Starting phenix.real_space_refine
on Thu Sep 18 00:40:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgv_44524/09_2025/9bgv_44524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgv_44524/09_2025/9bgv_44524.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bgv_44524/09_2025/9bgv_44524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgv_44524/09_2025/9bgv_44524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgv_44524/09_2025/9bgv_44524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgv_44524/09_2025/9bgv_44524.cif"
  }
  resolution = 3.65
  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=   0.014
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
     Fe      2      7.16       5
     S      66      5.16       5
     C    7984      2.51       5
     N    2192      2.21       5
     O    2344      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12588
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6251
          Classifications: {'peptide': 787}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 751}
    Chain: "B"
      Number of atoms: 6251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6251
          Classifications: {'peptide': 787}
          Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 751}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'HEM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.82, per 1000 atoms: 0.22
  Number of scatterers: 12588
  At special positions: 0
  Unit cell: (87.9038, 102.554, 203.777, 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)
     Fe      2     26.01
     S      66     16.00
     O    2344      8.00
     N    2192      7.00
     C    7984      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.12
  Conformation dependent library (CDL) restraints added in 660.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2968

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 15 sheets defined
      46.8% alpha, 19.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 28
      removed outlier: 3.983A  pdb=" N   GLN A  28 " --> pdb=" O   PRO A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 54
    Processing helix  chain 'A' and resid 56 through 61
    Processing helix  chain 'A' and resid 64 through 69
      removed outlier: 3.610A  pdb=" N   MET A  67 " --> pdb=" O   ASN A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 74
    Processing helix  chain 'A' and resid 76 through 88
    Processing helix  chain 'A' and resid 133 through 153
      removed outlier: 4.566A  pdb=" N   GLN A 139 " --> pdb=" O   VAL A 135 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   ILE A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 149 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   LEU A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 201 through 210
      removed outlier: 3.993A  pdb=" N   GLN A 207 " --> pdb=" O   ARG A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 274
    Processing helix  chain 'A' and resid 278 through 294
      removed outlier: 3.556A  pdb=" N   GLU A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 381
      removed outlier: 3.561A  pdb=" N   HIS A 379 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE A 380 " --> pdb=" O   SER A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 408
    Processing helix  chain 'A' and resid 421 through 429
      removed outlier: 4.004A  pdb=" N   VAL A 425 " --> pdb=" O   HIS A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 448
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 514 through 531
      removed outlier: 4.349A  pdb=" N   ALA A 520 " --> pdb=" O   LEU A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 562
      removed outlier: 3.693A  pdb=" N   LYS A 547 " --> pdb=" O   ASN A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 610
      Proline residue:  A 604  - end of helix
      removed outlier: 3.569A  pdb=" N   GLY A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 632
      removed outlier: 3.819A  pdb=" N   ILE A 615 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   ILE A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A 623 " --> pdb=" O   VAL A 619 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   SER A 632 " --> pdb=" O   ALA A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 666
      removed outlier: 4.097A  pdb=" N   GLN A 657 " --> pdb=" O   GLN A 653 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL A 658 " --> pdb=" O   LEU A 654 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   MET A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   HIS A 663 " --> pdb=" O   SER A 659 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TRP A 665 " --> pdb=" O   ALA A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 687 through 699
      removed outlier: 3.798A  pdb=" N   ILE A 694 " --> pdb=" O   LYS A 690 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU A 695 " --> pdb=" O   ARG A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 733
      removed outlier: 3.859A  pdb=" N   VAL A 732 " --> pdb=" O   ASP A 728 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 728 through 733'
    Processing helix  chain 'A' and resid 740 through 756
      removed outlier: 3.804A  pdb=" N   LEU A 744 " --> pdb=" O   ARG A 740 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE A 751 " --> pdb=" O   ALA A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 766 through 776
      removed outlier: 4.118A  pdb=" N   ILE A 776 " --> pdb=" O   MET A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 793
      No H-bonds generated for 'chain 'A' and resid 791 through 793'
    Processing helix  chain 'A' and resid 794 through 802
      removed outlier: 4.419A  pdb=" N   SER A 800 " --> pdb=" O   PRO A 796 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 28
    Processing helix  chain 'B' and resid 46 through 54
    Processing helix  chain 'B' and resid 56 through 61
      removed outlier: 3.805A  pdb=" N   VAL B  60 " --> pdb=" O   LYS B  56 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 88
      removed outlier: 4.132A  pdb=" N   GLY B  88 " --> pdb=" O   ASN B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 152
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 180 through 185
    Processing helix  chain 'B' and resid 188 through 193
    Processing helix  chain 'B' and resid 201 through 208
    Processing helix  chain 'B' and resid 256 through 274
    Processing helix  chain 'B' and resid 278 through 294
      removed outlier: 3.675A  pdb=" N   GLU B 284 " --> pdb=" O   HIS B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 382
      removed outlier: 4.172A  pdb=" N   LEU B 369 " --> pdb=" O   HIS B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 408
      removed outlier: 4.194A  pdb=" N   ASN B 400 " --> pdb=" O   ASN B 396 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ASP B 404 " --> pdb=" O   ASN B 400 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LYS B 408 " --> pdb=" O   ASP B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 429
    Processing helix  chain 'B' and resid 430 through 449
    Processing helix  chain 'B' and resid 471 through 485
      removed outlier: 3.510A  pdb=" N   GLN B 477 " --> pdb=" O   SER B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 512 through 531
      removed outlier: 3.595A  pdb=" N   LEU B 516 " --> pdb=" O   ASN B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 563
      removed outlier: 4.610A  pdb=" N   MET B 545 " --> pdb=" O   ALA B 541 " (cutoff:3.500A)
      removed outlier: 4.859A  pdb=" N   VAL B 546 " --> pdb=" O   MET B 542 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LYS B 547 " --> pdb=" O   ASN B 543 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 598 through 610
      Proline residue:  B 604  - end of helix
    Processing helix  chain 'B' and resid 611 through 633
      removed outlier: 3.692A  pdb=" N   TRP B 630 " --> pdb=" O   GLN B 626 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 666
      removed outlier: 3.689A  pdb=" N   VAL B 658 " --> pdb=" O   LEU B 654 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   TRP B 665 " --> pdb=" O   ALA B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 668 through 670
      No H-bonds generated for 'chain 'B' and resid 668 through 670'
    Processing helix  chain 'B' and resid 685 through 690
    Processing helix  chain 'B' and resid 691 through 699
      removed outlier: 4.197A  pdb=" N   LEU B 695 " --> pdb=" O   ARG B 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 714 through 719
    Processing helix  chain 'B' and resid 728 through 733
      removed outlier: 3.532A  pdb=" N   VAL B 732 " --> pdb=" O   ASP B 728 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 756
      removed outlier: 3.700A  pdb=" N   LEU B 744 " --> pdb=" O   ARG B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 766 through 777
    Processing helix  chain 'B' and resid 794 through 802
    Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 45
      removed outlier: 3.632A  pdb=" N   MET A  43 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   LEU A  35 " --> pdb=" O   MET A  43 " (cutoff:3.500A)
      removed outlier: 4.269A  pdb=" N   PHE A  45 " --> pdb=" O   ALA A  33 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   ALA A  33 " --> pdb=" O   PHE A  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169
      removed outlier: 6.386A  pdb=" N   VAL A 159 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   CYS A 169 " --> pdb=" O   VAL A 157 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   VAL A 157 " --> pdb=" O   CYS A 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 314
      removed outlier: 6.911A  pdb=" N   LEU A 301 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   SER A 314 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL A 299 " --> pdb=" O   SER A 314 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ALA A 339 " --> pdb=" O   LEU A 304 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ILE A 331 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ILE A 341 " --> pdb=" O   ALA A 329 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   ALA A 329 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   GLN A 343 " --> pdb=" O   TRP A 327 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   TRP A 327 " --> pdb=" O   GLN A 343 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LYS A 345 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   GLN A 325 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 454 through 459
      removed outlier: 5.394A  pdb=" N   LEU A 455 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 5.328A  pdb=" N   ARG A 457 " --> pdb=" O   VAL A 464 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   VAL A 464 " --> pdb=" O   ARG A 457 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   GLY A 504 " --> pdb=" O   LEU A 416 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   LEU A 501 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
      removed outlier: 8.228A  pdb=" N   GLN A 536 " --> pdb=" O   LEU A 501 " (cutoff:3.500A)
      removed outlier: 6.492A  pdb=" N   ILE A 503 " --> pdb=" O   GLN A 536 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 568
    Processing sheet with id=AA6, first strand: chain 'A' and resid 640 through 641
      removed outlier: 7.826A  pdb=" N   SER A 641 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE A 583 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
      removed outlier: 6.969A  pdb=" N   GLN A 572 " --> pdb=" O   TYR A 581 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ILE A 725 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 8.168A  pdb=" N   GLU A 762 " --> pdb=" O   ILE A 725 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 673 through 676
      removed outlier: 3.786A  pdb=" N   ILE A 676 " --> pdb=" O   SER A 703 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 42 through 45
      removed outlier: 6.024A  pdb=" N   LEU B  35 " --> pdb=" O   MET B  43 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE B  45 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA B  33 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 42 through 45
      removed outlier: 6.024A  pdb=" N   LEU B  35 " --> pdb=" O   MET B  43 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   PHE B  45 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ALA B  33 " --> pdb=" O   PHE B  45 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 158 through 160
      removed outlier: 3.666A  pdb=" N   SER B 235 " --> pdb=" O   THR B 252 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 308 through 314
      removed outlier: 6.651A  pdb=" N   LEU B 301 " --> pdb=" O   TRP B 312 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   SER B 314 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   VAL B 299 " --> pdb=" O   SER B 314 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   ALA B 339 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   ILE B 331 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   ILE B 341 " --> pdb=" O   ALA B 329 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ALA B 329 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   GLN B 343 " --> pdb=" O   TRP B 327 " (cutoff:3.500A)
      removed outlier: 6.686A  pdb=" N   TRP B 327 " --> pdb=" O   GLN B 343 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   LYS B 345 " --> pdb=" O   GLN B 325 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   GLN B 325 " --> pdb=" O   LYS B 345 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 454 through 459
      removed outlier: 7.001A  pdb=" N   GLN B 462 " --> pdb=" O   ILE B 458 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   THR B 500 " --> pdb=" O   ASP B 420 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 490 through 491
    Processing sheet with id=AB5, first strand: chain 'B' and resid 790 through 791
      removed outlier: 4.563A  pdb=" N   GLY B 783 " --> pdb=" O   PRO B 571 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   VAL B 759 " --> pdb=" O   VAL B 780 " (cutoff:3.500A)
      removed outlier: 7.833A  pdb=" N   GLN B 782 " --> pdb=" O   VAL B 759 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   ALA B 761 " --> pdb=" O   GLN B 782 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   ILE B 725 " --> pdb=" O   VAL B 760 " (cutoff:3.500A)
      removed outlier: 7.455A  pdb=" N   GLU B 762 " --> pdb=" O   ILE B 725 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ILE B 727 " --> pdb=" O   GLU B 762 " (cutoff:3.500A)
      removed outlier: 7.370A  pdb=" N   VAL B 764 " --> pdb=" O   ILE B 727 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   VAL B 704 " --> pdb=" O   LYS B 726 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   SER B 703 " --> pdb=" O   LEU B 672 " (cutoff:3.500A)
      removed outlier: 6.340A  pdb=" N   VAL B 674 " --> pdb=" O   SER B 703 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   GLU B 675 " --> pdb=" O   VAL B 642 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   LEU B 580 " --> pdb=" O   PHE B 574 " (cutoff:3.500A)
      removed outlier: 6.338A  pdb=" N   PHE B 574 " --> pdb=" O   LEU B 580 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 590 through 591
      removed outlier: 3.625A  pdb=" N   ASP B 591 " --> pdb=" O   GLY B 595 " (cutoff:3.500A)

    630 hydrogen bonds defined for protein.
    1800 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 1.45 seconds

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

  Histogram of bond lengths:
        1.21 -     1.39: 5149
        1.39 -     1.57: 7585
        1.57 -     1.75: 0
        1.75 -     1.92: 116
        1.92 -     2.10: 8
  Bond restraints: 12858
  Sorted by residual:
  bond pdb=" N   HIS A  77 "
       pdb=" CA  HIS A  77 "
    ideal  model  delta    sigma   weight residual
    1.462  1.486 -0.024 7.70e-03 1.69e+04 9.86e+00
  bond pdb=" N   GLU B 197 "
       pdb=" CA  GLU B 197 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.035 1.40e-02 5.10e+03 6.14e+00
  bond pdb=" N   PHE B 198 "
       pdb=" CA  PHE B 198 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.41e-02 5.03e+03 5.37e+00
  bond pdb=" CA  LEU A 210 "
       pdb=" C   LEU A 210 "
    ideal  model  delta    sigma   weight residual
    1.522  1.494  0.028 1.38e-02 5.25e+03 4.26e+00
  bond pdb=" N   ASP B 201 "
       pdb=" CA  ASP B 201 "
    ideal  model  delta    sigma   weight residual
    1.463  1.488 -0.024 1.31e-02 5.83e+03 3.47e+00
  ... (remaining 12853 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.71: 16897
        1.71 -     3.42: 467
        3.42 -     5.14: 65
        5.14 -     6.85: 13
        6.85 -     8.56: 8
  Bond angle restraints: 17450
  Sorted by residual:
  angle pdb=" N   VAL A 722 "
        pdb=" CA  VAL A 722 "
        pdb=" C   VAL A 722 "
      ideal   model   delta    sigma   weight residual
     111.91  106.86    5.05 8.90e-01 1.26e+00 3.22e+01
  angle pdb=" N   GLY B 336 "
        pdb=" CA  GLY B 336 "
        pdb=" C   GLY B 336 "
      ideal   model   delta    sigma   weight residual
     111.21  116.87   -5.66 1.04e+00 9.25e-01 2.96e+01
  angle pdb=" C   PRO B 199 "
        pdb=" CA  PRO B 199 "
        pdb=" CB  PRO B 199 "
      ideal   model   delta    sigma   weight residual
     113.09  107.87    5.22 1.36e+00 5.41e-01 1.48e+01
  angle pdb=" C   PRO A 540 "
        pdb=" N   ALA A 541 "
        pdb=" CA  ALA A 541 "
      ideal   model   delta    sigma   weight residual
     122.46  115.67    6.79 1.80e+00 3.09e-01 1.42e+01
  angle pdb=" CA  ASP B 201 "
        pdb=" C   ASP B 201 "
        pdb=" O   ASP B 201 "
      ideal   model   delta    sigma   weight residual
     122.37  118.23    4.14 1.15e+00 7.56e-01 1.30e+01
  ... (remaining 17445 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.73: 6955
       17.73 -    35.45: 663
       35.45 -    53.18: 106
       53.18 -    70.91: 27
       70.91 -    88.63: 17
  Dihedral angle restraints: 7768
    sinusoidal: 3196
      harmonic: 4572
  Sorted by residual:
  dihedral pdb=" CA  PRO B 199 "
           pdb=" C   PRO B 199 "
           pdb=" N   ALA B 200 "
           pdb=" CA  ALA B 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.89   27.11     0      5.00e+00 4.00e-02 2.94e+01
  dihedral pdb=" CA  HIS A 152 "
           pdb=" C   HIS A 152 "
           pdb=" N   LEU A 153 "
           pdb=" CA  LEU A 153 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.64  -22.36     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  GLN A 536 "
           pdb=" C   GLN A 536 "
           pdb=" N   PHE A 537 "
           pdb=" CA  PHE A 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.98   22.02     0      5.00e+00 4.00e-02 1.94e+01
  ... (remaining 7765 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1183
       0.035 -    0.069: 479
       0.069 -    0.104: 199
       0.104 -    0.139: 64
       0.139 -    0.173: 5
  Chirality restraints: 1930
  Sorted by residual:
  chirality pdb=" CB  VAL B 718 "
            pdb=" CA  VAL B 718 "
            pdb=" CG1 VAL B 718 "
            pdb=" CG2 VAL B 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.46   -0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CB  ILE B 503 "
            pdb=" CA  ILE B 503 "
            pdb=" CG1 ILE B 503 "
            pdb=" CG2 ILE B 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.62e-01
  chirality pdb=" CA  ASN B 756 "
            pdb=" N   ASN B 756 "
            pdb=" C   ASN B 756 "
            pdb=" CB  ASN B 756 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.96e-01
  ... (remaining 1927 not shown)

  Planarity restraints: 2270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 392 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.69e+00
        pdb=" N   PRO A 393 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO A 393 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 393 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 161 "   -0.027 5.00e-02 4.00e+02   4.07e-02 2.65e+00
        pdb=" N   PRO B 162 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO B 162 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B 162 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A 161 "   -0.026 5.00e-02 4.00e+02   3.88e-02 2.40e+00
        pdb=" N   PRO A 162 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 162 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 162 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 2267 not shown)

  Histogram of nonbonded interaction distances:
        1.89 -     2.49: 69
        2.49 -     3.09: 9171
        3.09 -     3.70: 19374
        3.70 -     4.30: 26440
        4.30 -     4.90: 43835
  Nonbonded interactions: 98889
  Sorted by model distance:
  nonbonded pdb=" CE1 PHE B 198 "
            pdb=" CB  ALA B 200 "
     model   vdw
     1.891 3.760
  nonbonded pdb=" CZ  PHE B 198 "
            pdb=" CB  ALA B 200 "
     model   vdw
     1.960 3.760
  nonbonded pdb=" NE2 GLN A 142 "
            pdb=" OE1 GLN B 168 "
     model   vdw
     2.158 3.120
  nonbonded pdb=" OG1 THR A 226 "
            pdb=" OE1 GLU A 228 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER B 297 "
            pdb=" O   LYS B 345 "
     model   vdw
     2.203 3.040
  ... (remaining 98884 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: 0.03
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:             2.460
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     12.770
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
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      :  0.007   0.650  12859  Z= 0.610
  Angle     :  0.692   8.560  17450  Z= 0.385
  Chirality :  0.046   0.173   1930
  Planarity :  0.005   0.048   2270
  Dihedral  : 14.633  88.633   4800
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  2.05 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.54 (0.22), residues: 1570
  helix:  0.66 (0.21), residues: 656
  sheet: -0.67 (0.28), residues: 308
  loop : -1.23 (0.27), residues: 606

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 444 
 TYR   0.020   0.002   TYR A 507 
 PHE   0.018   0.002   PHE B 602 
 TRP   0.017   0.002   TRP B 589 
 HIS   0.004   0.001   HIS A 521 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (12858)
  covalent geometry    : angle       0.69162 (17450)
  hydrogen bonds       : bond        0.11846 (  623)
  hydrogen bonds       : angle       5.88331 ( 1800)
  Misc. bond           : bond        0.64989 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 323
  time to evaluate  : 0.506 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.3936 (tpt) cc_final: 0.3576 (tpt)
REVERT: A   95 MET cc_start: 0.3926 (mtp) cc_final: 0.3675 (mtp)
REVERT: A  185 SER cc_start: 0.7496 (t) cc_final: 0.7225 (p)
REVERT: A  279 PHE cc_start: 0.7197 (t80) cc_final: 0.6638 (t80)
REVERT: A  282 MET cc_start: 0.8093 (tpp) cc_final: 0.7270 (ttm)
REVERT: A  364 GLN cc_start: 0.7732 (pp30) cc_final: 0.7057 (tm-30)
REVERT: A  452 ASP cc_start: 0.7166 (t70) cc_final: 0.6828 (t0)
REVERT: A  457 ARG cc_start: 0.5662 (ttt-90) cc_final: 0.4641 (ttt-90)
REVERT: A  524 MET cc_start: 0.7178 (tmm) cc_final: 0.6810 (tmm)
REVERT: A  557 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8189 (ttmm)
REVERT: A  571 PRO cc_start: 0.8100 (Cg_endo) cc_final: 0.7869 (Cg_exo)
REVERT: A  596 HIS cc_start: 0.4704 (t70) cc_final: 0.4450 (t70)
REVERT: A  687 GLU cc_start: 0.6108 (pm20) cc_final: 0.5806 (pm20)
REVERT: A  729 LYS cc_start: 0.7147 (tptp) cc_final: 0.6398 (tptt)
REVERT: A  745 LEU cc_start: 0.8142 (mt) cc_final: 0.7848 (mt)
REVERT: A  762 GLU cc_start: 0.6901 (tm-30) cc_final: 0.6600 (tm-30)
REVERT: A  778 CYS cc_start: 0.7713 (t) cc_final: 0.7465 (t)
REVERT: A  794 GLU cc_start: 0.7176 (mt-10) cc_final: 0.6874 (mt-10)
REVERT: B   98 GLU cc_start: 0.8123 (pm20) cc_final: 0.7915 (pm20)
REVERT: B  279 PHE cc_start: 0.7435 (t80) cc_final: 0.7132 (t80)
REVERT: B  282 MET cc_start: 0.5374 (tpt) cc_final: 0.5102 (tpt)
REVERT: B  298 HIS cc_start: 0.7041 (t-90) cc_final: 0.6658 (t-90)
REVERT: B  345 LYS cc_start: 0.7875 (ptpp) cc_final: 0.7059 (ptpp)
REVERT: B  448 LYS cc_start: 0.7884 (mtpp) cc_final: 0.7655 (ttmm)
REVERT: B  449 LEU cc_start: 0.7849 (pp) cc_final: 0.7604 (tp)
REVERT: B  480 ASP cc_start: 0.6985 (m-30) cc_final: 0.6469 (m-30)
REVERT: B  493 ASP cc_start: 0.6854 (t0) cc_final: 0.6552 (t0)
REVERT: B  495 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7476 (ttmm)
REVERT: B  529 LYS cc_start: 0.8113 (tmtt) cc_final: 0.7644 (tmtt)
REVERT: B  590 HIS cc_start: 0.6636 (t70) cc_final: 0.6393 (t70)
REVERT: B  614 ASN cc_start: 0.7347 (m-40) cc_final: 0.6977 (m-40)
REVERT: B  716 ARG cc_start: 0.7086 (mmm160) cc_final: 0.6636 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 324
  average time/residue: 0.1345
  time to fit residues: 59.6769
Evaluate side-chains
  285 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.9990
   chunk 124 optimal weight:    0.5980
   chunk 103 optimal weight:    0.2980
   chunk 77 optimal weight:    0.0370
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.5980
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
A 142 GLN
A 562 ASN
A 670 HIS
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 474 ASN
B 521 HIS
B 564 GLN
B 626 GLN
B 670 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.179475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.149543 restraints weight = 20705.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.154106 restraints weight = 11525.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.157284 restraints weight = 7584.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.159342 restraints weight = 5557.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.160738 restraints weight = 4453.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6527
moved from start:          0.1403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  12859  Z= 0.168
  Angle     :  0.679  12.990  17450  Z= 0.340
  Chirality :  0.046   0.179   1930
  Planarity :  0.005   0.071   2270
  Dihedral  :  6.280  71.050   1712
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 12.68 %
    Favored  : 85.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.41 (0.22), residues: 1570
  helix:  0.71 (0.21), residues: 656
  sheet: -0.53 (0.28), residues: 318
  loop : -1.13 (0.27), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 131 
 TYR   0.015   0.002   TYR A 507 
 PHE   0.028   0.002   PHE B 602 
 TRP   0.015   0.001   TRP B 231 
 HIS   0.011   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 (12858)
  covalent geometry    : angle       0.67917 (17450)
  hydrogen bonds       : bond        0.04417 (  623)
  hydrogen bonds       : angle       5.16967 ( 1800)
  Misc. bond           : bond        0.00054 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 305
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 MET cc_start: 0.3814 (mtp) cc_final: 0.3567 (mtp)
REVERT: A  163 GLU cc_start: 0.7257 (mp0) cc_final: 0.7014 (mp0)
REVERT: A  279 PHE cc_start: 0.7209 (t80) cc_final: 0.6440 (t80)
REVERT: A  282 MET cc_start: 0.8270 (tpp) cc_final: 0.7818 (ttm)
REVERT: A  345 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7859 (mttt)
REVERT: A  364 GLN cc_start: 0.7695 (pp30) cc_final: 0.7076 (tm-30)
REVERT: A  429 LEU cc_start: 0.6560 (mm) cc_final: 0.6117 (mm)
REVERT: A  452 ASP cc_start: 0.7250 (t70) cc_final: 0.6872 (t0)
REVERT: A  525 ASP cc_start: 0.6131 (t70) cc_final: 0.5734 (t0)
REVERT: A  665 TRP cc_start: 0.5893 (m-90) cc_final: 0.5663 (m-90)
REVERT: A  716 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6757 (mmm160)
REVERT: A  729 LYS cc_start: 0.7152 (tptp) cc_final: 0.6580 (tptt)
REVERT: A  745 LEU cc_start: 0.8075 (mt) cc_final: 0.7815 (mt)
REVERT: A  751 ILE cc_start: 0.5428 (OUTLIER) cc_final: 0.5141 (mp)
REVERT: A  762 GLU cc_start: 0.6713 (tm-30) cc_final: 0.6438 (tm-30)
REVERT: A  778 CYS cc_start: 0.7756 (t) cc_final: 0.7469 (t)
REVERT: A  794 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6927 (mt-10)
REVERT: B   98 GLU cc_start: 0.8289 (pm20) cc_final: 0.7977 (pm20)
REVERT: B  112 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7342 (mtp85)
REVERT: B  139 GLN cc_start: 0.7670 (tp-100) cc_final: 0.7392 (tp-100)
REVERT: B  141 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7480 (mm-30)
REVERT: B  260 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7218 (tpp80)
REVERT: B  279 PHE cc_start: 0.7446 (t80) cc_final: 0.7192 (t80)
REVERT: B  282 MET cc_start: 0.5295 (tpt) cc_final: 0.5048 (tpt)
REVERT: B  298 HIS cc_start: 0.7110 (t-90) cc_final: 0.6691 (t-90)
REVERT: B  311 HIS cc_start: 0.6773 (t-90) cc_final: 0.6463 (t-90)
REVERT: B  345 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7083 (ptpp)
REVERT: B  417 ILE cc_start: 0.7989 (tp) cc_final: 0.7732 (tp)
REVERT: B  493 ASP cc_start: 0.6735 (t0) cc_final: 0.6405 (t0)
REVERT: B  495 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7353 (ttmm)
REVERT: B  529 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7610 (tmtt)
REVERT: B  590 HIS cc_start: 0.6595 (t70) cc_final: 0.6331 (t70)
REVERT: B  614 ASN cc_start: 0.7598 (m-40) cc_final: 0.7167 (m-40)
REVERT: B  644 LEU cc_start: 0.7529 (mp) cc_final: 0.7310 (mp)
REVERT: B  689 PHE cc_start: 0.7577 (t80) cc_final: 0.7228 (t80)
REVERT: B  726 LYS cc_start: 0.8356 (mttt) cc_final: 0.7935 (ttmt)
  outliers start: 23
  outliers final: 10
  residues processed: 310
  average time/residue: 0.1327
  time to fit residues: 56.4875
Evaluate side-chains
  292 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 280
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 LYS
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  580 LEU
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  751 ILE
Chi-restraints excluded: chain A residue  758 THR
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 56 optimal weight:    0.2980
   chunk 113 optimal weight:    0.8980
   chunk 151 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 127 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    0.4980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
B 470 ASN
B 564 GLN
B 626 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.178317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.148383 restraints weight = 20821.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.152802 restraints weight = 11919.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.155953 restraints weight = 8015.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.158083 restraints weight = 5932.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.159324 restraints weight = 4762.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6532
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083  12859  Z= 0.157
  Angle     :  0.652  11.644  17450  Z= 0.328
  Chirality :  0.046   0.178   1930
  Planarity :  0.005   0.066   2270
  Dihedral  :  6.236  73.735   1712
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 15.10 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1570
  helix:  0.67 (0.20), residues: 667
  sheet: -0.44 (0.28), residues: 321
  loop : -1.13 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 131 
 TYR   0.029   0.002   TYR B  80 
 PHE   0.026   0.002   PHE B 602 
 TRP   0.024   0.001   TRP B 231 
 HIS   0.006   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (12858)
  covalent geometry    : angle       0.65243 (17450)
  hydrogen bonds       : bond        0.04183 (  623)
  hydrogen bonds       : angle       5.08913 ( 1800)
  Misc. bond           : bond        0.00058 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 288
  time to evaluate  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.3483 (tpt) cc_final: 0.3281 (tpt)
REVERT: A  163 GLU cc_start: 0.7213 (mp0) cc_final: 0.7012 (mp0)
REVERT: A  176 MET cc_start: 0.8306 (ttm) cc_final: 0.8034 (ttt)
REVERT: A  279 PHE cc_start: 0.7128 (t80) cc_final: 0.6357 (t80)
REVERT: A  282 MET cc_start: 0.8248 (tpp) cc_final: 0.7778 (ttm)
REVERT: A  364 GLN cc_start: 0.7661 (pp30) cc_final: 0.7089 (tm-30)
REVERT: A  450 LYS cc_start: 0.7153 (OUTLIER) cc_final: 0.6827 (ttmm)
REVERT: A  452 ASP cc_start: 0.7198 (t70) cc_final: 0.6926 (t0)
REVERT: A  495 LYS cc_start: 0.8163 (mttm) cc_final: 0.7863 (mttm)
REVERT: A  525 ASP cc_start: 0.6109 (t70) cc_final: 0.5760 (t0)
REVERT: A  665 TRP cc_start: 0.5877 (m-90) cc_final: 0.5652 (m-90)
REVERT: A  729 LYS cc_start: 0.7185 (tptp) cc_final: 0.6506 (tptt)
REVERT: A  751 ILE cc_start: 0.5369 (OUTLIER) cc_final: 0.5056 (mp)
REVERT: A  762 GLU cc_start: 0.6709 (tm-30) cc_final: 0.6356 (tm-30)
REVERT: A  776 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7839 (pt)
REVERT: A  778 CYS cc_start: 0.7705 (t) cc_final: 0.6508 (m)
REVERT: A  794 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6881 (mt-10)
REVERT: B   77 HIS cc_start: 0.8179 (OUTLIER) cc_final: 0.7290 (m-70)
REVERT: B   98 GLU cc_start: 0.8308 (pm20) cc_final: 0.7998 (pm20)
REVERT: B  141 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7456 (mm-30)
REVERT: B  177 PHE cc_start: 0.7516 (m-80) cc_final: 0.7163 (m-10)
REVERT: B  220 PHE cc_start: 0.7464 (m-10) cc_final: 0.6990 (m-80)
REVERT: B  260 ARG cc_start: 0.7433 (ttm170) cc_final: 0.7200 (tpp80)
REVERT: B  279 PHE cc_start: 0.7553 (t80) cc_final: 0.7266 (t80)
REVERT: B  282 MET cc_start: 0.5247 (tpt) cc_final: 0.5018 (tpt)
REVERT: B  298 HIS cc_start: 0.7103 (t-90) cc_final: 0.6718 (t-90)
REVERT: B  345 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7059 (ptpp)
REVERT: B  357 GLU cc_start: 0.7464 (tp30) cc_final: 0.6878 (tp30)
REVERT: B  417 ILE cc_start: 0.7994 (tp) cc_final: 0.7736 (tp)
REVERT: B  495 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7409 (ttmm)
REVERT: B  529 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7602 (tmtt)
REVERT: B  590 HIS cc_start: 0.6627 (t70) cc_final: 0.6352 (t70)
REVERT: B  614 ASN cc_start: 0.7686 (m-40) cc_final: 0.7080 (m110)
REVERT: B  643 ASN cc_start: 0.7259 (p0) cc_final: 0.6968 (p0)
REVERT: B  689 PHE cc_start: 0.7672 (t80) cc_final: 0.7328 (t80)
REVERT: B  726 LYS cc_start: 0.8348 (mttt) cc_final: 0.7877 (ttmt)
  outliers start: 32
  outliers final: 18
  residues processed: 301
  average time/residue: 0.1382
  time to fit residues: 57.1046
Evaluate side-chains
  304 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 282
  time to evaluate  : 0.468 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  450 LYS
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  470 ASN
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  712 SER
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 130 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 35 optimal weight:    1.9990
   chunk 128 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.176549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.145852 restraints weight = 20695.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.150587 restraints weight = 11435.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.153863 restraints weight = 7516.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.156100 restraints weight = 5509.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.157103 restraints weight = 4368.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.1906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.113  12859  Z= 0.221
  Angle     :  0.700  11.190  17450  Z= 0.355
  Chirality :  0.047   0.179   1930
  Planarity :  0.005   0.049   2270
  Dihedral  :  6.361  73.783   1712
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 16.57 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.74 (0.21), residues: 1570
  helix:  0.36 (0.20), residues: 679
  sheet: -0.66 (0.28), residues: 331
  loop : -1.30 (0.27), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  71 
 TYR   0.032   0.002   TYR B  80 
 PHE   0.027   0.002   PHE B 602 
 TRP   0.020   0.002   TRP B 231 
 HIS   0.013   0.001   HIS B 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00517 (12858)
  covalent geometry    : angle       0.69958 (17450)
  hydrogen bonds       : bond        0.04562 (  623)
  hydrogen bonds       : angle       5.23784 ( 1800)
  Misc. bond           : bond        0.00155 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 299
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  131 ARG cc_start: 0.6467 (tpp80) cc_final: 0.6166 (tpp80)
REVERT: A  163 GLU cc_start: 0.7321 (mp0) cc_final: 0.7012 (mp0)
REVERT: A  176 MET cc_start: 0.8291 (ttm) cc_final: 0.8030 (ttt)
REVERT: A  279 PHE cc_start: 0.7297 (t80) cc_final: 0.6452 (t80)
REVERT: A  282 MET cc_start: 0.8228 (tpp) cc_final: 0.7806 (ttm)
REVERT: A  364 GLN cc_start: 0.7701 (pp30) cc_final: 0.7177 (tm-30)
REVERT: A  382 GLN cc_start: 0.6900 (tm-30) cc_final: 0.6536 (tm-30)
REVERT: A  450 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6893 (ttmm)
REVERT: A  452 ASP cc_start: 0.7267 (t70) cc_final: 0.6870 (t0)
REVERT: A  495 LYS cc_start: 0.8230 (mttm) cc_final: 0.7923 (mttm)
REVERT: A  525 ASP cc_start: 0.6129 (t70) cc_final: 0.5749 (t0)
REVERT: A  596 HIS cc_start: 0.4890 (t70) cc_final: 0.4549 (t70)
REVERT: A  665 TRP cc_start: 0.5953 (m-90) cc_final: 0.5700 (m-90)
REVERT: A  745 LEU cc_start: 0.8070 (mt) cc_final: 0.7850 (mp)
REVERT: A  751 ILE cc_start: 0.5115 (OUTLIER) cc_final: 0.4612 (mm)
REVERT: A  776 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7745 (pt)
REVERT: A  778 CYS cc_start: 0.7808 (t) cc_final: 0.6514 (m)
REVERT: A  794 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6991 (mt-10)
REVERT: B   77 HIS cc_start: 0.8160 (OUTLIER) cc_final: 0.7282 (m-70)
REVERT: B   98 GLU cc_start: 0.8334 (pm20) cc_final: 0.8030 (pm20)
REVERT: B  118 VAL cc_start: 0.4227 (OUTLIER) cc_final: 0.3964 (t)
REVERT: B  141 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7527 (mm-30)
REVERT: B  177 PHE cc_start: 0.7497 (m-80) cc_final: 0.7126 (m-10)
REVERT: B  187 MET cc_start: 0.6084 (ttp) cc_final: 0.5824 (tmm)
REVERT: B  201 ASP cc_start: 0.6821 (p0) cc_final: 0.6257 (p0)
REVERT: B  220 PHE cc_start: 0.7680 (m-10) cc_final: 0.7184 (m-80)
REVERT: B  260 ARG cc_start: 0.7354 (ttm170) cc_final: 0.7109 (tpp80)
REVERT: B  279 PHE cc_start: 0.7455 (t80) cc_final: 0.7143 (t80)
REVERT: B  282 MET cc_start: 0.5374 (tpt) cc_final: 0.5150 (tpt)
REVERT: B  298 HIS cc_start: 0.7107 (t-90) cc_final: 0.6741 (t-90)
REVERT: B  345 LYS cc_start: 0.7882 (ptpp) cc_final: 0.7106 (ptpp)
REVERT: B  357 GLU cc_start: 0.7431 (tp30) cc_final: 0.6824 (tp30)
REVERT: B  371 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7269 (mm)
REVERT: B  417 ILE cc_start: 0.8061 (tp) cc_final: 0.7776 (tp)
REVERT: B  495 LYS cc_start: 0.7824 (ttmm) cc_final: 0.7426 (ttmm)
REVERT: B  529 LYS cc_start: 0.8191 (tmtt) cc_final: 0.7606 (tmtt)
REVERT: B  590 HIS cc_start: 0.6651 (t70) cc_final: 0.6323 (t70)
REVERT: B  614 ASN cc_start: 0.7831 (m-40) cc_final: 0.7512 (m110)
REVERT: B  689 PHE cc_start: 0.7734 (t80) cc_final: 0.7463 (t80)
REVERT: B  726 LYS cc_start: 0.8375 (mttt) cc_final: 0.7909 (ttmt)
  outliers start: 43
  outliers final: 22
  residues processed: 321
  average time/residue: 0.1307
  time to fit residues: 58.4591
Evaluate side-chains
  313 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 285
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  450 LYS
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  364 GLN
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  712 SER
Chi-restraints excluded: chain B residue  729 LYS
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 77 optimal weight:    0.0770
   chunk 155 optimal weight:    0.0970
   chunk 97 optimal weight:    0.0970
   chunk 15 optimal weight:    0.5980
   chunk 142 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0980
   overall best weight:    0.1934

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

Flipped N/Q/H residues before XYZ refinement:
A  77 HIS
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 564 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.182634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.152843 restraints weight = 20793.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.157671 restraints weight = 11388.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.160899 restraints weight = 7429.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.162841 restraints weight = 5461.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.164428 restraints weight = 4401.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.4085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6496
moved from start:          0.2166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  12859  Z= 0.126
  Angle     :  0.654  11.301  17450  Z= 0.326
  Chirality :  0.045   0.234   1930
  Planarity :  0.005   0.065   2270
  Dihedral  :  6.178  73.585   1712
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.62 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1570
  helix:  0.76 (0.20), residues: 664
  sheet: -0.50 (0.28), residues: 331
  loop : -1.20 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 716 
 TYR   0.031   0.001   TYR B  80 
 PHE   0.060   0.002   PHE A 445 
 TRP   0.021   0.001   TRP B 618 
 HIS   0.005   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (12858)
  covalent geometry    : angle       0.65353 (17450)
  hydrogen bonds       : bond        0.03782 (  623)
  hydrogen bonds       : angle       4.93883 ( 1800)
  Misc. bond           : bond        0.00173 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 287
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LEU cc_start: 0.7332 (mt) cc_final: 0.7120 (mp)
REVERT: A  161 ASP cc_start: 0.6337 (p0) cc_final: 0.6132 (p0)
REVERT: A  279 PHE cc_start: 0.6928 (t80) cc_final: 0.6188 (t80)
REVERT: A  282 MET cc_start: 0.8052 (tpp) cc_final: 0.7613 (ttm)
REVERT: A  364 GLN cc_start: 0.7623 (pp30) cc_final: 0.7115 (tm-30)
REVERT: A  452 ASP cc_start: 0.7189 (t70) cc_final: 0.6895 (t0)
REVERT: A  525 ASP cc_start: 0.6084 (t70) cc_final: 0.5714 (t0)
REVERT: A  557 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8135 (ttmm)
REVERT: A  596 HIS cc_start: 0.4811 (t70) cc_final: 0.4488 (t70)
REVERT: A  598 PRO cc_start: 0.7927 (Cg_exo) cc_final: 0.7618 (Cg_endo)
REVERT: A  611 GLU cc_start: 0.6601 (mp0) cc_final: 0.6177 (mp0)
REVERT: A  665 TRP cc_start: 0.5881 (m-90) cc_final: 0.5667 (m-90)
REVERT: A  745 LEU cc_start: 0.8003 (mt) cc_final: 0.7706 (mp)
REVERT: A  751 ILE cc_start: 0.4808 (OUTLIER) cc_final: 0.4528 (mp)
REVERT: A  776 ILE cc_start: 0.8342 (OUTLIER) cc_final: 0.7973 (pt)
REVERT: A  778 CYS cc_start: 0.7685 (t) cc_final: 0.6440 (m)
REVERT: A  794 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6831 (mt-10)
REVERT: B   77 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7250 (m-70)
REVERT: B   98 GLU cc_start: 0.8305 (pm20) cc_final: 0.8035 (pm20)
REVERT: B  118 VAL cc_start: 0.4109 (OUTLIER) cc_final: 0.3809 (t)
REVERT: B  141 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7456 (mm-30)
REVERT: B  177 PHE cc_start: 0.7342 (m-80) cc_final: 0.7115 (m-10)
REVERT: B  187 MET cc_start: 0.6218 (ttp) cc_final: 0.5962 (tmm)
REVERT: B  201 ASP cc_start: 0.6911 (p0) cc_final: 0.6302 (p0)
REVERT: B  220 PHE cc_start: 0.7584 (m-10) cc_final: 0.7132 (m-80)
REVERT: B  260 ARG cc_start: 0.7416 (ttm170) cc_final: 0.7189 (tpp80)
REVERT: B  279 PHE cc_start: 0.7536 (t80) cc_final: 0.7220 (t80)
REVERT: B  298 HIS cc_start: 0.7111 (t-90) cc_final: 0.6674 (t-90)
REVERT: B  345 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7084 (ptpp)
REVERT: B  357 GLU cc_start: 0.7351 (tp30) cc_final: 0.6892 (tp30)
REVERT: B  417 ILE cc_start: 0.8047 (tp) cc_final: 0.7735 (tp)
REVERT: B  495 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7405 (ttmm)
REVERT: B  529 LYS cc_start: 0.8124 (tmtt) cc_final: 0.7579 (tmtt)
REVERT: B  590 HIS cc_start: 0.6541 (t70) cc_final: 0.6283 (t70)
REVERT: B  614 ASN cc_start: 0.7685 (m-40) cc_final: 0.7235 (m110)
REVERT: B  689 PHE cc_start: 0.7631 (t80) cc_final: 0.7360 (t80)
REVERT: B  744 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7891 (tp)
  outliers start: 35
  outliers final: 20
  residues processed: 307
  average time/residue: 0.1268
  time to fit residues: 54.4640
Evaluate side-chains
  306 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 281
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  364 GLN
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 53 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 97 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 397 ASN
B 564 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.180040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.150019 restraints weight = 20616.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.154852 restraints weight = 11363.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.158056 restraints weight = 7450.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.160096 restraints weight = 5485.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.161662 restraints weight = 4411.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.110  12859  Z= 0.217
  Angle     :  0.715  14.630  17450  Z= 0.363
  Chirality :  0.047   0.192   1930
  Planarity :  0.005   0.058   2270
  Dihedral  :  6.333  72.854   1712
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 19.35 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.74 (0.21), residues: 1570
  helix:  0.44 (0.20), residues: 672
  sheet: -0.66 (0.28), residues: 331
  loop : -1.41 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 131 
 TYR   0.031   0.002   TYR B  80 
 PHE   0.027   0.002   PHE B 602 
 TRP   0.021   0.002   TRP B 618 
 HIS   0.006   0.001   HIS B  77 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (12858)
  covalent geometry    : angle       0.71452 (17450)
  hydrogen bonds       : bond        0.04419 (  623)
  hydrogen bonds       : angle       5.21994 ( 1800)
  Misc. bond           : bond        0.00136 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 289
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.7245 (ttm170) cc_final: 0.7023 (mtt-85)
REVERT: A  279 PHE cc_start: 0.7157 (t80) cc_final: 0.6341 (t80)
REVERT: A  282 MET cc_start: 0.8182 (tpp) cc_final: 0.7768 (ttm)
REVERT: A  364 GLN cc_start: 0.7694 (pp30) cc_final: 0.7240 (tm-30)
REVERT: A  452 ASP cc_start: 0.7187 (t70) cc_final: 0.6900 (t0)
REVERT: A  495 LYS cc_start: 0.8200 (mttm) cc_final: 0.7877 (mttm)
REVERT: A  525 ASP cc_start: 0.6116 (t70) cc_final: 0.5727 (t0)
REVERT: A  596 HIS cc_start: 0.4955 (t70) cc_final: 0.4437 (t70)
REVERT: A  598 PRO cc_start: 0.8028 (Cg_exo) cc_final: 0.7753 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6127 (m-90) cc_final: 0.5845 (m-90)
REVERT: A  745 LEU cc_start: 0.8061 (mt) cc_final: 0.7727 (mp)
REVERT: A  751 ILE cc_start: 0.5154 (OUTLIER) cc_final: 0.4799 (pt)
REVERT: A  776 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8039 (pt)
REVERT: A  778 CYS cc_start: 0.7779 (t) cc_final: 0.6638 (m)
REVERT: A  794 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6920 (mt-10)
REVERT: B   77 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7425 (m-70)
REVERT: B   98 GLU cc_start: 0.8290 (pm20) cc_final: 0.8008 (pm20)
REVERT: B  118 VAL cc_start: 0.4091 (OUTLIER) cc_final: 0.3814 (t)
REVERT: B  136 GLU cc_start: 0.6826 (tp30) cc_final: 0.6572 (tp30)
REVERT: B  141 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7565 (mm-30)
REVERT: B  177 PHE cc_start: 0.7346 (m-80) cc_final: 0.7057 (m-10)
REVERT: B  187 MET cc_start: 0.6208 (ttp) cc_final: 0.6007 (tmm)
REVERT: B  220 PHE cc_start: 0.7656 (m-10) cc_final: 0.7208 (m-80)
REVERT: B  260 ARG cc_start: 0.7309 (ttm170) cc_final: 0.7073 (tpp80)
REVERT: B  279 PHE cc_start: 0.7482 (t80) cc_final: 0.7248 (t80)
REVERT: B  298 HIS cc_start: 0.7087 (t-90) cc_final: 0.6670 (t-90)
REVERT: B  345 LYS cc_start: 0.7924 (ptpp) cc_final: 0.7109 (ptpp)
REVERT: B  371 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7339 (mm)
REVERT: B  417 ILE cc_start: 0.8051 (tp) cc_final: 0.7756 (tp)
REVERT: B  495 LYS cc_start: 0.7807 (ttmm) cc_final: 0.7413 (ttmm)
REVERT: B  529 LYS cc_start: 0.8147 (tmtt) cc_final: 0.7731 (tmtt)
REVERT: B  614 ASN cc_start: 0.7718 (m-40) cc_final: 0.7197 (m110)
REVERT: B  689 PHE cc_start: 0.7676 (t80) cc_final: 0.7191 (t80)
  outliers start: 49
  outliers final: 34
  residues processed: 314
  average time/residue: 0.1248
  time to fit residues: 54.4708
Evaluate side-chains
  325 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 286
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  397 ASN
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  545 MET
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  605 LEU
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  181 ILE
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  364 GLN
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  692 ILE
Chi-restraints excluded: chain B residue  712 SER
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 89 optimal weight:    2.9990
   chunk 132 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    0.1980
   chunk 24 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9990
   chunk 139 optimal weight:    0.0270
   chunk 31 optimal weight:    0.2980
   chunk 3 optimal weight:    0.4980
   chunk 104 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   overall best weight:    0.3238

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 626 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.179528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.149445 restraints weight = 20578.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.154175 restraints weight = 11253.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.157332 restraints weight = 7295.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.159476 restraints weight = 5337.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.160839 restraints weight = 4225.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6509
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072  12859  Z= 0.143
  Angle     :  0.687  12.553  17450  Z= 0.346
  Chirality :  0.046   0.174   1930
  Planarity :  0.005   0.048   2270
  Dihedral  :  6.262  73.253   1712
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 21.19 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.48 (0.21), residues: 1570
  helix:  0.71 (0.20), residues: 667
  sheet: -0.49 (0.28), residues: 321
  loop : -1.34 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 131 
 TYR   0.030   0.001   TYR B  80 
 PHE   0.058   0.002   PHE A 445 
 TRP   0.031   0.001   TRP B 231 
 HIS   0.007   0.001   HIS A 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (12858)
  covalent geometry    : angle       0.68682 (17450)
  hydrogen bonds       : bond        0.03890 (  623)
  hydrogen bonds       : angle       5.03698 ( 1800)
  Misc. bond           : bond        0.00178 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 289
  time to evaluate  : 0.470 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 LEU cc_start: 0.7415 (mt) cc_final: 0.7173 (mp)
REVERT: A  279 PHE cc_start: 0.6980 (t80) cc_final: 0.6178 (t80)
REVERT: A  282 MET cc_start: 0.8015 (tpp) cc_final: 0.7619 (ttm)
REVERT: A  364 GLN cc_start: 0.7654 (pp30) cc_final: 0.7179 (tm-30)
REVERT: A  452 ASP cc_start: 0.7115 (t70) cc_final: 0.6872 (t0)
REVERT: A  525 ASP cc_start: 0.6083 (t70) cc_final: 0.5711 (t0)
REVERT: A  596 HIS cc_start: 0.4843 (t70) cc_final: 0.4374 (t70)
REVERT: A  598 PRO cc_start: 0.7932 (Cg_exo) cc_final: 0.7636 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6089 (m-90) cc_final: 0.5831 (m-90)
REVERT: A  745 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: A  776 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7997 (pt)
REVERT: A  778 CYS cc_start: 0.7721 (t) cc_final: 0.6621 (m)
REVERT: A  794 GLU cc_start: 0.7101 (mt-10) cc_final: 0.6812 (mt-10)
REVERT: B   77 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7345 (m-70)
REVERT: B  118 VAL cc_start: 0.4017 (OUTLIER) cc_final: 0.3747 (t)
REVERT: B  141 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7592 (mm-30)
REVERT: B  187 MET cc_start: 0.6327 (ttp) cc_final: 0.6098 (tmm)
REVERT: B  201 ASP cc_start: 0.6992 (p0) cc_final: 0.6371 (p0)
REVERT: B  220 PHE cc_start: 0.7556 (m-10) cc_final: 0.7142 (m-80)
REVERT: B  260 ARG cc_start: 0.7433 (ttm170) cc_final: 0.7171 (tpp80)
REVERT: B  279 PHE cc_start: 0.7478 (t80) cc_final: 0.7215 (t80)
REVERT: B  298 HIS cc_start: 0.7071 (t-90) cc_final: 0.6650 (t-90)
REVERT: B  345 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7086 (ptpp)
REVERT: B  371 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7414 (mm)
REVERT: B  372 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6725 (tm-30)
REVERT: B  417 ILE cc_start: 0.8060 (tp) cc_final: 0.7741 (tp)
REVERT: B  495 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7404 (ttmm)
REVERT: B  529 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7566 (tmtt)
REVERT: B  536 GLN cc_start: 0.7010 (mm110) cc_final: 0.6800 (mm-40)
REVERT: B  590 HIS cc_start: 0.6797 (t-90) cc_final: 0.6336 (t70)
REVERT: B  591 ASP cc_start: 0.6731 (t70) cc_final: 0.6200 (p0)
REVERT: B  614 ASN cc_start: 0.7636 (m-40) cc_final: 0.7134 (m110)
REVERT: B  689 PHE cc_start: 0.7667 (t80) cc_final: 0.7222 (t80)
  outliers start: 40
  outliers final: 24
  residues processed: 312
  average time/residue: 0.1330
  time to fit residues: 57.2778
Evaluate side-chains
  311 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 282
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  366 MET
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  364 GLN
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  712 SER
Chi-restraints excluded: chain B residue  718 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 138 optimal weight:    0.5980
   chunk 81 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 155 optimal weight:    0.0070
   chunk 29 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0270
   chunk 112 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 385 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.178500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.148400 restraints weight = 20432.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.153125 restraints weight = 11212.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156267 restraints weight = 7301.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.158365 restraints weight = 5351.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.159841 restraints weight = 4246.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.2494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.089  12859  Z= 0.177
  Angle     :  0.723  12.365  17450  Z= 0.364
  Chirality :  0.047   0.303   1930
  Planarity :  0.005   0.049   2270
  Dihedral  :  6.327  75.312   1712
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 21.92 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.61 (0.21), residues: 1570
  helix:  0.58 (0.20), residues: 668
  sheet: -0.61 (0.28), residues: 325
  loop : -1.33 (0.26), residues: 577

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 131 
 TYR   0.031   0.002   TYR B  80 
 PHE   0.028   0.002   PHE A 770 
 TRP   0.024   0.002   TRP B 618 
 HIS   0.006   0.001   HIS B 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 (12858)
  covalent geometry    : angle       0.72341 (17450)
  hydrogen bonds       : bond        0.04117 (  623)
  hydrogen bonds       : angle       5.08950 ( 1800)
  Misc. bond           : bond        0.00154 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 282
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 PHE cc_start: 0.7106 (t80) cc_final: 0.6272 (t80)
REVERT: A  282 MET cc_start: 0.8166 (tpp) cc_final: 0.7772 (ttm)
REVERT: A  364 GLN cc_start: 0.7653 (pp30) cc_final: 0.7193 (tm-30)
REVERT: A  452 ASP cc_start: 0.7131 (t70) cc_final: 0.6922 (t0)
REVERT: A  495 LYS cc_start: 0.8169 (mttm) cc_final: 0.7859 (mttm)
REVERT: A  525 ASP cc_start: 0.6085 (t70) cc_final: 0.5721 (t0)
REVERT: A  596 HIS cc_start: 0.4826 (t70) cc_final: 0.4382 (t70)
REVERT: A  598 PRO cc_start: 0.7983 (Cg_exo) cc_final: 0.7692 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6121 (m-90) cc_final: 0.5824 (m-90)
REVERT: A  745 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7761 (mp)
REVERT: A  776 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8004 (pt)
REVERT: A  778 CYS cc_start: 0.7706 (t) cc_final: 0.6600 (m)
REVERT: A  794 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6843 (mt-10)
REVERT: B   77 HIS cc_start: 0.8022 (OUTLIER) cc_final: 0.7298 (m-70)
REVERT: B   98 GLU cc_start: 0.8185 (pm20) cc_final: 0.7791 (pm20)
REVERT: B  118 VAL cc_start: 0.3748 (OUTLIER) cc_final: 0.3432 (t)
REVERT: B  141 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7591 (mm-30)
REVERT: B  177 PHE cc_start: 0.7322 (m-80) cc_final: 0.7062 (m-10)
REVERT: B  187 MET cc_start: 0.6392 (ttp) cc_final: 0.6177 (tmm)
REVERT: B  220 PHE cc_start: 0.7555 (m-10) cc_final: 0.7151 (m-80)
REVERT: B  260 ARG cc_start: 0.7281 (ttm170) cc_final: 0.7004 (tpp80)
REVERT: B  279 PHE cc_start: 0.7517 (t80) cc_final: 0.7243 (t80)
REVERT: B  288 ARG cc_start: 0.6271 (ptp-110) cc_final: 0.5973 (ptp-110)
REVERT: B  298 HIS cc_start: 0.7075 (t-90) cc_final: 0.6658 (t-90)
REVERT: B  345 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7108 (ptpp)
REVERT: B  371 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7422 (mm)
REVERT: B  372 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6745 (tm-30)
REVERT: B  417 ILE cc_start: 0.8050 (tp) cc_final: 0.7753 (tp)
REVERT: B  495 LYS cc_start: 0.7780 (ttmm) cc_final: 0.7431 (ttmm)
REVERT: B  529 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7582 (tmtt)
REVERT: B  614 ASN cc_start: 0.7632 (m-40) cc_final: 0.7148 (m110)
REVERT: B  675 GLU cc_start: 0.6744 (mp0) cc_final: 0.6273 (mm-30)
REVERT: B  689 PHE cc_start: 0.7673 (t80) cc_final: 0.7230 (t80)
  outliers start: 41
  outliers final: 28
  residues processed: 305
  average time/residue: 0.1285
  time to fit residues: 54.3588
Evaluate side-chains
  319 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 286
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  682 MET
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  725 ILE
Chi-restraints excluded: chain A residue  745 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  364 GLN
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  663 HIS
Chi-restraints excluded: chain B residue  712 SER
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 120 optimal weight:    0.0970
   chunk 134 optimal weight:    0.0670
   chunk 113 optimal weight:    0.9990
   chunk 29 optimal weight:    0.0010
   chunk 5 optimal weight:    0.0870
   chunk 140 optimal weight:    0.1980
   chunk 107 optimal weight:    0.8980
   chunk 78 optimal weight:    0.0770
   chunk 110 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 141 optimal weight:    0.9980
   overall best weight:    0.0658

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 248 ASN
** A 298 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 570 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 397 ASN
B 564 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.181559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.151879 restraints weight = 20744.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.156611 restraints weight = 11321.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.159780 restraints weight = 7312.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.161894 restraints weight = 5303.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.163238 restraints weight = 4210.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.4092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  12859  Z= 0.131
  Angle     :  0.697  11.330  17450  Z= 0.349
  Chirality :  0.045   0.240   1930
  Planarity :  0.005   0.048   2270
  Dihedral  :  6.166  75.760   1712
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.46 %
    Favored  : 74.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.38 (0.22), residues: 1570
  helix:  0.77 (0.21), residues: 671
  sheet: -0.39 (0.29), residues: 323
  loop : -1.30 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 131 
 TYR   0.028   0.001   TYR B  80 
 PHE   0.028   0.002   PHE A 770 
 TRP   0.032   0.002   TRP B 231 
 HIS   0.008   0.001   HIS B 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (12858)
  covalent geometry    : angle       0.69671 (17450)
  hydrogen bonds       : bond        0.03532 (  623)
  hydrogen bonds       : angle       4.82159 ( 1800)
  Misc. bond           : bond        0.00176 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 285
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.1986 (tpt) cc_final: 0.0534 (tpt)
REVERT: A   66 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6354 (t0)
REVERT: A  210 LEU cc_start: 0.7936 (mp) cc_final: 0.7581 (tt)
REVERT: A  279 PHE cc_start: 0.6621 (t80) cc_final: 0.5840 (t80)
REVERT: A  282 MET cc_start: 0.7948 (tpp) cc_final: 0.7497 (ttm)
REVERT: A  364 GLN cc_start: 0.7545 (pp30) cc_final: 0.7044 (tm-30)
REVERT: A  374 GLU cc_start: 0.7818 (tp30) cc_final: 0.7575 (tp30)
REVERT: A  389 MET cc_start: 0.5539 (ttm) cc_final: 0.5181 (tmm)
REVERT: A  452 ASP cc_start: 0.7059 (t70) cc_final: 0.6828 (t70)
REVERT: A  461 THR cc_start: 0.6826 (p) cc_final: 0.6619 (m)
REVERT: A  525 ASP cc_start: 0.6038 (t70) cc_final: 0.5667 (t0)
REVERT: A  557 LYS cc_start: 0.8333 (mtpp) cc_final: 0.8056 (ttmm)
REVERT: A  596 HIS cc_start: 0.4829 (t70) cc_final: 0.4436 (t70)
REVERT: A  598 PRO cc_start: 0.7802 (Cg_exo) cc_final: 0.7484 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6094 (m-90) cc_final: 0.5784 (m-90)
REVERT: A  678 GLU cc_start: 0.7125 (pp20) cc_final: 0.6664 (tm-30)
REVERT: A  729 LYS cc_start: 0.7071 (tptt) cc_final: 0.6636 (tptt)
REVERT: A  740 ARG cc_start: 0.5345 (mpp-170) cc_final: 0.4466 (mpp-170)
REVERT: A  745 LEU cc_start: 0.8011 (mt) cc_final: 0.7703 (mp)
REVERT: A  776 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7985 (pt)
REVERT: A  778 CYS cc_start: 0.7487 (t) cc_final: 0.6905 (m)
REVERT: B   77 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7311 (m-70)
REVERT: B   98 GLU cc_start: 0.8219 (pm20) cc_final: 0.7806 (pm20)
REVERT: B  118 VAL cc_start: 0.4102 (OUTLIER) cc_final: 0.3822 (t)
REVERT: B  136 GLU cc_start: 0.6627 (tp30) cc_final: 0.6400 (tp30)
REVERT: B  187 MET cc_start: 0.6192 (ttp) cc_final: 0.5965 (tmm)
REVERT: B  220 PHE cc_start: 0.7544 (m-10) cc_final: 0.7172 (m-80)
REVERT: B  288 ARG cc_start: 0.6323 (ptp-110) cc_final: 0.5968 (ptp-110)
REVERT: B  298 HIS cc_start: 0.7095 (t-90) cc_final: 0.6700 (t-90)
REVERT: B  345 LYS cc_start: 0.7915 (ptpp) cc_final: 0.7119 (ptpp)
REVERT: B  371 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7348 (mm)
REVERT: B  417 ILE cc_start: 0.8209 (tp) cc_final: 0.7860 (tp)
REVERT: B  495 LYS cc_start: 0.7720 (ttmm) cc_final: 0.7362 (ttmm)
REVERT: B  529 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7518 (tmtt)
REVERT: B  590 HIS cc_start: 0.6612 (t-90) cc_final: 0.6289 (t70)
REVERT: B  614 ASN cc_start: 0.7573 (m-40) cc_final: 0.7172 (m110)
REVERT: B  675 GLU cc_start: 0.6682 (mp0) cc_final: 0.6246 (mm-30)
REVERT: B  689 PHE cc_start: 0.7688 (t80) cc_final: 0.7328 (t80)
REVERT: B  786 PHE cc_start: 0.6567 (m-10) cc_final: 0.6033 (m-10)
  outliers start: 31
  outliers final: 18
  residues processed: 305
  average time/residue: 0.1472
  time to fit residues: 61.3109
Evaluate side-chains
  297 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 274
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  712 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 155 optimal weight:    0.0970
   chunk 73 optimal weight:    0.8980
   chunk 151 optimal weight:    0.5980
   chunk 152 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 141 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** B 365 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.177385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.147070 restraints weight = 20715.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.151725 restraints weight = 11424.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.154869 restraints weight = 7486.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.156764 restraints weight = 5482.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.158440 restraints weight = 4424.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6542
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098  12859  Z= 0.208
  Angle     :  0.764   9.937  17450  Z= 0.387
  Chirality :  0.048   0.236   1930
  Planarity :  0.005   0.054   2270
  Dihedral  :  6.294  78.382   1712
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 12.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 23.46 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.63 (0.21), residues: 1570
  helix:  0.54 (0.20), residues: 674
  sheet: -0.67 (0.28), residues: 327
  loop : -1.31 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 131 
 TYR   0.031   0.002   TYR B  80 
 PHE   0.024   0.002   PHE B 602 
 TRP   0.033   0.002   TRP B 231 
 HIS   0.008   0.001   HIS B 590 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (12858)
  covalent geometry    : angle       0.76412 (17450)
  hydrogen bonds       : bond        0.04283 (  623)
  hydrogen bonds       : angle       5.08262 ( 1800)
  Misc. bond           : bond        0.00138 (    1)

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 282
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.2005 (tpt) cc_final: 0.0222 (tpt)
REVERT: A  131 ARG cc_start: 0.6567 (tpp80) cc_final: 0.5806 (tpp80)
REVERT: A  279 PHE cc_start: 0.7141 (t80) cc_final: 0.6283 (t80)
REVERT: A  282 MET cc_start: 0.8192 (tpp) cc_final: 0.7776 (ttm)
REVERT: A  364 GLN cc_start: 0.7640 (pp30) cc_final: 0.7168 (tm-30)
REVERT: A  452 ASP cc_start: 0.7108 (t70) cc_final: 0.6902 (t0)
REVERT: A  525 ASP cc_start: 0.6066 (t70) cc_final: 0.5715 (t0)
REVERT: A  557 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8148 (ttmm)
REVERT: A  596 HIS cc_start: 0.4811 (t70) cc_final: 0.4402 (t70)
REVERT: A  598 PRO cc_start: 0.7963 (Cg_exo) cc_final: 0.7680 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6162 (m-90) cc_final: 0.5854 (m-90)
REVERT: A  745 LEU cc_start: 0.8022 (mt) cc_final: 0.7695 (mp)
REVERT: A  770 PHE cc_start: 0.6848 (t80) cc_final: 0.6645 (t80)
REVERT: A  776 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.8018 (pt)
REVERT: A  778 CYS cc_start: 0.7694 (t) cc_final: 0.6777 (m)
REVERT: B   77 HIS cc_start: 0.8092 (OUTLIER) cc_final: 0.7348 (m-70)
REVERT: B  118 VAL cc_start: 0.3927 (OUTLIER) cc_final: 0.3622 (t)
REVERT: B  136 GLU cc_start: 0.6794 (tp30) cc_final: 0.6515 (tp30)
REVERT: B  141 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7618 (mm-30)
REVERT: B  187 MET cc_start: 0.6315 (ttp) cc_final: 0.6105 (tmm)
REVERT: B  220 PHE cc_start: 0.7594 (m-10) cc_final: 0.7247 (m-80)
REVERT: B  279 PHE cc_start: 0.7592 (t80) cc_final: 0.7379 (t80)
REVERT: B  288 ARG cc_start: 0.6410 (ptp-110) cc_final: 0.6106 (ptp-110)
REVERT: B  298 HIS cc_start: 0.7021 (t-90) cc_final: 0.6703 (t-90)
REVERT: B  345 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7172 (ptpp)
REVERT: B  371 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7281 (mm)
REVERT: B  417 ILE cc_start: 0.8083 (tp) cc_final: 0.7761 (tp)
REVERT: B  495 LYS cc_start: 0.7653 (ttmm) cc_final: 0.7335 (ttmm)
REVERT: B  529 LYS cc_start: 0.8127 (tmtt) cc_final: 0.7683 (tmtt)
REVERT: B  590 HIS cc_start: 0.6729 (t-90) cc_final: 0.6355 (t70)
REVERT: B  614 ASN cc_start: 0.7617 (m-40) cc_final: 0.7118 (m-40)
REVERT: B  675 GLU cc_start: 0.6733 (mp0) cc_final: 0.6246 (mm-30)
REVERT: B  689 PHE cc_start: 0.7704 (t80) cc_final: 0.7343 (t80)
REVERT: B  706 ASP cc_start: 0.6846 (t0) cc_final: 0.6576 (t0)
  outliers start: 30
  outliers final: 21
  residues processed: 299
  average time/residue: 0.1500
  time to fit residues: 61.5813
Evaluate side-chains
  302 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 277
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  636 HIS
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  730 SER
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  416 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  712 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 109 optimal weight:    0.5980
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 118 optimal weight:    0.0970
   chunk 27 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   chunk 112 optimal weight:    0.7980
   chunk 57 optimal weight:    0.5980
   chunk 51 optimal weight:    0.4980
   chunk 147 optimal weight:    1.9990
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
A 562 ASN
B 168 GLN
B 364 GLN
B 365 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.178883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148565 restraints weight = 20744.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.153196 restraints weight = 11399.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156320 restraints weight = 7447.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.158307 restraints weight = 5486.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.159870 restraints weight = 4427.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6510
moved from start:          0.2837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  12859  Z= 0.157
  Angle     :  0.752   9.380  17450  Z= 0.380
  Chirality :  0.047   0.212   1930
  Planarity :  0.005   0.054   2270
  Dihedral  :  6.265  77.059   1712
  Min Nonbonded Distance : 2.306

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 24.56 %
    Favored  : 72.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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 aren not related in a simple way.
  whole: -0.56 (0.21), residues: 1570
  helix:  0.59 (0.20), residues: 672
  sheet: -0.61 (0.28), residues: 325
  loop : -1.28 (0.27), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 131 
 TYR   0.030   0.001   TYR B  80 
 PHE   0.023   0.002   PHE B 602 
 TRP   0.033   0.002   TRP B 231 
 HIS   0.012   0.001   HIS B 365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12858)
  covalent geometry    : angle       0.75168 (17450)
  hydrogen bonds       : bond        0.03996 (  623)
  hydrogen bonds       : angle       4.99614 ( 1800)
  Misc. bond           : bond        0.00142 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2436.62 seconds
wall clock time: 42 minutes 43.91 seconds (2563.91 seconds total)