Starting phenix.real_space_refine (version: dev)
on Sun Dec 11 16:56:51 2022 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/12_2022/7bzx_30262.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/12_2022/7bzx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/12_2022/7bzx_30262.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/12_2022/7bzx_30262.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/12_2022/7bzx_30262.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bzx_30262/12_2022/7bzx_30262.pdb"
  }
  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
-------------------------------------------------------------------------------
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
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 4.07, per 1000 atoms: 0.72
  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  - 3.50
        Amino acid           : False - 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: 2.56
  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: 0.66
  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: 2.15

  Time building geometry restraints manager: 2.68 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:
       99.71 -   106.32: 228
      106.32 -   112.92: 2800
      112.92 -   119.52: 1814
      119.52 -   126.12: 2853
      126.12 -   132.72: 131
  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
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
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.
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:             0.270
  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:          2.110
  Check model and map are aligned:         0.100
  Convert atoms to be neutral:             0.050
  Process input model:                     21.410
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2479
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 %
  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

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.624 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0582
  time to fit residues: 4.5562
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.632 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8062
-------------------------------------------------------------------------------
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:    0.9990
   chunk 48 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    3.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3202
moved from start:          0.4301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.016   5646  Z= 0.177
  Angle     :  0.595   5.322   7826  Z= 0.361
  Chirality :  0.046   0.138   1038
  Planarity :  0.003   0.013   1148
  Dihedral  :  5.514  26.963   1148
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.25 %
    Favored  : 94.48 %
  Rotamer Outliers :  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: -1.18 (0.24), residues: 1142
  helix:  0.34 (0.22), residues: 502
  sheet: -1.80 (0.39), residues: 163
  loop : -1.55 (0.27), residues: 477

*********************** 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 fitting.
    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: 0.0560
  time to fit residues: 4.3446
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.597 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8163
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 86 optimal weight:   10.0000
   chunk 71 optimal weight:   20.0000
   chunk 28 optimal weight:    6.9990
   chunk 104 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 93 optimal weight:    0.9990
   chunk 103 optimal weight:   30.0000
   chunk 35 optimal weight:   30.0000
   chunk 83 optimal weight:   40.0000
   overall best weight:    6.5992

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4209
moved from start:          1.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.040   5646  Z= 0.273
  Angle     :  0.732   6.878   7826  Z= 0.454
  Chirality :  0.048   0.144   1038
  Planarity :  0.004   0.028   1148
  Dihedral  :  7.172  29.706   1148
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  9.54 %
    Favored  : 90.19 %
  Rotamer Outliers :  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: -2.23 (0.23), residues: 1142
  helix: -0.71 (0.21), residues: 505
  sheet: -1.18 (0.39), residues: 153
  loop : -2.38 (0.27), residues: 484

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.593 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0581
  time to fit residues: 4.5520
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.640 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8304
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:   20.0000
   chunk 78 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 49 optimal weight:   30.0000
   chunk 70 optimal weight:   10.0000
   chunk 104 optimal weight:    9.9990
   chunk 111 optimal weight:   30.0000
   chunk 99 optimal weight:   30.0000
   chunk 29 optimal weight:   30.0000
   chunk 92 optimal weight:    0.3980
   overall best weight:    7.2790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4502
moved from start:          1.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5646  Z= 0.252
  Angle     :  0.692   5.895   7826  Z= 0.430
  Chirality :  0.048   0.139   1038
  Planarity :  0.004   0.017   1148
  Dihedral  :  7.095  27.771   1148
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 10.95 %
    Favored  : 88.88 %
  Rotamer Outliers :  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: -2.45 (0.24), residues: 1142
  helix: -0.79 (0.22), residues: 478
  sheet: -1.34 (0.41), residues: 142
  loop : -2.51 (0.27), residues: 522

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.662 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0549
  time to fit residues: 4.3971
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.610 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8270
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 82 optimal weight:   40.0000
   chunk 45 optimal weight:   40.0000
   chunk 94 optimal weight:   40.0000
   chunk 76 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 56 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 28 optimal weight:   10.0000
   chunk 37 optimal weight:   20.0000
   overall best weight:    9.9792

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4834
moved from start:          1.5669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.065   5646  Z= 0.329
  Angle     :  0.849   8.082   7826  Z= 0.524
  Chirality :  0.050   0.155   1038
  Planarity :  0.005   0.021   1148
  Dihedral  :  8.299  36.639   1148
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 22.76
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  : 16.55 %
    Favored  : 83.10 %
  Rotamer Outliers :  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: -3.38 (0.23), residues: 1142
  helix: -1.62 (0.22), residues: 453
  sheet: -2.39 (0.42), residues: 135
  loop : -2.74 (0.27), residues: 554

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.627 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0593
  time to fit residues: 4.5168
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.621 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8017
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 65 optimal weight:   40.0000
   chunk 27 optimal weight:    8.9990
   chunk 111 optimal weight:    0.0270
   chunk 92 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 58 optimal weight:   20.0000
   chunk 107 optimal weight:    7.9990
   overall best weight:    2.9842

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4556
moved from start:          1.5343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5646  Z= 0.132
  Angle     :  0.525   6.586   7826  Z= 0.318
  Chirality :  0.046   0.139   1038
  Planarity :  0.002   0.010   1148
  Dihedral  :  5.909  23.911   1148
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.58 %
    Favored  : 91.42 %
  Rotamer Outliers :  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: -2.39 (0.24), residues: 1142
  helix: -0.62 (0.23), residues: 482
  sheet: -1.57 (0.46), residues: 128
  loop : -2.52 (0.27), residues: 532

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.649 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0604
  time to fit residues: 4.6970
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.631 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8763
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 63 optimal weight:    6.9990
   chunk 81 optimal weight:    7.9990
   chunk 62 optimal weight:   10.0000
   chunk 93 optimal weight:    0.3980
   chunk 110 optimal weight:    5.9990
   chunk 69 optimal weight:   50.0000
   chunk 67 optimal weight:   30.0000
   chunk 51 optimal weight:   30.0000
   chunk 68 optimal weight:    7.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    5.4788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4720
moved from start:          1.6001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5646  Z= 0.198
  Angle     :  0.598   6.277   7826  Z= 0.367
  Chirality :  0.047   0.141   1038
  Planarity :  0.003   0.013   1148
  Dihedral  :  6.486  24.589   1148
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.36 %
    Favored  : 85.64 %
  Rotamer Outliers :  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: -2.75 (0.24), residues: 1142
  helix: -0.82 (0.23), residues: 459
  sheet: -1.92 (0.46), residues: 122
  loop : -2.71 (0.25), residues: 561

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.588 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0573
  time to fit residues: 4.4672
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.642 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8797
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:   40.0000
   chunk 33 optimal weight:   10.0000
   chunk 21 optimal weight:   20.0000
   chunk 70 optimal weight:   40.0000
   chunk 75 optimal weight:   30.0000
   chunk 54 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 100 optimal weight:    9.9990
   chunk 106 optimal weight:   10.0000
   chunk 96 optimal weight:   30.0000
   overall best weight:   13.9998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5088
moved from start:          1.7610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.092   5646  Z= 0.446
  Angle     :  1.027   9.740   7826  Z= 0.636
  Chirality :  0.054   0.201   1038
  Planarity :  0.006   0.025   1148
  Dihedral  :  9.396  37.959   1148
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 30.79
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  : 22.33 %
    Favored  : 77.41 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.82 %
    Twisted General : 0.37 %

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: -4.66 (0.21), residues: 1142
  helix: -2.57 (0.20), residues: 442
  sheet: -2.65 (0.45), residues: 116
  loop : -3.70 (0.23), residues: 584

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.628 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0569
  time to fit residues: 4.4395
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.639 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7834
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:   20.0000
   chunk 106 optimal weight:   20.0000
   chunk 62 optimal weight:   30.0000
   chunk 44 optimal weight:    6.9990
   chunk 81 optimal weight:   30.0000
   chunk 31 optimal weight:   20.0000
   chunk 93 optimal weight:    1.9990
   chunk 97 optimal weight:    8.9990
   chunk 102 optimal weight:    6.9990
   chunk 67 optimal weight:    1.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    5.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4833
moved from start:          1.7347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5646  Z= 0.195
  Angle     :  0.629   7.584   7826  Z= 0.384
  Chirality :  0.047   0.138   1038
  Planarity :  0.003   0.017   1148
  Dihedral  :  7.160  32.736   1148
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 13.66
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 15.24 %
    Favored  : 84.68 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  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: -3.95 (0.22), residues: 1142
  helix: -1.83 (0.21), residues: 456
  sheet: -2.41 (0.43), residues: 125
  loop : -3.41 (0.24), residues: 561

*********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.648 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0584
  time to fit residues: 4.5509
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.645 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.8318
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:   40.0000
   chunk 51 optimal weight:   20.0000
   chunk 75 optimal weight:   40.0000
   chunk 114 optimal weight:   30.0000
   chunk 105 optimal weight:   20.0000
   chunk 91 optimal weight:   30.0000
   chunk 9 optimal weight:   40.0000
   chunk 70 optimal weight:   50.0000
   chunk 55 optimal weight:   20.0000
   chunk 72 optimal weight:    7.9990
   chunk 97 optimal weight:   30.0000
   overall best weight:   19.5998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5314
moved from start:          1.9056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.008   0.119   5646  Z= 0.562
  Angle     :  1.228  16.612   7826  Z= 0.762
  Chirality :  0.058   0.234   1038
  Planarity :  0.008   0.038   1148
  Dihedral  : 10.974  50.573   1148
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 46.24
  Ramachandran Plot:
    Outliers :  1.49 %
    Allowed  : 28.72 %
    Favored  : 69.79 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.91 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.64 %
    Twisted General : 0.91 %

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: -5.71 (0.19), residues: 1142
  helix: -3.39 (0.18), residues: 420
  sheet: -3.04 (0.49), residues: 94
  loop : -4.38 (0.20), residues: 628

********************** 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 fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.587 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 34
  average time/residue: 0.0568
  time to fit residues: 4.3770
Evaluate side-chains
  34 residues out of total 927 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.677 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 0.7859
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:   20.0000
   chunk 84 optimal weight:   10.0000
   chunk 13 optimal weight:   30.0000
   chunk 25 optimal weight:    9.9990
   chunk 91 optimal weight:    0.5980
   chunk 38 optimal weight:   20.0000
   chunk 93 optimal weight:   30.0000
   chunk 11 optimal weight:   30.0000
   chunk 16 optimal weight:    6.9990
   chunk 80 optimal weight:    8.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    7.3190

-------------------------------------------------------------------------------
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 = 0.093492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.084306 restraints weight = 37108.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.085224 restraints weight = 29293.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.085890 restraints weight = 23956.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5741
moved from start:          1.8678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5646  Z= 0.259
  Angle     :  0.755  11.752   7826  Z= 0.461
  Chirality :  0.048   0.143   1038
  Planarity :  0.004   0.017   1148
  Dihedral  :  8.412  43.453   1148
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 18.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 18.39 %
    Favored  : 81.52 %
  Rotamer Outliers :  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: -5.13 (0.20), residues: 1142
  helix: -2.78 (0.19), residues: 443
  sheet: -3.04 (0.44), residues: 106
  loop : -4.11 (0.21), residues: 593

===============================================================================
Job complete
usr+sys time: 861.46 seconds
wall clock time: 16 minutes 8.11 seconds (968.11 seconds total)