Starting phenix.real_space_refine
on Tue Feb 11 11:46:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bzx_30262/02_2025/7bzx_30262.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bzx_30262/02_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_30262/02_2025/7bzx_30262.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bzx_30262/02_2025/7bzx_30262.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bzx_30262/02_2025/7bzx_30262.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bzx_30262/02_2025/7bzx_30262.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 16, 'ARG:plan': 27, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 17, 'PHE:plan': 22, 'GLU:plan': 26, 'ASP:plan': 38}
          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: {'GLN:plan1': 16, 'ARG:plan': 27, 'TYR:plan': 17, 'ASN:plan1': 21, 'TRP:plan': 2, 'HIS:plan': 17, 'PHE:plan': 22, 'GLU:plan': 26, 'ASP:plan': 38}
          Unresolved non-hydrogen planarities: 834
  Time building chain proxies: 4.30, per 1000 atoms: 0.76
  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: 1.76
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 0.91
  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: 1.82

  Time building geometry restraints manager: 1.98 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:                  0.010
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.620
  Find NCS groups from input model:        0.270
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.570
-------------------------------------------------------------------------------
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= 1.391
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.000   0.000   TRP B 142 
 PHE   0.000   0.000   PHE B 107 
 TYR   0.000   0.000   TYR B  82 

*********************** 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  : 0.596 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0585
  time to fit residues: 4.4775
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  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 46 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 34 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   overall best weight:    4.7988

-------------------------------------------------------------------------------
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 = 0.4653 r_free = 0.4653 target = 0.125773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.113377 restraints weight = 33166.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4438 r_free = 0.4438 target = 0.114428 restraints weight = 27309.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.115249 restraints weight = 23147.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.4447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4347
moved from start:          0.6608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5646  Z= 0.229
  Angle     :  0.758   8.003   7826  Z= 0.460
  Chirality :  0.048   0.163   1038
  Planarity :  0.004   0.019   1148
  Dihedral  :  6.766  28.735   1148
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  6.30 %
    Favored  : 93.35 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.23), residues: 1142
  helix: -0.53 (0.21), residues: 516
  sheet: -1.92 (0.41), residues: 154
  loop : -1.93 (0.27), residues: 472

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

*********************** 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  : 0.607 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0626
  time to fit residues: 4.6170
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  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 17 optimal weight:   20.0000
   chunk 30 optimal weight:   20.0000
   chunk 107 optimal weight:    7.9990
   chunk 83 optimal weight:   40.0000
   chunk 97 optimal weight:   30.0000
   chunk 78 optimal weight:   40.0000
   chunk 33 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0170
   chunk 38 optimal weight:   20.0000
   chunk 108 optimal weight:   20.0000
   overall best weight:    8.6028

-------------------------------------------------------------------------------
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 = 0.4385 r_free = 0.4385 target = 0.106852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.096000 restraints weight = 35209.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.096783 restraints weight = 29194.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.097578 restraints weight = 25095.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5115
moved from start:          1.2790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5646  Z= 0.320
  Angle     :  0.844   9.246   7826  Z= 0.523
  Chirality :  0.050   0.151   1038
  Planarity :  0.005   0.023   1148
  Dihedral  :  8.026  29.586   1148
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 11.21 %
    Favored  : 88.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.06 (0.22), residues: 1142
  helix: -1.37 (0.21), residues: 494
  sheet: -2.39 (0.41), residues: 122
  loop : -2.56 (0.26), residues: 526

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

*********************** 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  : 0.547 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0569
  time to fit residues: 4.4111
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  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 43 optimal weight:    9.9990
   chunk 38 optimal weight:   40.0000
   chunk 31 optimal weight:   20.0000
   chunk 45 optimal weight:   30.0000
   chunk 46 optimal weight:   20.0000
   chunk 33 optimal weight:    8.9990
   chunk 76 optimal weight:    0.0030
   chunk 85 optimal weight:    3.9990
   chunk 22 optimal weight:   50.0000
   chunk 112 optimal weight:   40.0000
   chunk 18 optimal weight:   20.0000
   overall best weight:    8.6000

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.102679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.092527 restraints weight = 36577.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.093472 restraints weight = 29747.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4157 r_free = 0.4157 target = 0.094123 restraints weight = 24932.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.4153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5271
moved from start:          1.4149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   5646  Z= 0.286
  Angle     :  0.753   6.687   7826  Z= 0.468
  Chirality :  0.049   0.156   1038
  Planarity :  0.004   0.018   1148
  Dihedral  :  7.428  28.492   1148
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 12.00 %
    Favored  : 87.83 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.19 (0.23), residues: 1142
  helix: -1.33 (0.22), residues: 479
  sheet: -2.47 (0.39), residues: 146
  loop : -2.74 (0.26), residues: 517

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

*********************** 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  : 0.615 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0542
  time to fit residues: 4.1529
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  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    6.9990
   chunk 56 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 22 optimal weight:   40.0000
   chunk 108 optimal weight:    7.9990
   chunk 2 optimal weight:    8.9990
   chunk 26 optimal weight:   20.0000
   chunk 103 optimal weight:    9.9990
   chunk 43 optimal weight:    0.4980
   chunk 101 optimal weight:   20.0000
   overall best weight:    3.6988

-------------------------------------------------------------------------------
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 = 0.4386 r_free = 0.4386 target = 0.105065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.094116 restraints weight = 35178.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.095215 restraints weight = 27815.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.096114 restraints weight = 22853.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5179
moved from start:          1.4338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   5646  Z= 0.144
  Angle     :  0.524   4.855   7826  Z= 0.322
  Chirality :  0.045   0.131   1038
  Planarity :  0.003   0.015   1148
  Dihedral  :  5.734  22.763   1148
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  9.54 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.40 (0.24), residues: 1142
  helix: -0.60 (0.23), residues: 497
  sheet: -1.97 (0.43), residues: 140
  loop : -2.49 (0.27), residues: 505

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

*********************** 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  : 0.652 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0570
  time to fit residues: 4.4649
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  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 7 optimal weight:   40.0000
   chunk 66 optimal weight:   20.0000
   chunk 84 optimal weight:   30.0000
   chunk 35 optimal weight:    8.9990
   chunk 42 optimal weight:   50.0000
   chunk 57 optimal weight:    0.6980
   chunk 89 optimal weight:   30.0000
   chunk 64 optimal weight:    0.0030
   chunk 102 optimal weight:   30.0000
   chunk 71 optimal weight:   30.0000
   chunk 0 optimal weight:   50.0000
   overall best weight:   11.9400

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.096741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.087201 restraints weight = 36741.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.088118 restraints weight = 29712.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.088795 restraints weight = 24772.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5582
moved from start:          1.6570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.086   5646  Z= 0.386
  Angle     :  0.914   9.049   7826  Z= 0.569
  Chirality :  0.052   0.188   1038
  Planarity :  0.005   0.022   1148
  Dihedral  :  8.885  35.383   1148
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 17.01
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 18.04 %
    Favored  : 81.79 %
  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 : 0.46 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.91 (0.22), residues: 1142
  helix: -1.94 (0.21), residues: 463
  sheet: -2.54 (0.41), residues: 128
  loop : -3.22 (0.25), residues: 551

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

*********************** 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  : 0.643 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0573
  time to fit residues: 4.5178
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  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 107 optimal weight:   20.0000
   chunk 102 optimal weight:   20.0000
   chunk 25 optimal weight:    5.9990
   chunk 31 optimal weight:    7.9990
   chunk 59 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 43 optimal weight:    9.9990
   chunk 76 optimal weight:   30.0000
   chunk 6 optimal weight:    5.9990
   chunk 44 optimal weight:    0.0870
   chunk 65 optimal weight:    1.9990
   overall best weight:    4.4166

-------------------------------------------------------------------------------
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 = 0.4310 r_free = 0.4310 target = 0.099803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.089141 restraints weight = 36584.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.090288 restraints weight = 28492.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.091164 restraints weight = 23021.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.4121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5413
moved from start:          1.6324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5646  Z= 0.172
  Angle     :  0.591   6.266   7826  Z= 0.362
  Chirality :  0.046   0.140   1038
  Planarity :  0.003   0.015   1148
  Dihedral  :  6.652  28.589   1148
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.05 %
    Favored  : 86.95 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.23 (0.23), residues: 1142
  helix: -1.19 (0.22), residues: 477
  sheet: -2.23 (0.46), residues: 110
  loop : -3.05 (0.25), residues: 555

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

*********************** 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  : 0.586 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0551
  time to fit residues: 4.2394
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  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 37 optimal weight:   30.0000
   chunk 87 optimal weight:   10.0000
   chunk 102 optimal weight:   50.0000
   chunk 58 optimal weight:   20.0000
   chunk 27 optimal weight:   20.0000
   chunk 93 optimal weight:   30.0000
   chunk 23 optimal weight:   20.0000
   chunk 49 optimal weight:   30.0000
   chunk 110 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 97 optimal weight:   30.0000
   overall best weight:   10.5794

-------------------------------------------------------------------------------
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 = 0.4226 r_free = 0.4226 target = 0.095533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.086222 restraints weight = 37549.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.087133 restraints weight = 29505.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.087868 restraints weight = 24146.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5610
moved from start:          1.7292

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= 0.342
  Angle     :  0.816   7.835   7826  Z= 0.509
  Chirality :  0.050   0.171   1038
  Planarity :  0.005   0.020   1148
  Dihedral  :  8.272  33.109   1148
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 20.40 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.08 (0.22), residues: 1142
  helix: -1.92 (0.21), residues: 454
  sheet: -2.73 (0.44), residues: 99
  loop : -3.44 (0.23), residues: 589

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

*********************** 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  : 0.597 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0564
  time to fit residues: 4.3113
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  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 90 optimal weight:    7.9990
   chunk 52 optimal weight:   30.0000
   chunk 32 optimal weight:   20.0000
   chunk 36 optimal weight:    3.9990
   chunk 88 optimal weight:   10.0000
   chunk 94 optimal weight:   30.0000
   chunk 91 optimal weight:    0.5980
   chunk 111 optimal weight:    0.3980
   chunk 8 optimal weight:   40.0000
   overall best weight:    2.7584

-------------------------------------------------------------------------------
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 = 0.4306 r_free = 0.4306 target = 0.099718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.089980 restraints weight = 36302.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.091023 restraints weight = 28115.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.091884 restraints weight = 22537.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5342
moved from start:          1.6920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.014   5646  Z= 0.129
  Angle     :  0.519   6.004   7826  Z= 0.317
  Chirality :  0.046   0.134   1038
  Planarity :  0.002   0.013   1148
  Dihedral  :  5.937  25.390   1148
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.23), residues: 1142
  helix: -0.97 (0.23), residues: 482
  sheet: -2.14 (0.44), residues: 111
  loop : -3.13 (0.25), residues: 549

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

*********************** 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  : 0.607 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0550
  time to fit residues: 4.2718
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  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 15 optimal weight:    7.9990
   chunk 95 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 38 optimal weight:    7.9990
   chunk 35 optimal weight:   30.0000
   chunk 58 optimal weight:   20.0000
   chunk 108 optimal weight:   30.0000
   chunk 56 optimal weight:    5.9990
   chunk 114 optimal weight:    1.9990
   overall best weight:    4.9988

-------------------------------------------------------------------------------
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 = 0.4270 r_free = 0.4270 target = 0.097806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.088231 restraints weight = 37371.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.089310 restraints weight = 28906.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.090149 restraints weight = 23132.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5448
moved from start:          1.7222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5646  Z= 0.184
  Angle     :  0.563   5.200   7826  Z= 0.348
  Chirality :  0.046   0.131   1038
  Planarity :  0.003   0.013   1148
  Dihedral  :  6.305  25.343   1148
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.20 %
    Favored  : 83.80 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.24), residues: 1142
  helix: -0.98 (0.23), residues: 473
  sheet: -2.21 (0.47), residues: 99
  loop : -3.11 (0.25), residues: 570

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

********************** 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  : 0.634 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0565
  time to fit residues: 4.3701
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  : 0.630 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 76 optimal weight:   30.0000
   chunk 70 optimal weight:   40.0000
   chunk 23 optimal weight:   20.0000
   chunk 73 optimal weight:    5.9990
   chunk 52 optimal weight:   30.0000
   chunk 56 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 5 optimal weight:   40.0000
   chunk 37 optimal weight:    7.9990
   chunk 84 optimal weight:    7.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    5.3788

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.096873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.087271 restraints weight = 37327.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.088335 restraints weight = 28938.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.089166 restraints weight = 23289.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5488
moved from start:          1.7684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5646  Z= 0.189
  Angle     :  0.582   5.788   7826  Z= 0.359
  Chirality :  0.046   0.134   1038
  Planarity :  0.003   0.015   1148
  Dihedral  :  6.498  26.273   1148
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.15 %
    Favored  : 84.85 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.17 (0.24), residues: 1142
  helix: -0.97 (0.23), residues: 466
  sheet: -2.51 (0.48), residues: 86
  loop : -3.10 (0.25), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP B 142 
 PHE   0.000   0.000   PHE B 107 
 TYR   0.000   0.000   TYR B  82 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1481.43 seconds
wall clock time: 26 minutes 58.37 seconds (1618.37 seconds total)