
   chunk 100 optimal weight:    0.0010
   chunk 33 optimal weight:    7.9990
   chunk 25 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   overall best weight:    5.7192

-------------------------------------------------------------------------------
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 = 0.4480 r_free = 0.4480 target = 0.113787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.102131 restraints weight = 33912.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.103031 restraints weight = 27846.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.103835 restraints weight = 23729.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.104456 restraints weight = 20664.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.104860 restraints weight = 18421.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4768
moved from start:          1.0736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5646  Z= 0.237
  Angle     :  0.715   7.074   7826  Z= 0.439
  Chirality :  0.047   0.140   1038
  Planarity :  0.004   0.022   1148
  Dihedral  :  7.058  24.917   1148
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  9.28 %
    Favored  : 90.37 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.10 (0.23), residues: 1142
  helix: -0.64 (0.21), residues: 501
  sheet: -1.52 (0.38), residues: 159
  loop : -2.07 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5646)
  covalent geometry    : angle       0.71460 ( 7826)
  hydrogen bonds       : bond        0.05191 (  356)
  hydrogen bonds       : angle       7.36089 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.217 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0288
  time to fit residues: 2.0723
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:   30.0000
   chunk 9 optimal weight:   40.0000
   chunk 76 optimal weight:   20.0000
   chunk 17 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 15 optimal weight:    6.9990
   chunk 8 optimal weight:    7.9990
   chunk 31 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:    7.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
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 = 0.4463 r_free = 0.4463 target = 0.111644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.100788 restraints weight = 34131.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.101647 restraints weight = 28235.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.102371 restraints weight = 24068.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.102978 restraints weight = 21041.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.103440 restraints weight = 18758.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.4301
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4841
moved from start:          1.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   5646  Z= 0.166
  Angle     :  0.525   4.399   7826  Z= 0.324
  Chirality :  0.046   0.133   1038
  Planarity :  0.003   0.015   1148
  Dihedral  :  5.362  21.844   1148
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  6.48 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.24), residues: 1142
  helix:  0.05 (0.23), residues: 513
  sheet: -1.46 (0.38), residues: 171
  loop : -2.05 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 5646)
  covalent geometry    : angle       0.52477 ( 7826)
  hydrogen bonds       : bond        0.03435 (  356)
  hydrogen bonds       : angle       5.95105 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.194 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0292
  time to fit residues: 2.0268
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 88 optimal weight:   20.0000
   chunk 82 optimal weight:   30.0000
   chunk 1 optimal weight:    6.9990
   chunk 111 optimal weight:   40.0000
   chunk 68 optimal weight:   40.0000
   chunk 78 optimal weight:    7.9990
   chunk 8 optimal weight:   40.0000
   chunk 54 optimal weight:   20.0000
   chunk 47 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   overall best weight:   12.3994

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.098920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.089224 restraints weight = 37473.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.090043 restraints weight = 30344.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.090787 restraints weight = 25509.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.091407 restraints weight = 21934.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.091904 restraints weight = 19096.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.4114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5451
moved from start:          1.5643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.085   5646  Z= 0.395
  Angle     :  0.983  11.277   7826  Z= 0.609
  Chirality :  0.053   0.191   1038
  Planarity :  0.006   0.025   1148
  Dihedral  :  9.088  37.450   1148
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 16.65
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 15.24 %
    Favored  : 84.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.59 (0.23), residues: 1142
  helix: -1.77 (0.22), residues: 453
  sheet: -2.07 (0.41), residues: 130
  loop : -3.02 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 5646)
  covalent geometry    : angle       0.98297 ( 7826)
  hydrogen bonds       : bond        0.07625 (  356)
  hydrogen bonds       : angle       9.66872 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.209 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0286
  time to fit residues: 2.0501
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 42 optimal weight:   30.0000
   chunk 69 optimal weight:   10.0000
   chunk 94 optimal weight:    9.9990
   chunk 113 optimal weight:   30.0000
   chunk 71 optimal weight:   30.0000
   chunk 20 optimal weight:   30.0000
   chunk 50 optimal weight:    8.9990
   chunk 111 optimal weight:    0.0970
   chunk 62 optimal weight:   20.0000
   chunk 12 optimal weight:    7.9990
   overall best weight:    7.4188

-------------------------------------------------------------------------------
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 = 0.4285 r_free = 0.4285 target = 0.099498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.089470 restraints weight = 36768.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.090473 restraints weight = 29284.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.091273 restraints weight = 24133.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.091835 restraints weight = 20450.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.092359 restraints weight = 17888.232|
|-----------------------------------------------------------------------------|
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5380
moved from start:          1.5781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5646  Z= 0.241
  Angle     :  0.694   6.418   7826  Z= 0.428
  Chirality :  0.048   0.142   1038
  Planarity :  0.004   0.016   1148
  Dihedral  :  7.368  32.514   1148
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.19 %
    Favored  : 85.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.23), residues: 1142
  helix: -1.49 (0.22), residues: 477
  sheet: -1.96 (0.45), residues: 121
  loop : -3.10 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 5646)
  covalent geometry    : angle       0.69375 ( 7826)
  hydrogen bonds       : bond        0.05238 (  356)
  hydrogen bonds       : angle       8.01408 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.203 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0278
  time to fit residues: 1.9792
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 71 optimal weight:    8.9990
   chunk 94 optimal weight:   30.0000
   chunk 36 optimal weight:    6.9990
   chunk 56 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 62 optimal weight:   30.0000
   chunk 26 optimal weight:    5.9990
   chunk 5 optimal weight:   40.0000
   chunk 42 optimal weight:   30.0000
   chunk 92 optimal weight:    2.9990
   overall best weight:    2.9988

-------------------------------------------------------------------------------
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 = 0.4352 r_free = 0.4352 target = 0.102375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.091486 restraints weight = 36605.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.092662 restraints weight = 28664.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.093461 restraints weight = 23332.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.094289 restraints weight = 19717.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.094843 restraints weight = 16944.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.4193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5236
moved from start:          1.5707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   5646  Z= 0.129
  Angle     :  0.495   5.968   7826  Z= 0.302
  Chirality :  0.045   0.127   1038
  Planarity :  0.002   0.010   1148
  Dihedral  :  5.583  24.519   1148
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.98 %
    Favored  : 90.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.56 (0.24), residues: 1142
  helix: -0.58 (0.23), residues: 480
  sheet: -2.00 (0.44), residues: 122
  loop : -2.71 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00177 ( 5646)
  covalent geometry    : angle       0.49452 ( 7826)
  hydrogen bonds       : bond        0.03326 (  356)
  hydrogen bonds       : angle       6.37637 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.220 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0282
  time to fit residues: 2.0361
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 45 optimal weight:   50.0000
   chunk 27 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0570
   chunk 82 optimal weight:   40.0000
   chunk 25 optimal weight:    6.9990
   chunk 65 optimal weight:   30.0000
   chunk 78 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 31 optimal weight:    1.9990
   chunk 113 optimal weight:   30.0000
   overall best weight:    3.8106

-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.100865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.090681 restraints weight = 36455.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4126 r_free = 0.4126 target = 0.091739 restraints weight = 28723.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.092550 restraints weight = 23448.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.093192 restraints weight = 19795.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.093727 restraints weight = 17174.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4166
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5288
moved from start:          1.6111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5646  Z= 0.148
  Angle     :  0.511   4.770   7826  Z= 0.315
  Chirality :  0.045   0.133   1038
  Planarity :  0.002   0.010   1148
  Dihedral  :  5.701  22.712   1148
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.35 %
    Favored  : 87.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.36 (0.24), residues: 1142
  helix: -0.31 (0.24), residues: 471
  sheet: -2.35 (0.43), residues: 114
  loop : -2.57 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 5646)
  covalent geometry    : angle       0.51103 ( 7826)
  hydrogen bonds       : bond        0.03716 (  356)
  hydrogen bonds       : angle       6.57424 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.214 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0265
  time to fit residues: 1.9314
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:   40.0000
   chunk 45 optimal weight:   40.0000
   chunk 111 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 78 optimal weight:   20.0000
   chunk 39 optimal weight:    3.9990
   chunk 66 optimal weight:   20.0000
   chunk 50 optimal weight:   30.0000
   chunk 17 optimal weight:   20.0000
   chunk 19 optimal weight:    0.8980
   chunk 29 optimal weight:    8.9990
   overall best weight:    6.1788

-------------------------------------------------------------------------------
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 = 0.4270 r_free = 0.4270 target = 0.097616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.088130 restraints weight = 37661.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.089139 restraints weight = 29263.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.089988 restraints weight = 23604.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.090658 restraints weight = 19654.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.091182 restraints weight = 16780.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5429
moved from start:          1.6945

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5646  Z= 0.210
  Angle     :  0.613   5.731   7826  Z= 0.381
  Chirality :  0.047   0.132   1038
  Planarity :  0.003   0.015   1148
  Dihedral  :  6.796  27.856   1148
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.50 %
    Favored  : 84.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.23), residues: 1142
  helix: -1.00 (0.23), residues: 463
  sheet: -2.14 (0.48), residues: 102
  loop : -2.91 (0.24), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5646)
  covalent geometry    : angle       0.61337 ( 7826)
  hydrogen bonds       : bond        0.04869 (  356)
  hydrogen bonds       : angle       7.58921 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.206 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0280
  time to fit residues: 2.0177
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 56 optimal weight:    7.9990
   chunk 35 optimal weight:    8.9990
   chunk 33 optimal weight:   20.0000
   chunk 45 optimal weight:   50.0000
   chunk 1 optimal weight:   20.0000
   chunk 41 optimal weight:    7.9990
   chunk 70 optimal weight:   40.0000
   chunk 65 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 20 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.097184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.087783 restraints weight = 38376.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.088862 restraints weight = 29711.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.089707 restraints weight = 23727.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.090382 restraints weight = 19597.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.090909 restraints weight = 16642.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.4118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5433
moved from start:          1.7427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5646  Z= 0.198
  Angle     :  0.598   5.835   7826  Z= 0.369
  Chirality :  0.046   0.132   1038
  Planarity :  0.003   0.015   1148
  Dihedral  :  6.637  28.556   1148
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.27 %
    Favored  : 85.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.23), residues: 1142
  helix: -0.99 (0.23), residues: 459
  sheet: -2.56 (0.49), residues: 95
  loop : -3.01 (0.24), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 5646)
  covalent geometry    : angle       0.59753 ( 7826)
  hydrogen bonds       : bond        0.04644 (  356)
  hydrogen bonds       : angle       7.32944 ( 1014)

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

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

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2284 Ramachandran restraints generated.
    1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.206 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0268
  time to fit residues: 1.9555
Evaluate side-chains
  34 residues out of total 927 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:   50.0000
   chunk 3 optimal weight:    7.9990
   chunk 110 optimal weight:    7.9990
   chunk 105 optimal weight:    7.9990
   chunk 38 optimal weight:   30.0000
   chunk 18 optimal weight:   30.0000
   chunk 78 optimal weight:   20.0000
   chunk 8 optimal weight:   30.0000
   chunk 16 optimal weight:   40.0000
   chunk 84 optimal weight:    8.9990
   chunk 54 optimal weight:   30.0000
   overall best weight:   10.5992

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.093113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.083943 restraints weight = 38235.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.084974 restraints weight = 29662.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.085769 restraints weight = 23866.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.086410 restraints weight = 19762.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.086939 restraints weight = 16822.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5653
moved from start:          1.8413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076   5646  Z= 0.328
  Angle     :  0.822   7.579   7826  Z= 0.511
  Chirality :  0.050   0.164   1038
  Planarity :  0.005   0.018   1148
  Dihedral  :  8.444  35.826   1148
  Min Nonbonded Distance : 2.236

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 20.32 %
    Favored  : 79.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.26 (0.21), residues: 1142
  helix: -2.04 (0.21), residues: 456
  sheet: -2.79 (0.50), residues: 81
  loop : -3.59 (0.22), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TYR   0.000   0.000   TYR B  82 
 PHE   0.000   0.000   PHE B 107 
 TRP   0.000   0.000   TRP B 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 5646)
  covalent geometry    : angle       0.82232 ( 7826)
  hydrogen bonds       : bond        0.06924 (  356)
  hydrogen bonds       : angle       9.06205 ( 1014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 967.09 seconds
wall clock time: 17 minutes 11.70 seconds (1031.70 seconds total)