Starting phenix.real_space_refine
on Fri Oct 23 23:26:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/12rj_76709/10_2026/12rj_76709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/12rj_76709/10_2026/12rj_76709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/12rj_76709/10_2026/12rj_76709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/12rj_76709/10_2026/12rj_76709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/12rj_76709/10_2026/12rj_76709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/12rj_76709/10_2026/12rj_76709.cif"
  }
  resolution = 2.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.043
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: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    7234      2.51       5
     N    1868      2.21       5
     O    2132      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11292
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 705, 5646
          Classifications: {'peptide': 705}
          Link IDs: {'PCIS': 4, 'PTRANS': 27, 'TRANS': 673}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.17, per 1000 atoms: 0.46
  Number of scatterers: 11292
  At special positions: 0
  Unit cell: (99.96, 140.76, 79.56, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    2132      8.00
     N    1868      7.00
     C    7234      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 579.5 milliseconds
  

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2584

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 26 sheets defined
      38.4% alpha, 18.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 45
      removed outlier: 3.614A  pdb=" N   GLU A  45 " --> pdb=" O   GLN A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 130
      removed outlier: 3.594A  pdb=" N   SER A 130 " --> pdb=" O   LYS A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 246
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 3.834A  pdb=" N   ALA A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.691A  pdb=" N   LYS A 265 " --> pdb=" O   TYR A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 288
      removed outlier: 3.652A  pdb=" N   SER A 288 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 295
      removed outlier: 4.070A  pdb=" N   VAL A 292 " --> pdb=" O   SER A 288 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE A 293 " --> pdb=" O   TYR A 289 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR A 294 " --> pdb=" O   SER A 290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 324
      removed outlier: 5.039A  pdb=" N   TYR A 322 " --> pdb=" O   ASP A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 332 through 344
      removed outlier: 4.317A  pdb=" N   GLU A 336 " --> pdb=" O   PRO A 332 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE A 337 " --> pdb=" O   GLU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 385
    Processing helix  chain 'A' and resid 386 through 409
      removed outlier: 4.122A  pdb=" N   ALA A 390 " --> pdb=" O   ASN A 386 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU A 391 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASP A 392 " --> pdb=" O   GLN A 388 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ASP A 395 " --> pdb=" O   GLU A 391 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   VAL A 396 " --> pdb=" O   ASP A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 454
      removed outlier: 3.600A  pdb=" N   GLN A 438 " --> pdb=" O   TYR A 434 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 479
      Proline residue:  A 469  - end of helix
      removed outlier: 3.547A  pdb=" N   ASN A 476 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU A 477 " --> pdb=" O   LYS A 473 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA A 478 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU A 479 " --> pdb=" O   TYR A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 516
      removed outlier: 3.613A  pdb=" N   ALA A 516 " --> pdb=" O   GLY A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 525
      removed outlier: 4.136A  pdb=" N   TYR A 523 " --> pdb=" O   PRO A 520 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE A 525 " --> pdb=" O   ALA A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 542
      removed outlier: 3.628A  pdb=" N   GLU A 536 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 569
      Proline residue:  A 566  - end of helix
      removed outlier: 3.648A  pdb=" N   GLU A 569 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 578
      removed outlier: 3.980A  pdb=" N   THR A 578 " --> pdb=" O   TYR A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 582
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.574A  pdb=" N   TYR A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG A 599 " --> pdb=" O   SER A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 618
      removed outlier: 3.724A  pdb=" N   ASP A 608 " --> pdb=" O   GLN A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 647
      removed outlier: 3.826A  pdb=" N   LYS A 646 " --> pdb=" O   GLU A 643 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASP A 647 " --> pdb=" O   PRO A 644 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 643 through 647'
    Processing helix  chain 'A' and resid 654 through 661
      removed outlier: 3.905A  pdb=" N   TYR A 657 " --> pdb=" O   TYR A 654 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS A 658 " --> pdb=" O   PRO A 655 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   ALA A 660 " --> pdb=" O   TYR A 657 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   TRP A 661 " --> pdb=" O   LYS A 658 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 669
    Processing helix  chain 'B' and resid 39 through 45
      removed outlier: 3.614A  pdb=" N   GLU B  45 " --> pdb=" O   GLN B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 130
      removed outlier: 3.594A  pdb=" N   SER B 130 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 242 through 246
    Processing helix  chain 'B' and resid 249 through 260
      removed outlier: 3.834A  pdb=" N   ALA B 253 " --> pdb=" O   SER B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 273
      removed outlier: 3.691A  pdb=" N   LYS B 265 " --> pdb=" O   TYR B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 288
      removed outlier: 3.652A  pdb=" N   SER B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 295
      removed outlier: 4.070A  pdb=" N   VAL B 292 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ILE B 293 " --> pdb=" O   TYR B 289 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   THR B 294 " --> pdb=" O   SER B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 324
      removed outlier: 5.039A  pdb=" N   TYR B 322 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 331
    Processing helix  chain 'B' and resid 332 through 344
      removed outlier: 4.317A  pdb=" N   GLU B 336 " --> pdb=" O   PRO B 332 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE B 337 " --> pdb=" O   GLU B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 385
    Processing helix  chain 'B' and resid 386 through 409
      removed outlier: 4.122A  pdb=" N   ALA B 390 " --> pdb=" O   ASN B 386 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLU B 391 " --> pdb=" O   LEU B 387 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ASP B 392 " --> pdb=" O   GLN B 388 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   ASP B 395 " --> pdb=" O   GLU B 391 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   VAL B 396 " --> pdb=" O   ASP B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 454
      removed outlier: 3.600A  pdb=" N   GLN B 438 " --> pdb=" O   TYR B 434 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU B 440 " --> pdb=" O   ASN B 436 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   TYR B 441 " --> pdb=" O   ASN B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 479
      Proline residue:  B 469  - end of helix
      removed outlier: 3.547A  pdb=" N   ASN B 476 " --> pdb=" O   LEU B 472 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 477 " --> pdb=" O   LYS B 473 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ALA B 478 " --> pdb=" O   GLU B 474 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LEU B 479 " --> pdb=" O   TYR B 475 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 516
      removed outlier: 3.613A  pdb=" N   ALA B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 525
      removed outlier: 4.136A  pdb=" N   TYR B 523 " --> pdb=" O   PRO B 520 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ILE B 525 " --> pdb=" O   ALA B 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 527 through 542
      removed outlier: 3.628A  pdb=" N   GLU B 536 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 561 through 569
      Proline residue:  B 566  - end of helix
      removed outlier: 3.648A  pdb=" N   GLU B 569 " --> pdb=" O   PRO B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 578
      removed outlier: 3.980A  pdb=" N   THR B 578 " --> pdb=" O   TYR B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 582
    Processing helix  chain 'B' and resid 587 through 600
      removed outlier: 3.574A  pdb=" N   TYR B 598 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ARG B 599 " --> pdb=" O   SER B 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 618
      removed outlier: 3.725A  pdb=" N   ASP B 608 " --> pdb=" O   GLN B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 643 through 647
      removed outlier: 3.826A  pdb=" N   LYS B 646 " --> pdb=" O   GLU B 643 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ASP B 647 " --> pdb=" O   PRO B 644 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 643 through 647'
    Processing helix  chain 'B' and resid 654 through 661
      removed outlier: 3.904A  pdb=" N   TYR B 657 " --> pdb=" O   TYR B 654 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LYS B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA B 660 " --> pdb=" O   TYR B 657 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TRP B 661 " --> pdb=" O   LYS B 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 669
    Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 5
      removed outlier: 5.795A  pdb=" N   PHE A  92 " --> pdb=" O   SER A 107 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   SER A 107 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LYS A  94 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY A 178 " --> pdb=" O   HIS A 206 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 15
      removed outlier: 3.502A  pdb=" N   PHE A  22 " --> pdb=" O   PHE A  14 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 89
      removed outlier: 3.665A  pdb=" N   LYS A  88 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY A 153 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 150 " --> pdb=" O   GLN A 189 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN A 189 " --> pdb=" O   VAL A 150 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 210
    Processing sheet with id=AA5, first strand: chain 'A' and resid 275 through 276
      removed outlier: 3.808A  pdb=" N   ALA A 688 " --> pdb=" O   SER A 276 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLU A 691 " --> pdb=" O   LEU A 699 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU A 699 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   SER A 698 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   VAL A 730 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   SER A 700 " --> pdb=" O   VAL A 730 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   PHE A 732 " --> pdb=" O   SER A 700 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   SER A 702 " --> pdb=" O   PHE A 732 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 296 through 298
      removed outlier: 3.541A  pdb=" N   PHE A 305 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 431 through 432
    Processing sheet with id=AA8, first strand: chain 'A' and resid 458 through 459
    Processing sheet with id=AA9, first strand: chain 'A' and resid 480 through 481
      removed outlier: 3.653A  pdb=" N   TYR A 486 " --> pdb=" O   ASP A 481 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 505 through 506
    Processing sheet with id=AB2, first strand: chain 'A' and resid 543 through 546
      removed outlier: 3.726A  pdb=" N   TYR A 551 " --> pdb=" O   VAL A 546 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 584 through 586
      removed outlier: 6.916A  pdb=" N   CYS A 585 " --> pdb=" O   ASN A 628 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 671 through 672
    Processing sheet with id=AB5, first strand: chain 'B' and resid 4 through 5
      removed outlier: 5.795A  pdb=" N   PHE B  92 " --> pdb=" O   SER B 107 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   SER B 107 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   LYS B  94 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY B 178 " --> pdb=" O   HIS B 206 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 12 through 15
      removed outlier: 3.502A  pdb=" N   PHE B  22 " --> pdb=" O   PHE B  14 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 88 through 89
      removed outlier: 3.665A  pdb=" N   LYS B  88 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLY B 153 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL B 150 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   GLN B 189 " --> pdb=" O   VAL B 150 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 209 through 210
    Processing sheet with id=AB9, first strand: chain 'B' and resid 275 through 276
      removed outlier: 3.808A  pdb=" N   ALA B 688 " --> pdb=" O   SER B 276 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLU B 691 " --> pdb=" O   LEU B 699 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   LEU B 699 " --> pdb=" O   GLU B 691 " (cutoff:3.500A)
      removed outlier: 6.756A  pdb=" N   SER B 698 " --> pdb=" O   TYR B 728 " (cutoff:3.500A)
      removed outlier: 8.327A  pdb=" N   VAL B 730 " --> pdb=" O   SER B 698 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   SER B 700 " --> pdb=" O   VAL B 730 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   PHE B 732 " --> pdb=" O   SER B 700 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   SER B 702 " --> pdb=" O   PHE B 732 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 296 through 298
      removed outlier: 3.541A  pdb=" N   PHE B 305 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 431 through 432
    Processing sheet with id=AC3, first strand: chain 'B' and resid 458 through 459
    Processing sheet with id=AC4, first strand: chain 'B' and resid 480 through 481
      removed outlier: 3.653A  pdb=" N   TYR B 486 " --> pdb=" O   ASP B 481 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 505 through 506
    Processing sheet with id=AC6, first strand: chain 'B' and resid 543 through 546
      removed outlier: 3.726A  pdb=" N   TYR B 551 " --> pdb=" O   VAL B 546 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 584 through 586
      removed outlier: 6.916A  pdb=" N   CYS B 585 " --> pdb=" O   ASN B 628 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 671 through 672

    450 hydrogen bonds defined for protein.
    1200 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: 2.36

  Time building geometry restraints manager: 1.16 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: 3612
        1.34 -     1.46: 2270
        1.46 -     1.58: 5638
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 11608
  Sorted by residual:
  bond pdb=" N   SER A 120 "
       pdb=" CA  SER A 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.25e-02 6.40e+03 1.07e+01
  bond pdb=" N   SER B 120 "
       pdb=" CA  SER B 120 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.25e-02 6.40e+03 1.07e+01
  bond pdb=" C   GLY B  62 "
       pdb=" N   PRO B  63 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.025 7.80e-03 1.64e+04 1.05e+01
  bond pdb=" C   GLY A  62 "
       pdb=" N   PRO A  63 "
    ideal  model  delta    sigma   weight residual
    1.333  1.358 -0.025 7.80e-03 1.64e+04 1.05e+01
  bond pdb=" N   VAL B  64 "
       pdb=" CA  VAL B  64 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.037 1.22e-02 6.72e+03 9.22e+00
  ... (remaining 11603 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 14853
        1.03 -     2.06: 680
        2.06 -     3.09: 149
        3.09 -     4.11: 64
        4.11 -     5.14: 20
  Bond angle restraints: 15766
  Sorted by residual:
  angle pdb=" CA  VAL A  64 "
        pdb=" C   VAL A  64 "
        pdb=" O   VAL A  64 "
      ideal   model   delta    sigma   weight residual
     121.49  116.72    4.77 1.01e+00 9.80e-01 2.23e+01
  angle pdb=" CA  VAL B  64 "
        pdb=" C   VAL B  64 "
        pdb=" O   VAL B  64 "
      ideal   model   delta    sigma   weight residual
     121.49  116.72    4.77 1.01e+00 9.80e-01 2.23e+01
  angle pdb=" CA  VAL A  64 "
        pdb=" C   VAL A  64 "
        pdb=" N   ALA A  65 "
      ideal   model   delta    sigma   weight residual
     115.87  120.51   -4.64 1.29e+00 6.01e-01 1.29e+01
  angle pdb=" CA  VAL B  64 "
        pdb=" C   VAL B  64 "
        pdb=" N   ALA B  65 "
      ideal   model   delta    sigma   weight residual
     115.87  120.51   -4.64 1.29e+00 6.01e-01 1.29e+01
  angle pdb=" CA  PRO A  63 "
        pdb=" C   PRO A  63 "
        pdb=" O   PRO A  63 "
      ideal   model   delta    sigma   weight residual
     118.29  115.27    3.02 9.60e-01 1.09e+00 9.87e+00
  ... (remaining 15761 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 6186
       17.88 -    35.76: 466
       35.76 -    53.64: 72
       53.64 -    71.53: 10
       71.53 -    89.41: 12
  Dihedral angle restraints: 6746
    sinusoidal: 2664
      harmonic: 4082
  Sorted by residual:
  dihedral pdb=" CB  GLU B 391 "
           pdb=" CG  GLU B 391 "
           pdb=" CD  GLU B 391 "
           pdb=" OE1 GLU B 391 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.41   89.41     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A 391 "
           pdb=" CG  GLU A 391 "
           pdb=" CD  GLU A 391 "
           pdb=" OE1 GLU A 391 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.39   89.39     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASP A 697 "
           pdb=" CB  ASP A 697 "
           pdb=" CG  ASP A 697 "
           pdb=" OD1 ASP A 697 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.47   54.47     1      2.00e+01 2.50e-03 1.01e+01
  ... (remaining 6743 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1338
       0.055 -    0.110: 258
       0.110 -    0.165: 32
       0.165 -    0.221: 4
       0.221 -    0.276: 2
  Chirality restraints: 1634
  Sorted by residual:
  chirality pdb=" CA  VAL B  64 "
            pdb=" N   VAL B  64 "
            pdb=" C   VAL B  64 "
            pdb=" CB  VAL B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  VAL A  64 "
            pdb=" N   VAL A  64 "
            pdb=" C   VAL A  64 "
            pdb=" CB  VAL A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  CYS A  61 "
            pdb=" N   CYS A  61 "
            pdb=" C   CYS A  61 "
            pdb=" CB  CYS A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1631 not shown)

  Planarity restraints: 2032
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B  62 "    0.023 2.00e-02 2.50e+03   4.42e-02 1.95e+01
        pdb=" C   GLY B  62 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   GLY B  62 "    0.027 2.00e-02 2.50e+03
        pdb=" N   PRO B  63 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  62 "    0.023 2.00e-02 2.50e+03   4.42e-02 1.95e+01
        pdb=" C   GLY A  62 "   -0.076 2.00e-02 2.50e+03
        pdb=" O   GLY A  62 "    0.027 2.00e-02 2.50e+03
        pdb=" N   PRO A  63 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 119 "    0.014 2.00e-02 2.50e+03   2.74e-02 7.53e+00
        pdb=" C   SER B 119 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   SER B 119 "    0.018 2.00e-02 2.50e+03
        pdb=" N   SER B 120 "    0.016 2.00e-02 2.50e+03
  ... (remaining 2029 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2428
        2.79 -     3.31: 9306
        3.31 -     3.84: 17356
        3.84 -     4.37: 20520
        4.37 -     4.90: 36564
  Nonbonded interactions: 86174
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 650 "
            pdb=" O   PRO A 652 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" NH1 ARG B 650 "
            pdb=" O   PRO B 652 "
     model   vdw
     2.258 3.120
  nonbonded pdb=" OG1 THR A 324 "
            pdb=" OE1 GLU A 335 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OG1 THR B 324 "
            pdb=" OE1 GLU B 335 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" OH  TYR A 627 "
            pdb=" O   GLU A 643 "
     model   vdw
     2.324 3.040
  ... (remaining 86169 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             4.800
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.420
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  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:8.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
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      :  0.003   0.049  11608  Z= 0.183
  Angle     :  0.562   5.142  15766  Z= 0.338
  Chirality :  0.045   0.276   1634
  Planarity :  0.004   0.044   2032
  Dihedral  : 13.184  89.408   4162
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 2.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.00 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.21), residues: 1394
  helix:  0.11 (0.26), residues: 424
  sheet:  1.06 (0.37), residues: 194
  loop : -1.67 (0.19), residues: 776

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  75 
 TYR   0.016   0.001   TYR A 657 
 PHE   0.007   0.001   PHE A 506 
 TRP   0.017   0.001   TRP B 439 
 HIS   0.002   0.001   HIS A  27 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.18 (11608)
  covalent geometry    : angle       0.56175 /  0.34 (15766)
  hydrogen bonds       : bond        0.29863 / 19.47 (  450)
  hydrogen bonds       : angle       6.90579 /  4.96 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 76
  average time/residue: 0.7152
  time to fit residues: 58.1690
Evaluate side-chains
  51 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55]
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.0980
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    4.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   overall best weight:    3.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.055355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.043799 restraints weight = 41438.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 3.39
r_work: 0.2755 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9063
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  11608  Z= 0.210
  Angle     :  0.591   5.237  15766  Z= 0.332
  Chirality :  0.047   0.157   1634
  Planarity :  0.005   0.056   2032
  Dihedral  :  4.801  17.097   1558
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  3.97 %
    Favored  : 95.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.44 (0.22), residues: 1394
  helix:  0.71 (0.26), residues: 458
  sheet:  1.11 (0.32), residues: 256
  loop : -1.62 (0.21), residues: 680

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  91 
 TYR   0.022   0.002   TYR A 138 
 PHE   0.012   0.001   PHE A  29 
 TRP   0.015   0.001   TRP B 439 
 HIS   0.004   0.001   HIS A 621 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00488 /  0.21 (11608)
  covalent geometry    : angle       0.59124 /  0.33 (15766)
  hydrogen bonds       : bond        0.06910 /  4.55 (  450)
  hydrogen bonds       : angle       4.83595 /  3.40 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.383 
Fit side-chains
  outliers start: 10
  outliers final: 1
  residues processed: 56
  average time/residue: 0.6620
  time to fit residues: 39.9353
Evaluate side-chains
  51 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 50
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [131, 24, 95, 64, 6, 21, 70, 34, 112, 75, 18]
   chunk 131 optimal weight:    7.9990
   chunk 24 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 64 optimal weight:    3.9990
   chunk 6 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 70 optimal weight:   10.0000
   chunk 34 optimal weight:    5.9990
   chunk 112 optimal weight:    5.9990
   chunk 75 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.054256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2882 r_free = 0.2882 target = 0.042733 restraints weight = 41574.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.2853 rms_B_bonded: 3.40
r_work: 0.2727 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9093
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.027  11608  Z= 0.230
  Angle     :  0.594   6.042  15766  Z= 0.331
  Chirality :  0.047   0.168   1634
  Planarity :  0.005   0.050   2032
  Dihedral  :  4.893  18.035   1558
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  5.41 %
    Favored  : 93.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.22), residues: 1394
  helix:  0.85 (0.26), residues: 458
  sheet:  1.12 (0.33), residues: 242
  loop : -1.64 (0.21), residues: 694

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  91 
 TYR   0.021   0.002   TYR A 657 
 PHE   0.010   0.002   PHE B  29 
 TRP   0.015   0.001   TRP B 439 
 HIS   0.004   0.001   HIS B 206 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.23 (11608)
  covalent geometry    : angle       0.59358 /  0.33 (15766)
  hydrogen bonds       : bond        0.06896 /  4.54 (  450)
  hydrogen bonds       : angle       4.69901 /  3.27 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.422 
Fit side-chains
REVERT: A  570 MET cc_start: 0.7021 (OUTLIER) cc_final: 0.6772 (ptt)
REVERT: B  570 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6772 (ptt)
  outliers start: 14
  outliers final: 4
  residues processed: 57
  average time/residue: 0.6002
  time to fit residues: 37.2103
Evaluate side-chains
  54 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  574 VAL
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [93, 85, 82, 48, 60, 76, 71, 137, 94, 12, 129]
   chunk 93 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 82 optimal weight:    0.0370
   chunk 48 optimal weight:    6.9990
   chunk 60 optimal weight:   10.0000
   chunk 76 optimal weight:    0.9990
   chunk 71 optimal weight:    4.9990
   chunk 137 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9980
   chunk 12 optimal weight:    6.9990
   chunk 129 optimal weight:   10.0000
   overall best weight:    1.6064

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.056216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2945 r_free = 0.2945 target = 0.044764 restraints weight = 41451.579|
|-----------------------------------------------------------------------------|
r_work (start): 0.2915 rms_B_bonded: 3.44
r_work: 0.2792 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9039
moved from start:          0.2212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  11608  Z= 0.117
  Angle     :  0.487   6.165  15766  Z= 0.269
  Chirality :  0.044   0.142   1634
  Planarity :  0.004   0.037   2032
  Dihedral  :  4.454  17.350   1558
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 2.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.26 %
    Favored  : 91.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.22), residues: 1394
  helix:  1.27 (0.27), residues: 446
  sheet:  1.16 (0.32), residues: 242
  loop : -1.53 (0.21), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  91 
 TYR   0.017   0.001   TYR A 138 
 PHE   0.006   0.001   PHE A  29 
 TRP   0.014   0.001   TRP B 439 
 HIS   0.003   0.001   HIS B 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 (11608)
  covalent geometry    : angle       0.48746 /  0.27 (15766)
  hydrogen bonds       : bond        0.04481 /  2.94 (  450)
  hydrogen bonds       : angle       4.28724 /  3.00 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A  428 MET cc_start: 0.9100 (mmm) cc_final: 0.8879 (mtm)
REVERT: B  428 MET cc_start: 0.9103 (mmm) cc_final: 0.8887 (mtm)
  outliers start: 10
  outliers final: 2
  residues processed: 57
  average time/residue: 0.5518
  time to fit residues: 34.4553
Evaluate side-chains
  48 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [86, 104, 60, 19, 67, 8, 12, 114, 87, 110, 43]
   chunk 86 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 19 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0030
   chunk 12 optimal weight:    7.9990
   chunk 114 optimal weight:    3.9990
   chunk 87 optimal weight:    4.9990
   chunk 110 optimal weight:    8.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    3.9998

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.054229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.042509 restraints weight = 42338.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 3.50
r_work: 0.2721 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9100
moved from start:          0.2269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.028  11608  Z= 0.240
  Angle     :  0.593   6.746  15766  Z= 0.327
  Chirality :  0.047   0.173   1634
  Planarity :  0.004   0.044   2032
  Dihedral  :  4.822  20.508   1558
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 2.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  7.77 %
    Favored  : 91.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.35 (0.22), residues: 1394
  helix:  0.97 (0.26), residues: 458
  sheet:  0.95 (0.32), residues: 254
  loop : -1.61 (0.22), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.022   0.002   TYR A 138 
 PHE   0.011   0.002   PHE A  32 
 TRP   0.013   0.001   TRP B 439 
 HIS   0.012   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00562 /  0.24 (11608)
  covalent geometry    : angle       0.59277 /  0.33 (15766)
  hydrogen bonds       : bond        0.06640 /  4.38 (  450)
  hydrogen bonds       : angle       4.59986 /  3.20 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 52
  time to evaluate  : 0.321 
Fit side-chains
  outliers start: 12
  outliers final: 2
  residues processed: 58
  average time/residue: 0.5419
  time to fit residues: 34.5388
Evaluate side-chains
  52 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [24, 67, 52, 119, 66, 134, 55, 129, 13, 18, 58]
   chunk 24 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0870
   chunk 119 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 134 optimal weight:    3.9990
   chunk 55 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   chunk 13 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    2.5764

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.055147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.043501 restraints weight = 41771.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 3.40
r_work: 0.2750 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9075
moved from start:          0.2337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  11608  Z= 0.164
  Angle     :  0.530   7.211  15766  Z= 0.294
  Chirality :  0.045   0.163   1634
  Planarity :  0.004   0.039   2032
  Dihedral  :  4.644  19.926   1558
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  8.70 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.26 (0.22), residues: 1394
  helix:  1.08 (0.26), residues: 460
  sheet:  1.04 (0.32), residues: 242
  loop : -1.57 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  91 
 TYR   0.019   0.001   TYR A 138 
 PHE   0.008   0.001   PHE A  32 
 TRP   0.014   0.001   TRP A 439 
 HIS   0.010   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00379 /  0.16 (11608)
  covalent geometry    : angle       0.53013 /  0.29 (15766)
  hydrogen bonds       : bond        0.05377 /  3.54 (  450)
  hydrogen bonds       : angle       4.39509 /  3.06 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 50
  time to evaluate  : 0.450 
Fit side-chains
  outliers start: 10
  outliers final: 4
  residues processed: 56
  average time/residue: 0.5456
  time to fit residues: 33.6440
Evaluate side-chains
  52 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [26, 5, 54, 108, 133, 132, 48, 130, 109, 66, 83]
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0370
   chunk 54 optimal weight:    6.9990
   chunk 108 optimal weight:    9.9990
   chunk 133 optimal weight:    7.9990
   chunk 132 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 130 optimal weight:    8.9990
   chunk 109 optimal weight:    7.9990
   chunk 66 optimal weight:   10.0000
   chunk 83 optimal weight:    3.9990
   overall best weight:    3.2064

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.054785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.043135 restraints weight = 41737.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 3.41
r_work: 0.2738 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9087
moved from start:          0.2357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  11608  Z= 0.196
  Angle     :  0.558   7.714  15766  Z= 0.308
  Chirality :  0.046   0.165   1634
  Planarity :  0.004   0.041   2032
  Dihedral  :  4.715  18.535   1558
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  8.78 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.22), residues: 1394
  helix:  1.02 (0.26), residues: 460
  sheet:  1.00 (0.32), residues: 242
  loop : -1.58 (0.22), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.021   0.001   TYR A 138 
 PHE   0.011   0.001   PHE A  32 
 TRP   0.014   0.001   TRP B 439 
 HIS   0.009   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.20 (11608)
  covalent geometry    : angle       0.55832 /  0.31 (15766)
  hydrogen bonds       : bond        0.05919 /  3.90 (  450)
  hydrogen bonds       : angle       4.46203 /  3.10 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 50
  time to evaluate  : 0.480 
Fit side-chains
  outliers start: 12
  outliers final: 8
  residues processed: 58
  average time/residue: 0.5334
  time to fit residues: 33.9572
Evaluate side-chains
  56 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 THR
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  272 HIS
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue   50 THR
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  272 HIS
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [67, 78, 2, 73, 19, 95, 77, 51, 31, 123, 90]
   chunk 67 optimal weight:    4.9990
   chunk 78 optimal weight:    0.3980
   chunk 2 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 19 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 123 optimal weight:    0.8980
   chunk 90 optimal weight:    4.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  31 ASN
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  31 ASN
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.056741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.045263 restraints weight = 41034.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.34
r_work: 0.2803 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9031
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  11608  Z= 0.105
  Angle     :  0.483   8.191  15766  Z= 0.262
  Chirality :  0.044   0.137   1634
  Planarity :  0.004   0.034   2032
  Dihedral  :  4.318  18.566   1558
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 2.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  :  9.12 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.00 (0.23), residues: 1394
  helix:  1.32 (0.27), residues: 458
  sheet:  0.86 (0.31), residues: 280
  loop : -1.40 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.015   0.001   TYR A 138 
 PHE   0.006   0.001   PHE B 210 
 TRP   0.014   0.001   TRP B 439 
 HIS   0.007   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.11 (11608)
  covalent geometry    : angle       0.48331 /  0.26 (15766)
  hydrogen bonds       : bond        0.03937 /  2.59 (  450)
  hydrogen bonds       : angle       4.12779 /  2.88 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 0.443 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 52
  average time/residue: 0.5805
  time to fit residues: 32.8264
Evaluate side-chains
  49 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 46
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 HIS
Chi-restraints excluded: chain B residue  272 HIS
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [97, 112, 1, 33, 71, 2, 22, 14, 83, 9, 61]
   chunk 97 optimal weight:    6.9990
   chunk 112 optimal weight:    8.9990
   chunk 1 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 83 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   overall best weight:    2.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.055567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.044028 restraints weight = 40992.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 3.36
r_work: 0.2766 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9064
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11608  Z= 0.151
  Angle     :  0.529   9.475  15766  Z= 0.285
  Chirality :  0.045   0.153   1634
  Planarity :  0.004   0.036   2032
  Dihedral  :  4.449  17.878   1558
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  9.21 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.23), residues: 1394
  helix:  1.28 (0.27), residues: 458
  sheet:  0.82 (0.31), residues: 280
  loop : -1.43 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.019   0.001   TYR A 138 
 PHE   0.008   0.001   PHE A  32 
 TRP   0.012   0.001   TRP B 439 
 HIS   0.008   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.15 (11608)
  covalent geometry    : angle       0.52904 /  0.29 (15766)
  hydrogen bonds       : bond        0.05040 /  3.32 (  450)
  hydrogen bonds       : angle       4.24807 /  2.96 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.298 
Fit side-chains
  outliers start: 10
  outliers final: 6
  residues processed: 56
  average time/residue: 0.5526
  time to fit residues: 33.8700
Evaluate side-chains
  54 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  272 HIS
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  272 HIS
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [69, 80, 31, 3, 53, 55, 23, 32, 90, 112, 11]
   chunk 69 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 32 optimal weight:    0.2980
   chunk 90 optimal weight:    4.9990
   chunk 112 optimal weight:    7.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.3984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.056418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.044993 restraints weight = 41127.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.2920 rms_B_bonded: 3.37
r_work: 0.2800 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9034
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  11608  Z= 0.109
  Angle     :  0.482   9.390  15766  Z= 0.263
  Chirality :  0.044   0.139   1634
  Planarity :  0.004   0.033   2032
  Dihedral  :  4.268  18.068   1558
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  :  9.38 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.23), residues: 1394
  helix:  1.38 (0.27), residues: 458
  sheet:  0.90 (0.31), residues: 280
  loop : -1.35 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.016   0.001   TYR B 138 
 PHE   0.006   0.001   PHE B 210 
 TRP   0.013   0.001   TRP B 439 
 HIS   0.007   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 (11608)
  covalent geometry    : angle       0.48229 /  0.26 (15766)
  hydrogen bonds       : bond        0.04079 /  2.68 (  450)
  hydrogen bonds       : angle       4.09081 /  2.86 ( 1200)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.423 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 52
  average time/residue: 0.5782
  time to fit residues: 32.8407
Evaluate side-chains
  52 residues out of total 1184 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 46
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 VAL
Chi-restraints excluded: chain A residue  272 HIS
Chi-restraints excluded: chain A residue  593 MET
Chi-restraints excluded: chain B residue  197 VAL
Chi-restraints excluded: chain B residue  272 HIS
Chi-restraints excluded: chain B residue  593 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks: [130, 111, 129, 114, 11, 22, 96, 98, 10, 55, 87]
   chunk 130 optimal weight:    9.9990
   chunk 111 optimal weight:    6.9990
   chunk 129 optimal weight:    8.9990
   chunk 114 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 96 optimal weight:    0.9980
   chunk 98 optimal weight:    0.0870
   chunk 10 optimal weight:    4.9990
   chunk 55 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   overall best weight:    1.3962

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.056464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.044986 restraints weight = 41505.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.2922 rms_B_bonded: 3.41
r_work: 0.2802 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9032
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11608  Z= 0.109
  Angle     :  0.492   9.450  15766  Z= 0.263
  Chirality :  0.043   0.140   1634
  Planarity :  0.004   0.033   2032
  Dihedral  :  4.205  17.718   1558
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  9.54 %
    Favored  : 89.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 12.90 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.23), residues: 1394
  helix:  1.42 (0.27), residues: 458
  sheet:  0.89 (0.31), residues: 280
  loop : -1.29 (0.23), residues: 656

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  91 
 TYR   0.016   0.001   TYR A 138 
 PHE   0.006   0.001   PHE B 210 
 TRP   0.012   0.001   TRP A 439 
 HIS   0.007   0.001   HIS A 636 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.11 (11608)
  covalent geometry    : angle       0.49220 /  0.26 (15766)
  hydrogen bonds       : bond        0.04094 /  2.69 (  450)
  hydrogen bonds       : angle       4.05283 /  2.83 ( 1200)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3654.58 seconds
wall clock time: 63 minutes 19.45 seconds (3799.45 seconds total)