Starting phenix.real_space_refine
on Sat Jun  7 11:59:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t54_25694/06_2025/7t54_25694.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t54_25694/06_2025/7t54_25694.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t54_25694/06_2025/7t54_25694.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t54_25694/06_2025/7t54_25694.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t54_25694/06_2025/7t54_25694.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t54_25694/06_2025/7t54_25694.cif"
  }
  resolution = 4.5
  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=   0.001 sd=   0.034
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      20      5.16       5
     C    5310      2.51       5
     N    1570      2.21       5
     O    1646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8552
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 708, 4245
          Classifications: {'peptide': 708}
          Incomplete info: {'truncation_to_alanine': 386}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694}
          Chain breaks: 1
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1336
          Unresolved non-hydrogen angles: 1697
          Unresolved non-hydrogen dihedrals: 1098
          Unresolved non-hydrogen chiralities: 144
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 629
    Chain: "B"
      Number of atoms: 4245
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 708, 4245
          Classifications: {'peptide': 708}
          Incomplete info: {'truncation_to_alanine': 386}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 694}
          Chain breaks: 1
          Unresolved chain link angles: 10
          Unresolved non-hydrogen bonds: 1336
          Unresolved non-hydrogen angles: 1697
          Unresolved non-hydrogen dihedrals: 1098
          Unresolved non-hydrogen chiralities: 144
          Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 5, 'TYR:plan': 15, 'ASN:plan1': 22, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 22, 'GLU:plan': 19, 'ARG:plan': 12}
          Unresolved non-hydrogen planarities: 629
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.01, per 1000 atoms: 0.70
  Number of scatterers: 8552
  At special positions: 0
  Unit cell: (128.75, 87.55, 135.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      20     16.00
     P       6     15.00
     O    1646      8.00
     N    1570      7.00
     C    5310      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: 2.33
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2628

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 11 sheets defined
      62.7% alpha, 7.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 33
    Processing helix  chain 'A' and resid 38 through 47
      removed outlier: 4.059A  pdb=" N   ILE A  42 " --> pdb=" O   SER A  38 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   GLY A  47 " --> pdb=" O   ARG A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 66
      removed outlier: 3.592A  pdb=" N   LEU A  58 " --> pdb=" O   ASN A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 96
      No H-bonds generated for 'chain 'A' and resid 94 through 96'
    Processing helix  chain 'A' and resid 124 through 132
      removed outlier: 3.784A  pdb=" N   CYS A 129 " --> pdb=" O   MET A 125 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   SER A 130 " --> pdb=" O   ASP A 126 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   TRP A 132 " --> pdb=" O   PHE A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 163
    Processing helix  chain 'A' and resid 165 through 197
    Processing helix  chain 'A' and resid 202 through 250
      removed outlier: 3.509A  pdb=" N   SER A 248 " --> pdb=" O   MET A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 261
      removed outlier: 3.636A  pdb=" N   PHE A 258 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 272
      removed outlier: 4.337A  pdb=" N   ARG A 269 " --> pdb=" O   GLU A 265 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE A 270 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 305
      removed outlier: 3.934A  pdb=" N   ILE A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLN A 278 " --> pdb=" O   SER A 274 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ILE A 299 " --> pdb=" O   VAL A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 326
      removed outlier: 3.864A  pdb=" N   PHE A 326 " --> pdb=" O   ILE A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 354
      removed outlier: 3.912A  pdb=" N   ILE A 330 " --> pdb=" O   PHE A 326 " (cutoff:3.500A)
      removed outlier: 4.514A  pdb=" N   GLN A 331 " --> pdb=" O   ASN A 327 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ASN A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   GLN A 336 " --> pdb=" O   ASN A 332 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLU A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 361
      removed outlier: 3.604A  pdb=" N   PHE A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 418
      removed outlier: 3.845A  pdb=" N   THR A 371 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TYR A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 446
      Proline residue:  A 438  - end of helix
    Processing helix  chain 'A' and resid 448 through 463
      removed outlier: 3.762A  pdb=" N   VAL A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLU A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 533
      removed outlier: 3.811A  pdb=" N   LEU A 532 " --> pdb=" O   LEU A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 549 through 553
    Processing helix  chain 'A' and resid 554 through 561
    Processing helix  chain 'A' and resid 576 through 582
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.584A  pdb=" N   ILE A 592 " --> pdb=" O   ASP A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 608
      removed outlier: 4.251A  pdb=" N   LYS A 607 " --> pdb=" O   ASP A 603 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   LEU A 608 " --> pdb=" O   PHE A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 639
      removed outlier: 3.673A  pdb=" N   LYS A 639 " --> pdb=" O   ARG A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 669
      removed outlier: 3.812A  pdb=" N   HIS A 660 " --> pdb=" O   ILE A 656 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   ALA A 664 " --> pdb=" O   HIS A 660 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLU A 669 " --> pdb=" O   ILE A 665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 711
      removed outlier: 3.579A  pdb=" N   LYS A 711 " --> pdb=" O   LEU A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 722
    Processing helix  chain 'B' and resid 20 through 34
      removed outlier: 4.050A  pdb=" N   ALA B  24 " --> pdb=" O   ASP B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 38 through 47
      removed outlier: 3.611A  pdb=" N   ILE B  42 " --> pdb=" O   SER B  38 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLY B  47 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 54 through 66
      removed outlier: 3.648A  pdb=" N   LEU B  58 " --> pdb=" O   ASN B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 96
      No H-bonds generated for 'chain 'B' and resid 94 through 96'
    Processing helix  chain 'B' and resid 124 through 132
      removed outlier: 3.926A  pdb=" N   TRP B 132 " --> pdb=" O   PHE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 165 through 197
    Processing helix  chain 'B' and resid 202 through 252
      removed outlier: 3.574A  pdb=" N   LEU B 206 " --> pdb=" O   LYS B 202 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   TYR B 226 " --> pdb=" O   PHE B 222 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 261
      removed outlier: 3.866A  pdb=" N   PHE B 258 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 272
      removed outlier: 4.271A  pdb=" N   ARG B 269 " --> pdb=" O   GLU B 265 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   PHE B 270 " --> pdb=" O   ILE B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 305
      removed outlier: 3.712A  pdb=" N   ILE B 276 " --> pdb=" O   ASP B 272 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   LEU B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE B 299 " --> pdb=" O   VAL B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 354
      removed outlier: 4.679A  pdb=" N   LYS B 328 " --> pdb=" O   THR B 324 " (cutoff:3.500A)
      Proline residue:  B 329  - end of helix
      removed outlier: 3.728A  pdb=" N   ASN B 332 " --> pdb=" O   LYS B 328 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   GLN B 336 " --> pdb=" O   ASN B 332 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLU B 339 " --> pdb=" O   ARG B 335 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LYS B 343 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   GLU B 350 " --> pdb=" O   SER B 346 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 354 through 361
    Processing helix  chain 'B' and resid 363 through 418
      removed outlier: 3.508A  pdb=" N   SER B 382 " --> pdb=" O   VAL B 378 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   TYR B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 446
      Proline residue:  B 438  - end of helix
    Processing helix  chain 'B' and resid 448 through 460
      removed outlier: 3.691A  pdb=" N   VAL B 454 " --> pdb=" O   GLN B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 470
      removed outlier: 4.186A  pdb=" N   GLU B 470 " --> pdb=" O   ALA B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 533
      removed outlier: 3.825A  pdb=" N   LEU B 532 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 549 through 553
    Processing helix  chain 'B' and resid 554 through 561
    Processing helix  chain 'B' and resid 576 through 582
    Processing helix  chain 'B' and resid 588 through 599
      removed outlier: 3.546A  pdb=" N   ILE B 592 " --> pdb=" O   ASP B 588 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 607
      removed outlier: 4.320A  pdb=" N   LYS B 607 " --> pdb=" O   ASP B 603 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 624 through 639
      removed outlier: 3.592A  pdb=" N   LYS B 639 " --> pdb=" O   ARG B 635 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 657
    Processing helix  chain 'B' and resid 658 through 669
      removed outlier: 4.985A  pdb=" N   ALA B 664 " --> pdb=" O   HIS B 660 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLU B 669 " --> pdb=" O   ILE B 665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 703 through 711
      removed outlier: 3.565A  pdb=" N   LYS B 711 " --> pdb=" O   LEU B 707 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 722
    Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
      removed outlier: 3.951A  pdb=" N   ILE A  88 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115
    Processing sheet with id=AA4, first strand: chain 'A' and resid 502 through 505
      removed outlier: 4.066A  pdb=" N   ASN A 504 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   VAL A 491 " --> pdb=" O   ASN A 504 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   VAL A 491 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS A 540 " --> pdb=" O   VAL A 491 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 643 through 646
      removed outlier: 6.609A  pdb=" N   LEU A 644 " --> pdb=" O   ILE A 675 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   ILE A 677 " --> pdb=" O   LEU A 644 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   LEU A 646 " --> pdb=" O   ILE A 677 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   TYR A 691 " --> pdb=" O   THR A 514 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   ALA A 516 " --> pdb=" O   TYR A 691 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   LEU A 693 " --> pdb=" O   ALA A 516 " (cutoff:3.500A)
      removed outlier: 7.658A  pdb=" N   VAL A 518 " --> pdb=" O   LEU A 693 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   ILE A 690 " --> pdb=" O   SER A 701 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   SER A 701 " --> pdb=" O   ILE A 690 " (cutoff:3.500A)
      removed outlier: 7.204A  pdb=" N   LEU A 692 " --> pdb=" O   VAL A 699 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 574 through 575
      removed outlier: 3.688A  pdb=" N   GLY A 574 " --> pdb=" O   LEU A 616 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 71 through 72
      removed outlier: 3.899A  pdb=" N   ILE B  88 " --> pdb=" O   VAL B 137 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 111 through 113
      removed outlier: 4.072A  pdb=" N   ILE B 111 " --> pdb=" O   TYR B 123 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR B 123 " --> pdb=" O   ILE B 111 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL B 113 " --> pdb=" O   VAL B 121 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 502 through 505
      removed outlier: 4.063A  pdb=" N   ASN B 504 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   VAL B 491 " --> pdb=" O   ASN B 504 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL B 491 " --> pdb=" O   LYS B 540 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS B 540 " --> pdb=" O   VAL B 491 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 643 through 646
      removed outlier: 8.724A  pdb=" N   TYR B 691 " --> pdb=" O   THR B 514 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ALA B 516 " --> pdb=" O   TYR B 691 " (cutoff:3.500A)
      removed outlier: 8.359A  pdb=" N   LEU B 693 " --> pdb=" O   ALA B 516 " (cutoff:3.500A)
      removed outlier: 7.689A  pdb=" N   VAL B 518 " --> pdb=" O   LEU B 693 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE B 690 " --> pdb=" O   SER B 701 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   SER B 701 " --> pdb=" O   ILE B 690 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   LEU B 692 " --> pdb=" O   VAL B 699 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 574 through 575

    655 hydrogen bonds defined for protein.
    1908 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: 2.81

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3042
        1.34 -     1.46: 748
        1.46 -     1.58: 4780
        1.58 -     1.69: 12
        1.69 -     1.81: 36
  Bond restraints: 8618
  Sorted by residual:
  bond pdb=" N   ILE B 656 "
       pdb=" CA  ILE B 656 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.25e-02 6.40e+03 8.85e+00
  bond pdb=" N   ILE A 656 "
       pdb=" CA  ILE A 656 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.19e-02 7.06e+03 8.48e+00
  bond pdb=" N   VAL A 250 "
       pdb=" CA  VAL A 250 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.25e-02 6.40e+03 7.12e+00
  bond pdb=" N   LEU A 653 "
       pdb=" CA  LEU A 653 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.22e-02 6.72e+03 6.53e+00
  bond pdb=" N   SER A 655 "
       pdb=" CA  SER A 655 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.41e+00
  ... (remaining 8613 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 11545
        2.01 -     4.03: 245
        4.03 -     6.04: 20
        6.04 -     8.06: 8
        8.06 -    10.07: 2
  Bond angle restraints: 11820
  Sorted by residual:
  angle pdb=" N   PHE B 478 "
        pdb=" CA  PHE B 478 "
        pdb=" C   PHE B 478 "
      ideal   model   delta    sigma   weight residual
     111.36  121.43  -10.07 1.09e+00 8.42e-01 8.53e+01
  angle pdb=" N   ASP B 477 "
        pdb=" CA  ASP B 477 "
        pdb=" C   ASP B 477 "
      ideal   model   delta    sigma   weight residual
     109.07  118.60   -9.53 1.61e+00 3.86e-01 3.51e+01
  angle pdb=" C   ASP B 654 "
        pdb=" CA  ASP B 654 "
        pdb=" CB  ASP B 654 "
      ideal   model   delta    sigma   weight residual
     117.23  111.55    5.68 1.36e+00 5.41e-01 1.74e+01
  angle pdb=" C   GLU B 648 "
        pdb=" CA  GLU B 648 "
        pdb=" CB  GLU B 648 "
      ideal   model   delta    sigma   weight residual
     116.54  112.00    4.54 1.15e+00 7.56e-01 1.56e+01
  angle pdb=" C   GLU A  44 "
        pdb=" N   MET A  45 "
        pdb=" CA  MET A  45 "
      ideal   model   delta    sigma   weight residual
     122.38  115.67    6.71 1.81e+00 3.05e-01 1.37e+01
  ... (remaining 11815 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.13: 4793
       16.13 -    32.26: 231
       32.26 -    48.40: 58
       48.40 -    64.53: 24
       64.53 -    80.66: 2
  Dihedral angle restraints: 5108
    sinusoidal: 1048
      harmonic: 4060
  Sorted by residual:
  dihedral pdb=" N   SER B 481 "
           pdb=" C   SER B 481 "
           pdb=" CA  SER B 481 "
           pdb=" CB  SER B 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.61  -10.81     0      2.50e+00 1.60e-01 1.87e+01
  dihedral pdb=" C   SER B 481 "
           pdb=" N   SER B 481 "
           pdb=" CA  SER B 481 "
           pdb=" CB  SER B 481 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.85   10.25     0      2.50e+00 1.60e-01 1.68e+01
  dihedral pdb=" CA  GLU B 339 "
           pdb=" C   GLU B 339 "
           pdb=" N   ASP B 340 "
           pdb=" CA  ASP B 340 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.06   16.94     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 5105 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1381
       0.081 -    0.162: 123
       0.162 -    0.242: 4
       0.242 -    0.323: 1
       0.323 -    0.404: 1
  Chirality restraints: 1510
  Sorted by residual:
  chirality pdb=" CA  SER B 481 "
            pdb=" N   SER B 481 "
            pdb=" C   SER B 481 "
            pdb=" CB  SER B 481 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.11    0.40 2.00e-01 2.50e+01 4.08e+00
  chirality pdb=" CA  PHE B 478 "
            pdb=" N   PHE B 478 "
            pdb=" C   PHE B 478 "
            pdb=" CB  PHE B 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  ASP B 477 "
            pdb=" N   ASP B 477 "
            pdb=" C   ASP B 477 "
            pdb=" CB  ASP B 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1507 not shown)

  Planarity restraints: 1578
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 475 "    0.017 2.00e-02 2.50e+03   3.50e-02 1.22e+01
        pdb=" C   SER B 475 "   -0.060 2.00e-02 2.50e+03
        pdb=" O   SER B 475 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASP B 476 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 247 "    0.009 2.00e-02 2.50e+03   9.27e-03 1.72e+00
        pdb=" CG  TYR B 247 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 247 "    0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 247 "    0.008 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 247 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 247 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 247 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 247 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE B 480 "   -0.006 2.00e-02 2.50e+03   1.18e-02 1.40e+00
        pdb=" C   ILE B 480 "    0.020 2.00e-02 2.50e+03
        pdb=" O   ILE B 480 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   SER B 481 "   -0.007 2.00e-02 2.50e+03
  ... (remaining 1575 not shown)

  Histogram of nonbonded interaction distances:
        2.08 -     2.64: 49
        2.64 -     3.21: 8175
        3.21 -     3.77: 12763
        3.77 -     4.34: 14680
        4.34 -     4.90: 24423
  Nonbonded interactions: 60090
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 622 "
            pdb=" ND2 ASN A 622 "
     model   vdw
     2.078 3.120
  nonbonded pdb=" OH  TYR B 246 "
            pdb=" OE2 GLU B 461 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" N   SER B  68 "
            pdb=" O   GLU B 140 "
     model   vdw
     2.360 3.120
  nonbonded pdb=" NH1 ARG B 269 "
            pdb=" OD1 ASN B 457 "
     model   vdw
     2.418 3.120
  nonbonded pdb=" OE2 GLU B 339 "
            pdb=" ND2 ASN B 457 "
     model   vdw
     2.426 3.120
  ... (remaining 60085 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  Number of NCS constrained groups: 1
  pdb_interpretation.ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
Set refine NCS operators
  NCS operators will be refined.
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:             1.550
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.910
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6699
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      :  0.004   0.041   8618  Z= 0.248
  Angle     :  0.696  10.069  11820  Z= 0.464
  Chirality :  0.045   0.404   1510
  Planarity :  0.003   0.038   1578
  Dihedral  : 12.143  80.661   2480
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.40 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  0.68 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  0.70 (0.23), residues: 1408
  helix:  2.25 (0.19), residues: 786
  sheet: -1.46 (0.43), residues: 146
  loop : -2.09 (0.26), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 718 
 HIS   0.003   0.001   HIS B 249 
 PHE   0.009   0.001   PHE B 270 
 TYR   0.022   0.001   TYR B 247 
 ARG   0.008   0.001   ARG A 498 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14559 (  655)
  hydrogen bonds       : angle       4.72044 ( 1908)
  covalent geometry    : bond        0.00369 ( 8618)
  covalent geometry    : angle       0.69597 (11820)

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

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

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2816 Ramachandran restraints generated.
    1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1886
  time to fit residues: 13.4238
Evaluate side-chains
  29 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.4980
   chunk 106 optimal weight:    9.9990
   chunk 58 optimal weight:    0.0170
   chunk 36 optimal weight:   10.0000
   chunk 71 optimal weight:   40.0000
   chunk 56 optimal weight:    0.0370
   chunk 109 optimal weight:    7.9990
   chunk 42 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 81 optimal weight:    0.9990
   chunk 127 optimal weight:    0.0670
   overall best weight:    0.3236
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 652 ASN
B 679 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.039569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.032324 restraints weight = 59210.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2842 r_free = 0.2842 target = 0.032724 restraints weight = 49295.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.032979 restraints weight = 42742.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8618  Z= 0.146
  Angle     :  0.598   8.640  11820  Z= 0.354
  Chirality :  0.042   0.154   1510
  Planarity :  0.003   0.053   1578
  Dihedral  :  7.059  56.397   1518
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.43 %
    Allowed  :  3.84 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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:  0.99 (0.23), residues: 1408
  helix:  2.43 (0.18), residues: 822
  sheet: -1.09 (0.44), residues: 152
  loop : -2.34 (0.25), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 718 
 HIS   0.003   0.001   HIS A 249 
 PHE   0.008   0.001   PHE A 361 
 TYR   0.010   0.001   TYR A 536 
 ARG   0.005   0.001   ARG A 458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08818 (  655)
  hydrogen bonds       : angle       3.72241 ( 1908)
  covalent geometry    : bond        0.00251 ( 8618)
  covalent geometry    : angle       0.59828 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  536 TYR cc_start: 0.8599 (m-10) cc_final: 0.8265 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.1614
  time to fit residues: 7.1632
Evaluate side-chains
  26 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 137 optimal weight:   10.0000
   chunk 116 optimal weight:   40.0000
   chunk 118 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:   30.0000
   chunk 33 optimal weight:    9.9990
   chunk 132 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0170
   chunk 29 optimal weight:   40.0000
   chunk 111 optimal weight:   20.0000
   chunk 121 optimal weight:    0.0010
   overall best weight:    2.5628
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 679 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.037985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.031184 restraints weight = 61002.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2809 r_free = 0.2809 target = 0.031543 restraints weight = 51272.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.031844 restraints weight = 45147.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8618  Z= 0.138
  Angle     :  0.517   6.243  11820  Z= 0.316
  Chirality :  0.040   0.139   1510
  Planarity :  0.003   0.034   1578
  Dihedral  :  6.834  52.890   1518
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.26 %
    Favored  : 94.60 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  3.20 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.43 %

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:  1.01 (0.23), residues: 1408
  helix:  2.26 (0.18), residues: 836
  sheet:  0.07 (0.55), residues: 106
  loop : -2.34 (0.26), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 718 
 HIS   0.010   0.002   HIS A 679 
 PHE   0.011   0.001   PHE A 257 
 TYR   0.007   0.001   TYR B 612 
 ARG   0.003   0.001   ARG A 458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  655)
  hydrogen bonds       : angle       3.45416 ( 1908)
  covalent geometry    : bond        0.00250 ( 8618)
  covalent geometry    : angle       0.51735 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 29
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  536 TYR cc_start: 0.8215 (m-10) cc_final: 0.7777 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 30
  average time/residue: 0.1743
  time to fit residues: 7.0469
Evaluate side-chains
  26 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 64 optimal weight:    0.0070
   chunk 115 optimal weight:   20.0000
   chunk 41 optimal weight:   30.0000
   chunk 15 optimal weight:   20.0000
   chunk 28 optimal weight:   30.0000
   chunk 78 optimal weight:   50.0000
   chunk 56 optimal weight:    9.9990
   chunk 135 optimal weight:    8.9990
   chunk 17 optimal weight:   30.0000
   chunk 72 optimal weight:   40.0000
   overall best weight:    7.9406
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
** B 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.028249 restraints weight = 67140.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.028558 restraints weight = 58303.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.028656 restraints weight = 54780.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.7052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8618  Z= 0.317
  Angle     :  0.722   7.245  11820  Z= 0.432
  Chirality :  0.042   0.183   1510
  Planarity :  0.004   0.041   1578
  Dihedral  :  8.044  59.203   1518
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 12.77
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  8.24 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -0.94 (0.21), residues: 1408
  helix:  0.68 (0.17), residues: 834
  sheet: -1.48 (0.49), residues: 102
  loop : -2.84 (0.25), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 718 
 HIS   0.009   0.004   HIS B 679 
 PHE   0.031   0.003   PHE A 493 
 TYR   0.014   0.002   TYR B 612 
 ARG   0.004   0.001   ARG B 635 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04686 (  655)
  hydrogen bonds       : angle       4.99248 ( 1908)
  covalent geometry    : bond        0.00562 ( 8618)
  covalent geometry    : angle       0.72227 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.485 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1747
  time to fit residues: 6.1440
Evaluate side-chains
  19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 14 optimal weight:   40.0000
   chunk 91 optimal weight:   10.0000
   chunk 78 optimal weight:   50.0000
   chunk 59 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 27 optimal weight:   30.0000
   chunk 100 optimal weight:    0.0040
   chunk 77 optimal weight:   10.0000
   chunk 29 optimal weight:   50.0000
   chunk 85 optimal weight:   30.0000
   chunk 63 optimal weight:    5.9990
   overall best weight:    4.2002
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 457 ASN
** A 652 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.034311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.028132 restraints weight = 68500.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.028485 restraints weight = 58327.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.028633 restraints weight = 51457.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.7288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8618  Z= 0.168
  Angle     :  0.524   5.742  11820  Z= 0.315
  Chirality :  0.040   0.126   1510
  Planarity :  0.003   0.026   1578
  Dihedral  :  6.840  59.643   1518
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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:  0.22 (0.22), residues: 1408
  helix:  1.61 (0.17), residues: 836
  sheet: -1.25 (0.49), residues: 106
  loop : -2.32 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 718 
 HIS   0.003   0.002   HIS B 249 
 PHE   0.017   0.002   PHE B 257 
 TYR   0.006   0.001   TYR B 389 
 ARG   0.004   0.001   ARG A 458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  655)
  hydrogen bonds       : angle       3.87536 ( 1908)
  covalent geometry    : bond        0.00301 ( 8618)
  covalent geometry    : angle       0.52372 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8983 (tpt) cc_final: 0.8735 (tpp)
REVERT: A  271 MET cc_start: 0.9741 (mmp) cc_final: 0.9442 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1536
  time to fit residues: 5.2455
Evaluate side-chains
  20 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 87 optimal weight:   20.0000
   chunk 46 optimal weight:   30.0000
   chunk 124 optimal weight:    0.3980
   chunk 127 optimal weight:    9.9990
   chunk 102 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 120 optimal weight:    6.9990
   chunk 89 optimal weight:   30.0000
   chunk 27 optimal weight:   30.0000
   chunk 35 optimal weight:    0.6980
   chunk 76 optimal weight:   20.0000
   overall best weight:    2.1384
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.034610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.028223 restraints weight = 65459.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.028528 restraints weight = 55945.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.028674 restraints weight = 50843.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.7445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   8618  Z= 0.112
  Angle     :  0.471   4.543  11820  Z= 0.281
  Chirality :  0.039   0.123   1510
  Planarity :  0.002   0.029   1578
  Dihedral  :  6.437  59.001   1518
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.25 %
    Favored  : 93.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  0.60 (0.23), residues: 1408
  helix:  1.96 (0.18), residues: 842
  sheet: -1.12 (0.51), residues: 106
  loop : -2.31 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP B 718 
 HIS   0.002   0.001   HIS A 679 
 PHE   0.014   0.001   PHE B 257 
 TYR   0.007   0.001   TYR A 612 
 ARG   0.004   0.001   ARG B 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  655)
  hydrogen bonds       : angle       3.46691 ( 1908)
  covalent geometry    : bond        0.00200 ( 8618)
  covalent geometry    : angle       0.47060 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8901 (tpt) cc_final: 0.8656 (tpp)
REVERT: A  271 MET cc_start: 0.9759 (mmp) cc_final: 0.9488 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.1348
  time to fit residues: 4.6293
Evaluate side-chains
  20 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 82 optimal weight:   40.0000
   chunk 95 optimal weight:    4.9990
   chunk 99 optimal weight:   50.0000
   chunk 13 optimal weight:    0.0050
   chunk 94 optimal weight:    6.9990
   chunk 64 optimal weight:    0.3980
   chunk 29 optimal weight:   50.0000
   chunk 122 optimal weight:    4.9990
   chunk 96 optimal weight:   20.0000
   chunk 19 optimal weight:   30.0000
   overall best weight:    3.4800
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.027952 restraints weight = 66158.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.028226 restraints weight = 57243.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.028318 restraints weight = 55087.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.7904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8618  Z= 0.145
  Angle     :  0.504   7.711  11820  Z= 0.297
  Chirality :  0.039   0.130   1510
  Planarity :  0.002   0.020   1578
  Dihedral  :  6.591  58.696   1518
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  0.58 (0.23), residues: 1408
  helix:  1.99 (0.18), residues: 840
  sheet: -1.51 (0.49), residues: 106
  loop : -2.31 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 718 
 HIS   0.002   0.001   HIS A 548 
 PHE   0.016   0.001   PHE A 257 
 TYR   0.010   0.001   TYR B 612 
 ARG   0.003   0.001   ARG A 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03282 (  655)
  hydrogen bonds       : angle       3.55233 ( 1908)
  covalent geometry    : bond        0.00264 ( 8618)
  covalent geometry    : angle       0.50417 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8972 (tpt) cc_final: 0.8730 (tpp)
REVERT: A  271 MET cc_start: 0.9804 (mmp) cc_final: 0.9526 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0984
  time to fit residues: 3.7315
Evaluate side-chains
  20 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 8 optimal weight:   30.0000
   chunk 107 optimal weight:    0.7980
   chunk 103 optimal weight:    9.9990
   chunk 48 optimal weight:    0.1980
   chunk 68 optimal weight:    0.0570
   chunk 109 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 124 optimal weight:    7.9990
   overall best weight:    1.0100
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.034798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.028200 restraints weight = 63691.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.028405 restraints weight = 58925.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.028606 restraints weight = 54612.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.7876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   8618  Z= 0.100
  Angle     :  0.468   5.988  11820  Z= 0.274
  Chirality :  0.039   0.125   1510
  Planarity :  0.002   0.022   1578
  Dihedral  :  6.240  55.651   1518
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  0.64 (0.23), residues: 1408
  helix:  2.07 (0.17), residues: 848
  sheet: -1.39 (0.51), residues: 106
  loop : -2.47 (0.27), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 718 
 HIS   0.001   0.001   HIS A 679 
 PHE   0.015   0.001   PHE A 604 
 TYR   0.010   0.001   TYR A 389 
 ARG   0.003   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03140 (  655)
  hydrogen bonds       : angle       3.20844 ( 1908)
  covalent geometry    : bond        0.00178 ( 8618)
  covalent geometry    : angle       0.46832 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  255 MET cc_start: 0.8954 (tpt) cc_final: 0.8722 (tpp)
REVERT: A  271 MET cc_start: 0.9792 (mmp) cc_final: 0.9494 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.0887
  time to fit residues: 3.6000
Evaluate side-chains
  20 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 139 optimal weight:   20.0000
   chunk 87 optimal weight:   20.0000
   chunk 93 optimal weight:    2.9990
   chunk 110 optimal weight:   30.0000
   chunk 36 optimal weight:    5.9990
   chunk 66 optimal weight:    0.5980
   chunk 75 optimal weight:    3.9990
   chunk 18 optimal weight:   40.0000
   chunk 42 optimal weight:   20.0000
   chunk 71 optimal weight:   30.0000
   chunk 6 optimal weight:   20.0000
   overall best weight:    6.7190
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 567 GLN
** B 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.033424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027330 restraints weight = 67869.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.027458 restraints weight = 60324.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.027712 restraints weight = 56370.510|
|-----------------------------------------------------------------------------|
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.8550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8618  Z= 0.252
  Angle     :  0.626   7.840  11820  Z= 0.368
  Chirality :  0.040   0.126   1510
  Planarity :  0.003   0.020   1578
  Dihedral  :  7.354  53.898   1518
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.38 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.37 %
    Favored  : 98.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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: -0.09 (0.22), residues: 1408
  helix:  1.53 (0.17), residues: 846
  sheet: -2.07 (0.48), residues: 104
  loop : -2.72 (0.26), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP B 718 
 HIS   0.005   0.002   HIS B 602 
 PHE   0.022   0.003   PHE A 493 
 TYR   0.014   0.001   TYR A 612 
 ARG   0.004   0.001   ARG A 458 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  655)
  hydrogen bonds       : angle       4.14650 ( 1908)
  covalent geometry    : bond        0.00454 ( 8618)
  covalent geometry    : angle       0.62612 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  21 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.474 
Fit side-chains
REVERT: B  255 MET cc_start: 0.9111 (tpt) cc_final: 0.8872 (tpp)
REVERT: B  271 MET cc_start: 0.9835 (mmp) cc_final: 0.9573 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0928
  time to fit residues: 3.4594
Evaluate side-chains
  19 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 4 optimal weight:   30.0000
   chunk 59 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 45 optimal weight:   20.0000
   chunk 132 optimal weight:    0.9980
   chunk 66 optimal weight:    0.0570
   chunk 86 optimal weight:   20.0000
   chunk 134 optimal weight:   20.0000
   chunk 102 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0980
   overall best weight:    0.6098
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 249 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2901 r_free = 0.2901 target = 0.034379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.028014 restraints weight = 63770.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.028275 restraints weight = 54861.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2706 r_free = 0.2706 target = 0.028384 restraints weight = 54597.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.8349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8618  Z= 0.101
  Angle     :  0.485   6.158  11820  Z= 0.279
  Chirality :  0.040   0.127   1510
  Planarity :  0.002   0.027   1578
  Dihedral  :  6.379  59.949   1518
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  5.11 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  0.66 (0.23), residues: 1408
  helix:  2.14 (0.17), residues: 854
  sheet: -0.72 (0.58), residues: 74
  loop : -2.72 (0.25), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP A 718 
 HIS   0.001   0.000   HIS A 548 
 PHE   0.011   0.001   PHE B 257 
 TYR   0.011   0.001   TYR A 612 
 ARG   0.003   0.001   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03229 (  655)
  hydrogen bonds       : angle       3.23721 ( 1908)
  covalent geometry    : bond        0.00183 ( 8618)
  covalent geometry    : angle       0.48458 (11820)

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

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

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1408 Ramachandran restraints generated.
    704 Oldfield, 0 Emsley, 704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.516 
Fit side-chains
REVERT: A  255 MET cc_start: 0.9025 (tpt) cc_final: 0.8795 (tpp)
REVERT: A  271 MET cc_start: 0.9807 (mmp) cc_final: 0.9518 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0908
  time to fit residues: 3.5550
Evaluate side-chains
  20 residues out of total 605 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 46 optimal weight:   40.0000
   chunk 87 optimal weight:    9.9990
   chunk 107 optimal weight:    7.9990
   chunk 130 optimal weight:    2.9990
   chunk 136 optimal weight:    0.9990
   chunk 69 optimal weight:   40.0000
   chunk 111 optimal weight:   20.0000
   chunk 40 optimal weight:   20.0000
   chunk 74 optimal weight:   40.0000
   chunk 98 optimal weight:   20.0000
   overall best weight:    4.5788
-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** A 602 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.033621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.027432 restraints weight = 67549.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.027615 restraints weight = 58631.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.027846 restraints weight = 52879.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.8731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8618  Z= 0.180
  Angle     :  0.560  10.326  11820  Z= 0.322
  Chirality :  0.040   0.124   1510
  Planarity :  0.002   0.024   1578
  Dihedral  :  6.887  55.307   1518
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  8.38 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    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:  0.50 (0.23), residues: 1408
  helix:  2.05 (0.18), residues: 850
  sheet: -0.73 (0.70), residues: 52
  loop : -2.77 (0.24), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 718 
 HIS   0.002   0.001   HIS A 548 
 PHE   0.016   0.002   PHE B 493 
 TYR   0.015   0.001   TYR A 612 
 ARG   0.003   0.000   ARG B 489 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03400 (  655)
  hydrogen bonds       : angle       3.69315 ( 1908)
  covalent geometry    : bond        0.00326 ( 8618)
  covalent geometry    : angle       0.56028 (11820)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1995.47 seconds
wall clock time: 35 minutes 35.53 seconds (2135.53 seconds total)