Starting phenix.real_space_refine
on Wed Mar  4 05:54:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6p46_20244/03_2026/6p46_20244.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6p46_20244/03_2026/6p46_20244.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6p46_20244/03_2026/6p46_20244.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6p46_20244/03_2026/6p46_20244.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6p46_20244/03_2026/6p46_20244.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6p46_20244/03_2026/6p46_20244.cif"
  }
  resolution = 3.5
  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=   0.006
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
     Ca      2      9.91       5
     S      78      5.16       5
     C    7508      2.51       5
     N    1824      2.21       5
     O    1966      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11378
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 690, 5688
          Classifications: {'peptide': 690}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 659}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 5.04, per 1000 atoms: 0.44
  Number of scatterers: 11378
  At special positions: 0
  Unit cell: (81.543, 128.139, 111.195, 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)
     Ca      2     19.99
     S      78     16.00
     O    1966      8.00
     N    1824      7.00
     C    7508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 338 " - pdb=" SG  CYS A 365 " distance=1.56
    Simple disulfide: pdb=" SG  CYS A 349 " - pdb=" SG  CYS A 807 " distance=1.89
    Simple disulfide: pdb=" SG  CYS A 596 " - pdb=" SG  CYS A 601 " distance=1.32
    Simple disulfide: pdb=" SG  CYS B 338 " - pdb=" SG  CYS B 365 " distance=1.56
    Simple disulfide: pdb=" SG  CYS B 349 " - pdb=" SG  CYS B 807 " distance=1.89
    Simple disulfide: pdb=" SG  CYS B 596 " - pdb=" SG  CYS B 601 " distance=1.32

  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: 0.95
  Conformation dependent library (CDL) restraints added in 577.5 milliseconds
  

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2624

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      58.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 97
    Processing helix  chain 'A' and resid 131 through 140
      removed outlier: 3.911A  pdb=" N   THR A 137 " --> pdb=" O   GLU A 133 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   TYR A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 220
      removed outlier: 3.718A  pdb=" N   VAL A 213 " --> pdb=" O   ARG A 209 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   TYR A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG A 219 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   VAL A 220 " --> pdb=" O   ILE A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 237
      removed outlier: 4.608A  pdb=" N   ARG A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU A 236 " --> pdb=" O   GLY A 232 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   VAL A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 237'
    Processing helix  chain 'A' and resid 266 through 273
      removed outlier: 3.534A  pdb=" N   ARG A 271 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.687A  pdb=" N   ARG A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 312
      removed outlier: 3.906A  pdb=" N   TYR A 299 " --> pdb=" O   LYS A 295 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR A 306 " --> pdb=" O   TRP A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 327
      removed outlier: 4.101A  pdb=" N   PHE A 321 " --> pdb=" O   GLY A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 369
      removed outlier: 3.852A  pdb=" N   CYS A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   GLU A 366 " --> pdb=" O   ASN A 362 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   SER A 367 " --> pdb=" O   ILE A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 408
      removed outlier: 4.134A  pdb=" N   VAL A 384 " --> pdb=" O   LEU A 380 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   VAL A 388 " --> pdb=" O   VAL A 384 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   GLU A 395 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 489
      removed outlier: 3.683A  pdb=" N   PHE A 461 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE A 462 " --> pdb=" O   SER A 458 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   TRP A 463 " --> pdb=" O   ALA A 459 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 464 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   VAL A 471 " --> pdb=" O   ILE A 467 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   ILE A 472 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER A 486 " --> pdb=" O   PHE A 482 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR A 487 " --> pdb=" O   ILE A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 504 through 539
      removed outlier: 3.914A  pdb=" N   SER A 510 " --> pdb=" O   GLN A 506 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   SER A 514 " --> pdb=" O   SER A 510 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR A 526 " --> pdb=" O   MET A 522 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 532 " --> pdb=" O   TYR A 528 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE A 533 " --> pdb=" O   GLU A 529 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE A 538 " --> pdb=" O   MET A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 545 through 572
      removed outlier: 3.917A  pdb=" N   MET A 553 " --> pdb=" O   ASN A 549 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU A 557 " --> pdb=" O   MET A 553 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A 561 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER A 565 " --> pdb=" O   VAL A 561 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   SER A 566 " --> pdb=" O   ASN A 562 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   CYS A 567 " --> pdb=" O   TYR A 563 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE A 572 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
      removed outlier: 3.618A  pdb=" N   LEU A 588 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 614
      removed outlier: 3.661A  pdb=" N   GLN A 608 " --> pdb=" O   GLU A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 638
      removed outlier: 3.843A  pdb=" N   ASN A 621 " --> pdb=" O   ALA A 617 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   VAL A 625 " --> pdb=" O   ASN A 621 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A 627 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      Proline residue:  A 628  - end of helix
      removed outlier: 3.659A  pdb=" N   GLY A 635 " --> pdb=" O   MET A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 656
      removed outlier: 3.508A  pdb=" N   GLN A 652 " --> pdb=" O   PRO A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 679
      removed outlier: 4.205A  pdb=" N   MET A 671 " --> pdb=" O   GLU A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.972A  pdb=" N   ARG A 701 " --> pdb=" O   ILE A 697 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA A 704 " --> pdb=" O   ILE A 700 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU A 707 " --> pdb=" O   ASP A 703 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 748
      removed outlier: 3.767A  pdb=" N   ILE A 734 " --> pdb=" O   GLN A 730 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   VAL A 738 " --> pdb=" O   ILE A 734 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 748 " --> pdb=" O   ILE A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 760
      removed outlier: 3.759A  pdb=" N   TYR A 756 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 825 through 856
      removed outlier: 3.788A  pdb=" N   SER A 854 " --> pdb=" O   LYS A 850 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 866
    Processing helix  chain 'A' and resid 867 through 871
    Processing helix  chain 'B' and resid 90 through 97
    Processing helix  chain 'B' and resid 131 through 140
      removed outlier: 3.911A  pdb=" N   THR B 137 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   TYR B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 208 through 220
      removed outlier: 3.717A  pdb=" N   VAL B 213 " --> pdb=" O   ARG B 209 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   TYR B 214 " --> pdb=" O   SER B 210 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   ARG B 219 " --> pdb=" O   PHE B 215 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL B 220 " --> pdb=" O   ILE B 216 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 237
      removed outlier: 4.608A  pdb=" N   ARG B 235 " --> pdb=" O   PHE B 231 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   LEU B 236 " --> pdb=" O   GLY B 232 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 231 through 237'
    Processing helix  chain 'B' and resid 266 through 273
      removed outlier: 3.533A  pdb=" N   ARG B 271 " --> pdb=" O   TYR B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 290
      removed outlier: 3.687A  pdb=" N   ARG B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 312
      removed outlier: 3.905A  pdb=" N   TYR B 299 " --> pdb=" O   LYS B 295 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   TYR B 306 " --> pdb=" O   TRP B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 314 through 327
      removed outlier: 4.101A  pdb=" N   PHE B 321 " --> pdb=" O   GLY B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 369
      removed outlier: 3.852A  pdb=" N   CYS B 365 " --> pdb=" O   LEU B 361 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   GLU B 366 " --> pdb=" O   ASN B 362 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   SER B 367 " --> pdb=" O   ILE B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 408
      removed outlier: 4.133A  pdb=" N   VAL B 384 " --> pdb=" O   LEU B 380 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL B 388 " --> pdb=" O   VAL B 384 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR B 391 " --> pdb=" O   GLY B 387 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLU B 395 " --> pdb=" O   THR B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 489
      removed outlier: 3.682A  pdb=" N   PHE B 461 " --> pdb=" O   ALA B 457 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   PHE B 462 " --> pdb=" O   SER B 458 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   TRP B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE B 464 " --> pdb=" O   VAL B 460 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   VAL B 471 " --> pdb=" O   ILE B 467 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   ILE B 472 " --> pdb=" O   ILE B 468 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   VAL B 484 " --> pdb=" O   SER B 480 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   SER B 486 " --> pdb=" O   PHE B 482 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   THR B 487 " --> pdb=" O   ILE B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 504 through 539
      removed outlier: 3.914A  pdb=" N   SER B 510 " --> pdb=" O   GLN B 506 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   SER B 514 " --> pdb=" O   SER B 510 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   THR B 526 " --> pdb=" O   MET B 522 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA B 532 " --> pdb=" O   TYR B 528 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ILE B 533 " --> pdb=" O   GLU B 529 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   PHE B 538 " --> pdb=" O   MET B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 545 through 572
      removed outlier: 3.916A  pdb=" N   MET B 553 " --> pdb=" O   ASN B 549 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   LYS B 554 " --> pdb=" O   SER B 550 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   LEU B 557 " --> pdb=" O   MET B 553 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL B 561 " --> pdb=" O   LEU B 557 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   SER B 565 " --> pdb=" O   VAL B 561 " (cutoff:3.500A)
      removed outlier: 4.679A  pdb=" N   SER B 566 " --> pdb=" O   ASN B 562 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   CYS B 567 " --> pdb=" O   TYR B 563 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   PHE B 572 " --> pdb=" O   PHE B 568 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
      removed outlier: 3.619A  pdb=" N   LEU B 588 " --> pdb=" O   VAL B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 614
      removed outlier: 3.662A  pdb=" N   GLN B 608 " --> pdb=" O   GLU B 604 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 614 through 624
      removed outlier: 3.844A  pdb=" N   ASN B 621 " --> pdb=" O   ALA B 617 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 626 through 638
      removed outlier: 3.658A  pdb=" N   GLY B 635 " --> pdb=" O   MET B 631 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 648 through 656
      removed outlier: 3.508A  pdb=" N   GLN B 652 " --> pdb=" O   PRO B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 664 through 679
      removed outlier: 4.206A  pdb=" N   MET B 671 " --> pdb=" O   GLU B 667 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 3.972A  pdb=" N   ARG B 701 " --> pdb=" O   ILE B 697 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ALA B 704 " --> pdb=" O   ILE B 700 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   LEU B 707 " --> pdb=" O   ASP B 703 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 725 through 748
      removed outlier: 3.766A  pdb=" N   ILE B 734 " --> pdb=" O   GLN B 730 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   VAL B 738 " --> pdb=" O   ILE B 734 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER B 748 " --> pdb=" O   ILE B 744 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 750 through 760
      removed outlier: 3.759A  pdb=" N   TYR B 756 " --> pdb=" O   PRO B 752 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 825 through 856
      removed outlier: 3.788A  pdb=" N   SER B 854 " --> pdb=" O   LYS B 850 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 861 through 866
    Processing helix  chain 'B' and resid 867 through 871

    494 hydrogen bonds defined for protein.
    1464 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.32 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3090
        1.33 -     1.45: 2506
        1.45 -     1.57: 5970
        1.57 -     1.69: 0
        1.69 -     1.81: 120
  Bond restraints: 11686
  Sorted by residual:
  bond pdb=" CA  ASP A 375 "
       pdb=" C   ASP A 375 "
    ideal  model  delta    sigma   weight residual
    1.527  1.567 -0.041 1.21e-02 6.83e+03 1.14e+01
  bond pdb=" CA  ASP B 375 "
       pdb=" C   ASP B 375 "
    ideal  model  delta    sigma   weight residual
    1.527  1.567 -0.041 1.21e-02 6.83e+03 1.13e+01
  bond pdb=" CA  ALA B 571 "
       pdb=" C   ALA B 571 "
    ideal  model  delta    sigma   weight residual
    1.523  1.566 -0.043 1.34e-02 5.57e+03 1.01e+01
  bond pdb=" CA  ALA A 571 "
       pdb=" C   ALA A 571 "
    ideal  model  delta    sigma   weight residual
    1.523  1.565 -0.042 1.34e-02 5.57e+03 9.92e+00
  bond pdb=" N   SER A 376 "
       pdb=" CA  SER A 376 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.31e+00
  ... (remaining 11681 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 15203
        3.25 -     6.49: 510
        6.49 -     9.74: 93
        9.74 -    12.99: 24
       12.99 -    16.23: 2
  Bond angle restraints: 15832
  Sorted by residual:
  angle pdb=" N   ALA B 683 "
        pdb=" CA  ALA B 683 "
        pdb=" C   ALA B 683 "
      ideal   model   delta    sigma   weight residual
     112.93   96.70   16.23 1.33e+00 5.65e-01 1.49e+02
  angle pdb=" N   ALA A 683 "
        pdb=" CA  ALA A 683 "
        pdb=" C   ALA A 683 "
      ideal   model   delta    sigma   weight residual
     112.93   96.73   16.20 1.33e+00 5.65e-01 1.48e+02
  angle pdb=" N   LYS B 335 "
        pdb=" CA  LYS B 335 "
        pdb=" C   LYS B 335 "
      ideal   model   delta    sigma   weight residual
     112.68  100.25   12.43 1.33e+00 5.65e-01 8.73e+01
  angle pdb=" N   LYS A 335 "
        pdb=" CA  LYS A 335 "
        pdb=" C   LYS A 335 "
      ideal   model   delta    sigma   weight residual
     112.68  100.28   12.40 1.33e+00 5.65e-01 8.69e+01
  angle pdb=" N   ILE B 622 "
        pdb=" CA  ILE B 622 "
        pdb=" C   ILE B 622 "
      ideal   model   delta    sigma   weight residual
     111.90  104.77    7.13 8.10e-01 1.52e+00 7.75e+01
  ... (remaining 15827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 5906
       17.09 -    34.17: 744
       34.17 -    51.26: 168
       51.26 -    68.35: 42
       68.35 -    85.43: 16
  Dihedral angle restraints: 6876
    sinusoidal: 2800
      harmonic: 4076
  Sorted by residual:
  dihedral pdb=" CB  CYS A 596 "
           pdb=" SG  CYS A 596 "
           pdb=" SG  CYS A 601 "
           pdb=" CB  CYS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.23   73.23     1      1.00e+01 1.00e-02 6.83e+01
  dihedral pdb=" CB  CYS B 596 "
           pdb=" SG  CYS B 596 "
           pdb=" SG  CYS B 601 "
           pdb=" CB  CYS B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.23   73.23     1      1.00e+01 1.00e-02 6.83e+01
  dihedral pdb=" CB  CYS A 338 "
           pdb=" SG  CYS A 338 "
           pdb=" SG  CYS A 365 "
           pdb=" CB  CYS A 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.09   55.91     1      1.00e+01 1.00e-02 4.22e+01
  ... (remaining 6873 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.100: 1489
       0.100 -    0.200: 189
       0.200 -    0.301: 32
       0.301 -    0.401: 24
       0.401 -    0.501: 4
  Chirality restraints: 1738
  Sorted by residual:
  chirality pdb=" CA  PHE A 577 "
            pdb=" N   PHE A 577 "
            pdb=" C   PHE A 577 "
            pdb=" CB  PHE A 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.27e+00
  chirality pdb=" CA  PHE B 577 "
            pdb=" N   PHE B 577 "
            pdb=" C   PHE B 577 "
            pdb=" CB  PHE B 577 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.21e+00
  chirality pdb=" CA  ASN A 330 "
            pdb=" N   ASN A 330 "
            pdb=" C   ASN A 330 "
            pdb=" CB  ASN A 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.83e+00
  ... (remaining 1735 not shown)

  Planarity restraints: 1944
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 599 "    0.022 2.00e-02 2.50e+03   4.57e-02 2.09e+01
        pdb=" C   GLY A 599 "   -0.079 2.00e-02 2.50e+03
        pdb=" O   GLY A 599 "    0.030 2.00e-02 2.50e+03
        pdb=" N   GLY A 600 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 599 "   -0.022 2.00e-02 2.50e+03   4.55e-02 2.07e+01
        pdb=" C   GLY B 599 "    0.079 2.00e-02 2.50e+03
        pdb=" O   GLY B 599 "   -0.030 2.00e-02 2.50e+03
        pdb=" N   GLY B 600 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 570 "   -0.022 2.00e-02 2.50e+03   4.42e-02 1.95e+01
        pdb=" C   ILE A 570 "    0.076 2.00e-02 2.50e+03
        pdb=" O   ILE A 570 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   ALA A 571 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1941 not shown)

  Histogram of nonbonded interaction distances:
        1.80 -     2.42: 80
        2.42 -     3.04: 6753
        3.04 -     3.66: 17729
        3.66 -     4.28: 25929
        4.28 -     4.90: 41569
  Nonbonded interactions: 92060
  Sorted by model distance:
  nonbonded pdb=" C   GLU B 594 "
            pdb=" OE1 GLU B 595 "
     model   vdw
     1.800 3.270
  nonbonded pdb=" C   GLU A 594 "
            pdb=" OE1 GLU A 595 "
     model   vdw
     1.800 3.270
  nonbonded pdb=" OE1 GLU A 624 "
            pdb="CA    CA A1001 "
     model   vdw
     2.034 2.510
  nonbonded pdb=" OE1 GLU B 624 "
            pdb="CA    CA B1001 "
     model   vdw
     2.035 2.510
  nonbonded pdb=" N   GLU B 595 "
            pdb=" OE1 GLU B 595 "
     model   vdw
     2.079 3.120
  ... (remaining 92055 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 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:             1.400
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.920
  Find NCS groups from input model:        0.080
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
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      :  0.015   0.714  11692  Z= 0.719
  Angle     :  1.551  37.722  15844  Z= 0.930
  Chirality :  0.084   0.501   1738
  Planarity :  0.010   0.101   1944
  Dihedral  : 16.158  85.434   4234
  Min Nonbonded Distance : 1.800

Molprobity Statistics.
  All-atom Clashscore : 25.86
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  :  6.99 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 11.85 %
    Favored  : 84.44 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.45 (0.16), residues: 1344
  helix: -3.36 (0.14), residues: 724
  sheet:  None (None), residues: 0
  loop : -3.94 (0.18), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 266 
 TYR   0.034   0.003   TYR A 809 
 PHE   0.025   0.003   PHE B 760 
 TRP   0.024   0.003   TRP A 397 
 HIS   0.005   0.002   HIS A 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00941 (11686)
  covalent geometry    : angle       1.43371 (15832)
  SS BOND              : bond        0.50192 (    6)
  SS BOND              : angle      21.57957 (   12)
  hydrogen bonds       : bond        0.31387 (  494)
  hydrogen bonds       : angle      12.03939 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 280
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  523 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8792 (mp)
REVERT: A  534 MET cc_start: 0.7302 (mmt) cc_final: 0.7088 (mmt)
REVERT: A  546 ASP cc_start: 0.7978 (t0) cc_final: 0.7654 (t70)
REVERT: A  618 ILE cc_start: 0.9052 (mm) cc_final: 0.8779 (mt)
REVERT: B  224 VAL cc_start: 0.1020 (OUTLIER) cc_final: 0.0750 (t)
REVERT: B  305 TYR cc_start: 0.7810 (t80) cc_final: 0.7366 (t80)
REVERT: B  348 MET cc_start: 0.7175 (mpp) cc_final: 0.6651 (mmm)
REVERT: B  523 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8735 (mp)
REVERT: B  546 ASP cc_start: 0.7936 (t0) cc_final: 0.7646 (t0)
REVERT: B  555 MET cc_start: 0.7960 (tpp) cc_final: 0.7733 (tpt)
REVERT: B  855 TYR cc_start: 0.7063 (t80) cc_final: 0.6777 (t80)
  outliers start: 46
  outliers final: 25
  residues processed: 323
  average time/residue: 0.1062
  time to fit residues: 49.1778
Evaluate side-chains
  230 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 202
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  217 LEU
Chi-restraints excluded: chain A residue  349 CYS
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  464 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  475 ILE
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  488 THR
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  595 GLU
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  866 SER
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  464 ILE
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain B residue  475 ILE
Chi-restraints excluded: chain B residue  481 VAL
Chi-restraints excluded: chain B residue  488 THR
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  691 LEU
Chi-restraints excluded: chain B residue  747 THR
Chi-restraints excluded: chain B residue  866 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 130 optimal weight:    0.3980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 234 ASN
A 283 GLN
A 328 GLN
A 544 GLN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 710 GLN
A 740 ASN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 ASN
B 275 HIS
B 283 GLN
B 328 GLN
B 544 GLN
** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 674 GLN
B 696 ASN
B 710 GLN
B 740 ASN
** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 844 HIS

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.237887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.197603 restraints weight = 15507.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.199632 restraints weight = 10633.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.201294 restraints weight = 8068.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.201254 restraints weight = 6227.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.201571 restraints weight = 6431.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.4382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6890
moved from start:          0.2562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082  11692  Z= 0.176
  Angle     :  0.783  11.327  15844  Z= 0.413
  Chirality :  0.045   0.178   1738
  Planarity :  0.007   0.074   1944
  Dihedral  :  8.497  58.355   1560
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 17.18 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -4.41 (0.18), residues: 1344
  helix: -2.30 (0.15), residues: 776
  sheet: -5.10 (0.98), residues: 20
  loop : -3.72 (0.20), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 209 
 TYR   0.025   0.002   TYR A 406 
 PHE   0.017   0.002   PHE B 851 
 TRP   0.023   0.002   TRP A 397 
 HIS   0.004   0.001   HIS A 249 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (11686)
  covalent geometry    : angle       0.78271 (15832)
  SS BOND              : bond        0.01045 (    6)
  SS BOND              : angle       0.77477 (   12)
  hydrogen bonds       : bond        0.06254 (  494)
  hydrogen bonds       : angle       6.47256 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 237
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  347 LEU cc_start: 0.6176 (tt) cc_final: 0.5264 (mp)
REVERT: A  392 LEU cc_start: 0.8120 (mt) cc_final: 0.7785 (mt)
REVERT: A  523 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.8961 (mp)
REVERT: A  618 ILE cc_start: 0.9055 (mm) cc_final: 0.8719 (mt)
REVERT: A  659 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6447 (ptp)
REVERT: A  705 TRP cc_start: 0.7947 (t60) cc_final: 0.7652 (t60)
REVERT: A  773 MET cc_start: 0.7297 (mmm) cc_final: 0.6614 (tpp)
REVERT: B  305 TYR cc_start: 0.7737 (t80) cc_final: 0.7318 (t80)
REVERT: B  555 MET cc_start: 0.7891 (tpp) cc_final: 0.7683 (tpt)
REVERT: B  700 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7984 (tt)
REVERT: B  773 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4618 (mtp)
REVERT: B  855 TYR cc_start: 0.6740 (t80) cc_final: 0.6537 (t80)
  outliers start: 57
  outliers final: 25
  residues processed: 278
  average time/residue: 0.0955
  time to fit residues: 39.2719
Evaluate side-chains
  242 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 213
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 LYS
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  475 ILE
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  659 MET
Chi-restraints excluded: chain A residue  691 LEU
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  866 SER
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  250 ASP
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  475 ILE
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  773 MET
Chi-restraints excluded: chain B residue  866 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 109 optimal weight:    0.6980
   chunk 107 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 135 optimal weight:    1.9990
   chunk 29 optimal weight:   20.0000
   chunk 106 optimal weight:    8.9990
   chunk 115 optimal weight:    5.9990
   chunk 91 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 844 HIS
B 129 HIS
B 205 ASN
B 328 GLN
B 506 GLN
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 657 GLN
** B 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4695 r_free = 0.4695 target = 0.232839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.191307 restraints weight = 15609.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.191158 restraints weight = 10958.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.192928 restraints weight = 9635.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.193190 restraints weight = 7288.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.193529 restraints weight = 6820.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.4291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7064
moved from start:          0.3145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.076  11692  Z= 0.244
  Angle     :  0.769   8.397  15844  Z= 0.407
  Chirality :  0.047   0.161   1738
  Planarity :  0.007   0.069   1944
  Dihedral  :  7.477  58.800   1532
  Min Nonbonded Distance : 2.181

Molprobity Statistics.
  All-atom Clashscore : 15.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.08 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 19.84 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

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: -3.75 (0.19), residues: 1344
  helix: -1.77 (0.16), residues: 766
  sheet:  None (None), residues: 0
  loop : -3.50 (0.21), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 542 
 TYR   0.034   0.002   TYR A 242 
 PHE   0.028   0.002   PHE A 321 
 TRP   0.017   0.002   TRP A 397 
 HIS   0.006   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00551 (11686)
  covalent geometry    : angle       0.76915 (15832)
  SS BOND              : bond        0.00562 (    6)
  SS BOND              : angle       1.07291 (   12)
  hydrogen bonds       : bond        0.06208 (  494)
  hydrogen bonds       : angle       5.92222 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 226
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.8031 (t80) cc_final: 0.7656 (t80)
REVERT: A  523 ILE cc_start: 0.9248 (OUTLIER) cc_final: 0.8977 (mp)
REVERT: A  534 MET cc_start: 0.7428 (mmt) cc_final: 0.7003 (mmt)
REVERT: A  618 ILE cc_start: 0.9042 (mm) cc_final: 0.8722 (mt)
REVERT: A  632 ASN cc_start: 0.8057 (m-40) cc_final: 0.7825 (m-40)
REVERT: A  700 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7755 (tt)
REVERT: A  705 TRP cc_start: 0.8140 (t60) cc_final: 0.7755 (t60)
REVERT: A  721 ASP cc_start: 0.7876 (p0) cc_final: 0.7654 (p0)
REVERT: B   53 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.7008 (mp0)
REVERT: B   70 ARG cc_start: 0.7419 (ptm-80) cc_final: 0.6844 (ptt90)
REVERT: B  305 TYR cc_start: 0.7997 (t80) cc_final: 0.7552 (t80)
REVERT: B  555 MET cc_start: 0.7847 (tpp) cc_final: 0.7548 (tpt)
REVERT: B  700 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8038 (tt)
REVERT: B  742 MET cc_start: 0.7145 (mtp) cc_final: 0.6937 (mtp)
REVERT: B  839 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8214 (mm)
  outliers start: 60
  outliers final: 34
  residues processed: 267
  average time/residue: 0.0977
  time to fit residues: 38.5404
Evaluate side-chains
  246 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 207
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  405 GLU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain B residue   53 GLU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  134 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  573 PHE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  714 MET
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  839 ILE
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 55 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 72 optimal weight:   20.0000
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 73 optimal weight:    8.9990
   chunk 26 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 328 GLN
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 GLN
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 825 ASN ** 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 = 0.4712 r_free = 0.4712 target = 0.234760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.194034 restraints weight = 15665.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.193963 restraints weight = 10963.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.196029 restraints weight = 9336.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.196139 restraints weight = 7164.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.196672 restraints weight = 7142.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7034
moved from start:          0.3552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  11692  Z= 0.187
  Angle     :  0.712   7.884  15844  Z= 0.376
  Chirality :  0.045   0.158   1738
  Planarity :  0.006   0.065   1944
  Dihedral  :  7.054  58.812   1524
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.56 %
    Favored  : 91.44 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 20.73 %
    Favored  : 73.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.44 (0.20), residues: 1344
  helix: -1.46 (0.17), residues: 774
  sheet:  None (None), residues: 0
  loop : -3.48 (0.21), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 542 
 TYR   0.037   0.002   TYR A 242 
 PHE   0.021   0.002   PHE A 321 
 TRP   0.019   0.001   TRP A 397 
 HIS   0.004   0.001   HIS B 830 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (11686)
  covalent geometry    : angle       0.71232 (15832)
  SS BOND              : bond        0.00340 (    6)
  SS BOND              : angle       0.89965 (   12)
  hydrogen bonds       : bond        0.05679 (  494)
  hydrogen bonds       : angle       5.66262 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 221
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.7882 (t80) cc_final: 0.7582 (t80)
REVERT: A  347 LEU cc_start: 0.6289 (tt) cc_final: 0.5368 (mp)
REVERT: A  534 MET cc_start: 0.7314 (mmt) cc_final: 0.6917 (mmt)
REVERT: A  618 ILE cc_start: 0.8997 (mm) cc_final: 0.8692 (mt)
REVERT: A  632 ASN cc_start: 0.8015 (m-40) cc_final: 0.7783 (m-40)
REVERT: A  700 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7772 (tt)
REVERT: A  705 TRP cc_start: 0.8070 (t60) cc_final: 0.7619 (t60)
REVERT: B   70 ARG cc_start: 0.7345 (ptm-80) cc_final: 0.6825 (ptt90)
REVERT: B  305 TYR cc_start: 0.7872 (t80) cc_final: 0.7488 (t80)
REVERT: B  591 TYR cc_start: 0.5823 (p90) cc_final: 0.5349 (t80)
REVERT: B  659 MET cc_start: 0.6545 (ptm) cc_final: 0.5765 (ptt)
REVERT: B  700 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7932 (tt)
  outliers start: 66
  outliers final: 42
  residues processed: 264
  average time/residue: 0.0955
  time to fit residues: 36.8956
Evaluate side-chains
  250 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 206
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  363 ILE
Chi-restraints excluded: chain A residue  395 GLU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  548 GLU
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  768 HIS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  363 ILE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  403 GLU
Chi-restraints excluded: chain B residue  405 GLU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  509 THR
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  622 ILE
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  687 LEU
Chi-restraints excluded: chain B residue  697 ILE
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  812 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 127 optimal weight:    0.5980
   chunk 4 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   chunk 9 optimal weight:    7.9990
   chunk 74 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 117 optimal weight:    0.0770
   chunk 102 optimal weight:   10.0000
   chunk 26 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.6540

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
A 696 ASN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 825 ASN ** 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 = 0.4727 r_free = 0.4727 target = 0.235219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.197725 restraints weight = 15535.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.199089 restraints weight = 11673.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.200957 restraints weight = 9288.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.200872 restraints weight = 6912.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.201153 restraints weight = 6779.690|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11692  Z= 0.150
  Angle     :  0.678   8.181  15844  Z= 0.355
  Chirality :  0.044   0.167   1738
  Planarity :  0.006   0.062   1944
  Dihedral  :  6.838  59.506   1522
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  5.32 %
    Allowed  : 21.61 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -3.22 (0.20), residues: 1344
  helix: -1.25 (0.17), residues: 796
  sheet:  None (None), residues: 0
  loop : -3.50 (0.21), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 542 
 TYR   0.041   0.002   TYR A 242 
 PHE   0.027   0.001   PHE B 321 
 TRP   0.017   0.001   TRP A 397 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (11686)
  covalent geometry    : angle       0.67781 (15832)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       0.85494 (   12)
  hydrogen bonds       : bond        0.05184 (  494)
  hydrogen bonds       : angle       5.42743 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  284 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 218
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 TYR cc_start: 0.7796 (t80) cc_final: 0.7569 (t80)
REVERT: A  534 MET cc_start: 0.7294 (mmt) cc_final: 0.7016 (mmt)
REVERT: A  618 ILE cc_start: 0.9002 (mm) cc_final: 0.8699 (mt)
REVERT: A  632 ASN cc_start: 0.7993 (m-40) cc_final: 0.7783 (m-40)
REVERT: A  700 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7721 (tt)
REVERT: A  863 ILE cc_start: 0.6135 (OUTLIER) cc_final: 0.5749 (mp)
REVERT: B   70 ARG cc_start: 0.7269 (ptm-80) cc_final: 0.6844 (ptt90)
REVERT: B  305 TYR cc_start: 0.7831 (t80) cc_final: 0.7530 (t80)
REVERT: B  591 TYR cc_start: 0.5739 (p90) cc_final: 0.5385 (t80)
REVERT: B  700 ILE cc_start: 0.8153 (OUTLIER) cc_final: 0.7865 (tt)
REVERT: B  839 ILE cc_start: 0.9192 (OUTLIER) cc_final: 0.7467 (mm)
  outliers start: 66
  outliers final: 37
  residues processed: 260
  average time/residue: 0.0942
  time to fit residues: 36.2095
Evaluate side-chains
  245 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 204
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  768 HIS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  548 GLU
Chi-restraints excluded: chain B residue  573 PHE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  839 ILE
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 114 optimal weight:    3.9990
   chunk 57 optimal weight:    0.5980
   chunk 95 optimal weight:    0.9990
   chunk 54 optimal weight:    0.3980
   chunk 62 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 137 optimal weight:   20.0000
   chunk 69 optimal weight:   10.0000
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 205 ASN
A 328 GLN
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 825 ASN ** 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 = 0.4742 r_free = 0.4742 target = 0.236697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.199829 restraints weight = 15581.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.201052 restraints weight = 11825.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.202955 restraints weight = 9245.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.202966 restraints weight = 6954.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.203297 restraints weight = 7283.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6933
moved from start:          0.4180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11692  Z= 0.150
  Angle     :  0.679   8.349  15844  Z= 0.358
  Chirality :  0.044   0.182   1738
  Planarity :  0.006   0.061   1944
  Dihedral  :  6.744  59.726   1522
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 22.58 %
    Favored  : 72.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -3.00 (0.20), residues: 1344
  helix: -1.08 (0.17), residues: 794
  sheet:  None (None), residues: 0
  loop : -3.40 (0.21), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 542 
 TYR   0.033   0.002   TYR A 242 
 PHE   0.027   0.002   PHE B 321 
 TRP   0.016   0.001   TRP A 397 
 HIS   0.003   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11686)
  covalent geometry    : angle       0.67882 (15832)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       0.82528 (   12)
  hydrogen bonds       : bond        0.05074 (  494)
  hydrogen bonds       : angle       5.34582 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 209
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.7214 (ptm-80) cc_final: 0.6811 (ptm-80)
REVERT: A  305 TYR cc_start: 0.7782 (t80) cc_final: 0.7553 (t80)
REVERT: A  618 ILE cc_start: 0.8982 (mm) cc_final: 0.8656 (mt)
REVERT: A  632 ASN cc_start: 0.7942 (m-40) cc_final: 0.7720 (m-40)
REVERT: A  700 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7707 (tt)
REVERT: A  705 TRP cc_start: 0.7781 (t60) cc_final: 0.7453 (t60)
REVERT: A  750 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6938 (ptp)
REVERT: A  863 ILE cc_start: 0.6283 (OUTLIER) cc_final: 0.5874 (mp)
REVERT: B   70 ARG cc_start: 0.7283 (ptm-80) cc_final: 0.6890 (ptt90)
REVERT: B  305 TYR cc_start: 0.7808 (t80) cc_final: 0.7496 (t80)
REVERT: B  321 PHE cc_start: 0.6206 (OUTLIER) cc_final: 0.5899 (p90)
REVERT: B  358 PHE cc_start: 0.6232 (m-80) cc_final: 0.5872 (m-10)
REVERT: B  523 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8950 (mp)
REVERT: B  591 TYR cc_start: 0.5705 (p90) cc_final: 0.5401 (t80)
REVERT: B  700 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7839 (tt)
  outliers start: 59
  outliers final: 37
  residues processed: 245
  average time/residue: 0.0930
  time to fit residues: 33.8443
Evaluate side-chains
  242 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 199
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  750 MET
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  217 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  548 GLU
Chi-restraints excluded: chain B residue  573 PHE
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  697 ILE
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  811 ASP
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 82 optimal weight:    0.2980
   chunk 134 optimal weight:    0.5980
   chunk 121 optimal weight:    0.0670
   chunk 95 optimal weight:    1.9990
   chunk 78 optimal weight:   10.0000
   chunk 20 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0470
   chunk 21 optimal weight:    5.9990
   chunk 123 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.3216

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 657 GLN
** A 825 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 825 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4776 r_free = 0.4776 target = 0.242023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.203253 restraints weight = 15663.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.205090 restraints weight = 10894.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.206613 restraints weight = 8266.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.207060 restraints weight = 6395.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.207319 restraints weight = 6071.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.4430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.4440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11692  Z= 0.132
  Angle     :  0.659   9.434  15844  Z= 0.343
  Chirality :  0.044   0.175   1738
  Planarity :  0.006   0.061   1944
  Dihedral  :  6.466  56.232   1522
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 23.23 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.66 (0.21), residues: 1344
  helix: -0.83 (0.17), residues: 796
  sheet:  None (None), residues: 0
  loop : -3.22 (0.23), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 542 
 TYR   0.029   0.001   TYR A 242 
 PHE   0.033   0.001   PHE B 685 
 TRP   0.016   0.001   TRP B 705 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (11686)
  covalent geometry    : angle       0.65841 (15832)
  SS BOND              : bond        0.00239 (    6)
  SS BOND              : angle       0.80355 (   12)
  hydrogen bonds       : bond        0.04661 (  494)
  hydrogen bonds       : angle       5.23369 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 215
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.7195 (ptm-80) cc_final: 0.6812 (ptm-80)
REVERT: A  321 PHE cc_start: 0.6512 (OUTLIER) cc_final: 0.6221 (p90)
REVERT: A  613 MET cc_start: 0.8386 (ptm) cc_final: 0.8144 (ttp)
REVERT: A  618 ILE cc_start: 0.8897 (mm) cc_final: 0.8566 (mt)
REVERT: A  632 ASN cc_start: 0.7886 (m-40) cc_final: 0.7681 (m-40)
REVERT: A  700 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7666 (tt)
REVERT: A  705 TRP cc_start: 0.7628 (t60) cc_final: 0.7374 (t60)
REVERT: A  742 MET cc_start: 0.7085 (mtt) cc_final: 0.6738 (mtp)
REVERT: A  750 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6828 (ptp)
REVERT: A  863 ILE cc_start: 0.6181 (OUTLIER) cc_final: 0.5738 (mp)
REVERT: B   70 ARG cc_start: 0.7187 (ptm-80) cc_final: 0.6814 (ptt90)
REVERT: B  305 TYR cc_start: 0.7763 (t80) cc_final: 0.7488 (t80)
REVERT: B  321 PHE cc_start: 0.6050 (OUTLIER) cc_final: 0.5597 (p90)
REVERT: B  591 TYR cc_start: 0.5850 (p90) cc_final: 0.5391 (t80)
REVERT: B  700 ILE cc_start: 0.8074 (OUTLIER) cc_final: 0.7818 (tt)
  outliers start: 54
  outliers final: 35
  residues processed: 248
  average time/residue: 0.0905
  time to fit residues: 33.6842
Evaluate side-chains
  247 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 206
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  750 MET
Chi-restraints excluded: chain A residue  768 HIS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  842 MET
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  138 TYR
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  548 GLU
Chi-restraints excluded: chain B residue  573 PHE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  697 ILE
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  818 HIS
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9990
   chunk 1 optimal weight:    4.9990
   chunk 4 optimal weight:    7.9990
   chunk 49 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 105 optimal weight:    7.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 825 ASN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4746 r_free = 0.4746 target = 0.237474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.201733 restraints weight = 15460.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4399 r_free = 0.4399 target = 0.202411 restraints weight = 11629.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.204321 restraints weight = 9695.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.204287 restraints weight = 7302.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.204657 restraints weight = 6946.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.4426
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6912
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  11692  Z= 0.155
  Angle     :  0.664   9.922  15844  Z= 0.348
  Chirality :  0.044   0.162   1738
  Planarity :  0.006   0.061   1944
  Dihedral  :  6.188  56.894   1520
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.51 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 24.44 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.52 (0.21), residues: 1344
  helix: -0.72 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -3.15 (0.23), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 542 
 TYR   0.028   0.001   TYR A 305 
 PHE   0.033   0.002   PHE B 685 
 TRP   0.016   0.001   TRP B 705 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (11686)
  covalent geometry    : angle       0.66425 (15832)
  SS BOND              : bond        0.00329 (    6)
  SS BOND              : angle       0.86814 (   12)
  hydrogen bonds       : bond        0.04823 (  494)
  hydrogen bonds       : angle       5.21328 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 209
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.7111 (ptm-80) cc_final: 0.6788 (ptm-80)
REVERT: A  101 TYR cc_start: 0.5419 (t80) cc_final: 0.4690 (t80)
REVERT: A  321 PHE cc_start: 0.6529 (OUTLIER) cc_final: 0.6286 (p90)
REVERT: A  555 MET cc_start: 0.7709 (tpt) cc_final: 0.7378 (tpt)
REVERT: A  618 ILE cc_start: 0.8939 (mm) cc_final: 0.8601 (mt)
REVERT: A  700 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7721 (tt)
REVERT: A  705 TRP cc_start: 0.7723 (t60) cc_final: 0.7422 (t60)
REVERT: A  742 MET cc_start: 0.7043 (mtt) cc_final: 0.6688 (mtp)
REVERT: A  750 MET cc_start: 0.6970 (OUTLIER) cc_final: 0.6667 (ptp)
REVERT: A  863 ILE cc_start: 0.6162 (OUTLIER) cc_final: 0.5785 (mp)
REVERT: B  305 TYR cc_start: 0.7800 (t80) cc_final: 0.7527 (t80)
REVERT: B  321 PHE cc_start: 0.6089 (OUTLIER) cc_final: 0.5655 (p90)
REVERT: B  523 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8938 (mp)
REVERT: B  591 TYR cc_start: 0.5832 (p90) cc_final: 0.5349 (t80)
REVERT: B  700 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7799 (tt)
  outliers start: 46
  outliers final: 31
  residues processed: 238
  average time/residue: 0.0956
  time to fit residues: 34.2301
Evaluate side-chains
  242 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 204
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  700 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  750 MET
Chi-restraints excluded: chain A residue  768 HIS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  697 ILE
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 47 optimal weight:    0.0970
   chunk 54 optimal weight:    0.4980
   chunk 25 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 132 optimal weight:    0.0040
   chunk 134 optimal weight:    0.5980
   overall best weight:    0.2790

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 674 GLN
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.243872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4436 r_free = 0.4436 target = 0.205446 restraints weight = 15454.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.204577 restraints weight = 11815.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.206594 restraints weight = 8952.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4425 r_free = 0.4425 target = 0.207909 restraints weight = 6979.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.208150 restraints weight = 6315.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.4844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.080  11692  Z= 0.129
  Angle     :  0.651  11.655  15844  Z= 0.336
  Chirality :  0.043   0.152   1738
  Planarity :  0.006   0.060   1944
  Dihedral  :  6.008  56.547   1520
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 24.27 %
    Favored  : 72.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.27 (0.21), residues: 1344
  helix: -0.52 (0.18), residues: 796
  sheet:  None (None), residues: 0
  loop : -3.04 (0.23), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 209 
 TYR   0.022   0.001   TYR A 242 
 PHE   0.027   0.001   PHE B 321 
 TRP   0.020   0.001   TRP A 397 
 HIS   0.004   0.001   HIS A 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (11686)
  covalent geometry    : angle       0.65136 (15832)
  SS BOND              : bond        0.00285 (    6)
  SS BOND              : angle       0.66082 (   12)
  hydrogen bonds       : bond        0.04387 (  494)
  hydrogen bonds       : angle       5.13392 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 220
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   70 ARG cc_start: 0.7156 (ptm-80) cc_final: 0.6780 (ptm-80)
REVERT: A  101 TYR cc_start: 0.5546 (t80) cc_final: 0.4799 (t80)
REVERT: A  321 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5827 (p90)
REVERT: A  618 ILE cc_start: 0.8921 (mm) cc_final: 0.8555 (mt)
REVERT: A  742 MET cc_start: 0.6989 (mtt) cc_final: 0.6689 (mtp)
REVERT: A  863 ILE cc_start: 0.6081 (OUTLIER) cc_final: 0.5708 (mp)
REVERT: B   70 ARG cc_start: 0.6435 (ptt90) cc_final: 0.6042 (ptm-80)
REVERT: B  321 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.5266 (p90)
REVERT: B  523 ILE cc_start: 0.9079 (OUTLIER) cc_final: 0.8871 (mp)
REVERT: B  591 TYR cc_start: 0.5801 (p90) cc_final: 0.5297 (t80)
REVERT: B  629 TRP cc_start: 0.6862 (t60) cc_final: 0.5973 (t60)
REVERT: B  700 ILE cc_start: 0.7990 (OUTLIER) cc_final: 0.7723 (tt)
REVERT: B  742 MET cc_start: 0.7185 (mtt) cc_final: 0.6747 (mtt)
  outliers start: 44
  outliers final: 32
  residues processed: 246
  average time/residue: 0.1014
  time to fit residues: 36.7384
Evaluate side-chains
  242 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 205
  time to evaluate  : 0.431 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  321 PHE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  668 TYR
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  768 HIS
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  573 PHE
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  668 TYR
Chi-restraints excluded: chain B residue  697 ILE
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 8 optimal weight:    0.0570
   chunk 103 optimal weight:    9.9990
   chunk 39 optimal weight:    2.9990
   chunk 117 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 137 optimal weight:    8.9990
   chunk 68 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 24 optimal weight:    0.4980
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.1104

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 657 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.233950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.193710 restraints weight = 15602.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.193248 restraints weight = 11365.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.195112 restraints weight = 9449.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.195645 restraints weight = 7163.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.195925 restraints weight = 6635.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.4757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.095  11692  Z= 0.253
  Angle     :  0.772  12.082  15844  Z= 0.406
  Chirality :  0.049   0.222   1738
  Planarity :  0.006   0.063   1944
  Dihedral  :  6.380  59.697   1520
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 15.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.85 %
    Favored  : 91.15 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 24.68 %
    Favored  : 71.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.54 (0.21), residues: 1344
  helix: -0.81 (0.17), residues: 794
  sheet:  None (None), residues: 0
  loop : -3.02 (0.24), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 289 
 TYR   0.044   0.002   TYR B 305 
 PHE   0.036   0.002   PHE B 685 
 TRP   0.018   0.002   TRP A 397 
 HIS   0.007   0.002   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (11686)
  covalent geometry    : angle       0.77109 (15832)
  SS BOND              : bond        0.00448 (    6)
  SS BOND              : angle       1.32164 (   12)
  hydrogen bonds       : bond        0.05453 (  494)
  hydrogen bonds       : angle       5.42071 ( 1464)

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

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

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2688 Ramachandran restraints generated.
    1344 Oldfield, 0 Emsley, 1344 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 202
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   58 LYS cc_start: 0.6637 (tptp) cc_final: 0.6212 (mtmm)
REVERT: A   70 ARG cc_start: 0.7131 (ptm-80) cc_final: 0.6833 (ptm-80)
REVERT: A  101 TYR cc_start: 0.5606 (t80) cc_final: 0.4913 (t80)
REVERT: A  305 TYR cc_start: 0.8028 (t80) cc_final: 0.7749 (t80)
REVERT: A  632 ASN cc_start: 0.7942 (m-40) cc_final: 0.7708 (m-40)
REVERT: A  742 MET cc_start: 0.7134 (mtt) cc_final: 0.6770 (mtp)
REVERT: A  863 ILE cc_start: 0.6166 (OUTLIER) cc_final: 0.5757 (mp)
REVERT: B  321 PHE cc_start: 0.6282 (OUTLIER) cc_final: 0.5787 (p90)
REVERT: B  523 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.8985 (mp)
REVERT: B  591 TYR cc_start: 0.6024 (p90) cc_final: 0.5383 (t80)
REVERT: B  700 ILE cc_start: 0.8107 (OUTLIER) cc_final: 0.7837 (tt)
REVERT: B  742 MET cc_start: 0.7204 (mtt) cc_final: 0.6885 (mtt)
  outliers start: 46
  outliers final: 32
  residues processed: 233
  average time/residue: 0.0976
  time to fit residues: 34.0731
Evaluate side-chains
  235 residues out of total 1242 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 199
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  316 VAL
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  524 LEU
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  534 MET
Chi-restraints excluded: chain A residue  573 PHE
Chi-restraints excluded: chain A residue  596 CYS
Chi-restraints excluded: chain A residue  622 ILE
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  732 ILE
Chi-restraints excluded: chain A residue  769 THR
Chi-restraints excluded: chain A residue  818 HIS
Chi-restraints excluded: chain A residue  863 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  128 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  321 PHE
Chi-restraints excluded: chain B residue  384 VAL
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  523 ILE
Chi-restraints excluded: chain B residue  524 LEU
Chi-restraints excluded: chain B residue  526 THR
Chi-restraints excluded: chain B residue  548 GLU
Chi-restraints excluded: chain B residue  585 VAL
Chi-restraints excluded: chain B residue  596 CYS
Chi-restraints excluded: chain B residue  697 ILE
Chi-restraints excluded: chain B residue  700 ILE
Chi-restraints excluded: chain B residue  732 ILE
Chi-restraints excluded: chain B residue  769 THR
Chi-restraints excluded: chain B residue  777 ILE
Chi-restraints excluded: chain B residue  842 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   chunk 98 optimal weight:    9.9990
   chunk 64 optimal weight:    0.5980
   chunk 125 optimal weight:    0.9980
   chunk 28 optimal weight:    6.9990
   chunk 67 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 69 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 608 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 657 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.229994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.191660 restraints weight = 15455.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.192225 restraints weight = 12600.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.194001 restraints weight = 10417.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.194116 restraints weight = 7722.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.194367 restraints weight = 7358.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.4834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  11692  Z= 0.259
  Angle     :  0.793  12.232  15844  Z= 0.416
  Chirality :  0.049   0.207   1738
  Planarity :  0.007   0.063   1944
  Dihedral  :  6.539  59.512   1520
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 15.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 24.27 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.68 (0.21), residues: 1344
  helix: -0.96 (0.17), residues: 794
  sheet:  None (None), residues: 0
  loop : -3.02 (0.23), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 592 
 TYR   0.051   0.002   TYR B 477 
 PHE   0.035   0.002   PHE B 685 
 TRP   0.019   0.002   TRP B 705 
 HIS   0.006   0.001   HIS B 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 (11686)
  covalent geometry    : angle       0.79272 (15832)
  SS BOND              : bond        0.00380 (    6)
  SS BOND              : angle       1.28610 (   12)
  hydrogen bonds       : bond        0.05630 (  494)
  hydrogen bonds       : angle       5.56539 ( 1464)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1802.76 seconds
wall clock time: 32 minutes 4.73 seconds (1924.73 seconds total)