Starting phenix.real_space_refine
on Wed Jul 30 18:32:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgv_44524/07_2025/9bgv_44524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgv_44524/07_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_44524/07_2025/9bgv_44524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgv_44524/07_2025/9bgv_44524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgv_44524/07_2025/9bgv_44524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgv_44524/07_2025/9bgv_44524.cif"
  }
  resolution = 3.65
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.53, per 1000 atoms: 0.60
  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: 3.00
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  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: 1.59
  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: 4.57

  Time building geometry restraints manager: 3.60 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     31.020
  Find NCS groups from input model:        0.440
  Set up NCS constraints:                  0.060
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.190
-------------------------------------------------------------------------------
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 : 11.07
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (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
 TRP   0.017   0.002   TRP B 589 
 HIS   0.004   0.001   HIS A 521 
 PHE   0.018   0.002   PHE B 602 
 TYR   0.020   0.002   TYR A 507 
 ARG   0.006   0.000   ARG B 444 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11846 (  623)
  hydrogen bonds       : angle       5.88331 ( 1800)
  covalent geometry    : bond        0.00454 (12858)
  covalent geometry    : angle       0.69162 (17450)
  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  : 1.242 
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   31 MET cc_start: 0.3936 (tpt) cc_final: 0.3577 (tpt)
REVERT: A   95 MET cc_start: 0.3926 (mtp) cc_final: 0.3674 (mtp)
REVERT: A  185 SER cc_start: 0.7496 (t) cc_final: 0.7229 (p)
REVERT: A  279 PHE cc_start: 0.7197 (t80) cc_final: 0.6641 (t80)
REVERT: A  282 MET cc_start: 0.8093 (tpp) cc_final: 0.7272 (ttm)
REVERT: A  364 GLN cc_start: 0.7732 (pp30) cc_final: 0.7059 (tm-30)
REVERT: A  452 ASP cc_start: 0.7166 (t70) cc_final: 0.6829 (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: 0.6601 (tm-30)
REVERT: A  778 CYS cc_start: 0.7713 (t) cc_final: 0.7463 (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: 0.7914 (pm20)
REVERT: B  177 PHE cc_start: 0.7605 (m-80) cc_final: 0.7398 (m-80)
REVERT: B  279 PHE cc_start: 0.7435 (t80) cc_final: 0.7138 (t80)
REVERT: B  282 MET cc_start: 0.5374 (tpt) cc_final: 0.5110 (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: 0.7076 (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: 0.6470 (m-30)
REVERT: B  493 ASP cc_start: 0.6854 (t0) cc_final: 0.6551 (t0)
REVERT: B  495 LYS cc_start: 0.7951 (ttmm) cc_final: 0.7477 (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: 0.6701 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 324
  average time/residue: 0.2876
  time to fit residues: 126.8940
Evaluate side-chains
  286 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 286
  time to evaluate  : 1.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.5980
   chunk 118 optimal weight:    0.5980
   chunk 65 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 63 optimal weight:    0.4980
   chunk 122 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   chunk 91 optimal weight:    0.5980
   chunk 141 optimal weight:    0.9980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 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 = 0.4257 r_free = 0.4257 target = 0.178955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148868 restraints weight = 20641.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.153390 restraints weight = 11515.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.156530 restraints weight = 7603.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.1384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.095  12859  Z= 0.187
  Angle     :  0.691  12.908  17450  Z= 0.347
  Chirality :  0.047   0.180   1930
  Planarity :  0.005   0.074   2270
  Dihedral  :  6.329  70.963   1712
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 13.12 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.22), residues: 1570
  helix:  0.67 (0.21), residues: 654
  sheet: -0.57 (0.28), residues: 323
  loop : -1.13 (0.27), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 589 
 HIS   0.012   0.001   HIS B  77 
 PHE   0.029   0.002   PHE B 602 
 TYR   0.016   0.002   TYR A 507 
 ARG   0.008   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04560 (  623)
  hydrogen bonds       : angle       5.22625 ( 1800)
  covalent geometry    : bond        0.00435 (12858)
  covalent geometry    : angle       0.69102 (17450)
  Misc. bond           : bond        0.00462 (    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
  327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 303
  time to evaluate  : 1.378 
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: 0.3890 (mtp) cc_final: 0.3633 (mtp)
REVERT: A  163 GLU cc_start: 0.7317 (mp0) cc_final: 0.7031 (mp0)
REVERT: A  185 SER cc_start: 0.7428 (t) cc_final: 0.7204 (m)
REVERT: A  279 PHE cc_start: 0.7248 (t80) cc_final: 0.6478 (t80)
REVERT: A  282 MET cc_start: 0.8284 (tpp) cc_final: 0.7837 (ttm)
REVERT: A  345 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7874 (mttt)
REVERT: A  364 GLN cc_start: 0.7738 (pp30) cc_final: 0.7104 (tm-30)
REVERT: A  389 MET cc_start: 0.6996 (ttp) cc_final: 0.6635 (ttm)
REVERT: A  452 ASP cc_start: 0.7264 (t70) cc_final: 0.6892 (t0)
REVERT: A  502 SER cc_start: 0.7399 (t) cc_final: 0.7179 (t)
REVERT: A  525 ASP cc_start: 0.6172 (t70) cc_final: 0.5816 (t0)
REVERT: A  665 TRP cc_start: 0.5955 (m-90) cc_final: 0.5698 (m-90)
REVERT: A  678 GLU cc_start: 0.7469 (pm20) cc_final: 0.7242 (pp20)
REVERT: A  716 ARG cc_start: 0.7088 (tpp-160) cc_final: 0.6796 (mmm160)
REVERT: A  745 LEU cc_start: 0.8130 (mt) cc_final: 0.7859 (mt)
REVERT: A  751 ILE cc_start: 0.5636 (OUTLIER) cc_final: 0.5327 (mp)
REVERT: A  778 CYS cc_start: 0.7839 (t) cc_final: 0.7554 (t)
REVERT: A  794 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6968 (mt-10)
REVERT: B   98 GLU cc_start: 0.8300 (pm20) cc_final: 0.7979 (pm20)
REVERT: B  112 ARG cc_start: 0.7668 (mtp85) cc_final: 0.7378 (mtp85)
REVERT: B  139 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7401 (tp-100)
REVERT: B  141 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7507 (mm-30)
REVERT: B  177 PHE cc_start: 0.7537 (m-80) cc_final: 0.7104 (m-10)
REVERT: B  260 ARG cc_start: 0.7461 (ttm170) cc_final: 0.7227 (tpp80)
REVERT: B  279 PHE cc_start: 0.7462 (t80) cc_final: 0.7199 (t80)
REVERT: B  282 MET cc_start: 0.5363 (tpt) cc_final: 0.5113 (tpt)
REVERT: B  298 HIS cc_start: 0.7127 (t-90) cc_final: 0.6747 (t-90)
REVERT: B  311 HIS cc_start: 0.6777 (t-90) cc_final: 0.6528 (t-90)
REVERT: B  345 LYS cc_start: 0.7917 (ptpp) cc_final: 0.7068 (ptpp)
REVERT: B  493 ASP cc_start: 0.6743 (t0) cc_final: 0.6399 (t0)
REVERT: B  495 LYS cc_start: 0.7821 (ttmm) cc_final: 0.7371 (ttmm)
REVERT: B  529 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7624 (tmtt)
REVERT: B  590 HIS cc_start: 0.6655 (t70) cc_final: 0.6390 (t70)
REVERT: B  614 ASN cc_start: 0.7629 (m-40) cc_final: 0.7209 (m-40)
REVERT: B  689 PHE cc_start: 0.7667 (t80) cc_final: 0.7221 (t80)
REVERT: B  716 ARG cc_start: 0.7116 (mmm160) cc_final: 0.6727 (mmm160)
REVERT: B  726 LYS cc_start: 0.8322 (mttt) cc_final: 0.7868 (ttmt)
  outliers start: 24
  outliers final: 11
  residues processed: 308
  average time/residue: 0.3032
  time to fit residues: 126.7895
Evaluate side-chains
  291 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 278
  time to evaluate  : 1.264 
-------------------------------------------------------------------------------
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  310 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 91 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9990
   chunk 10 optimal weight:    7.9990
   chunk 137 optimal weight:    0.1980
   chunk 31 optimal weight:    0.9980
   chunk 123 optimal weight:    0.2980
   chunk 19 optimal weight:    0.4980
   chunk 12 optimal weight:    0.3980
   chunk 9 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.3580

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.182154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.152505 restraints weight = 20649.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.157290 restraints weight = 11391.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.160527 restraints weight = 7478.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6577
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  12859  Z= 0.142
  Angle     :  0.648  11.587  17450  Z= 0.325
  Chirality :  0.045   0.178   1930
  Planarity :  0.005   0.056   2270
  Dihedral  :  6.228  73.612   1712
  Min Nonbonded Distance : 2.342

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.22), residues: 1570
  helix:  0.70 (0.21), residues: 660
  sheet: -0.44 (0.28), residues: 321
  loop : -1.20 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 231 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.056   0.002   PHE A 445 
 TYR   0.029   0.002   TYR B  80 
 ARG   0.005   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04092 (  623)
  hydrogen bonds       : angle       5.02314 ( 1800)
  covalent geometry    : bond        0.00333 (12858)
  covalent geometry    : angle       0.64794 (17450)
  Misc. bond           : bond        0.00282 (    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
  325 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 298
  time to evaluate  : 1.265 
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: 0.3522 (tpt) cc_final: 0.3312 (tpt)
REVERT: A  279 PHE cc_start: 0.7076 (t80) cc_final: 0.6339 (t80)
REVERT: A  282 MET cc_start: 0.8118 (tpp) cc_final: 0.7660 (ttm)
REVERT: A  364 GLN cc_start: 0.7688 (pp30) cc_final: 0.7112 (tm-30)
REVERT: A  452 ASP cc_start: 0.7167 (t70) cc_final: 0.6816 (t0)
REVERT: A  457 ARG cc_start: 0.5845 (ttm-80) cc_final: 0.5574 (ttm-80)
REVERT: A  525 ASP cc_start: 0.6146 (t70) cc_final: 0.5789 (t0)
REVERT: A  611 GLU cc_start: 0.6684 (mp0) cc_final: 0.6308 (mp0)
REVERT: A  630 TRP cc_start: 0.7802 (m-10) cc_final: 0.7369 (m-10)
REVERT: A  665 TRP cc_start: 0.5931 (m-90) cc_final: 0.5691 (m-90)
REVERT: A  729 LYS cc_start: 0.7479 (tptt) cc_final: 0.6831 (tptp)
REVERT: A  762 GLU cc_start: 0.6608 (tm-30) cc_final: 0.6273 (tm-30)
REVERT: A  776 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.7846 (pt)
REVERT: A  778 CYS cc_start: 0.7739 (t) cc_final: 0.6538 (m)
REVERT: A  794 GLU cc_start: 0.7168 (mt-10) cc_final: 0.6907 (mt-10)
REVERT: B   77 HIS cc_start: 0.8180 (OUTLIER) cc_final: 0.7310 (m-70)
REVERT: B   98 GLU cc_start: 0.8304 (pm20) cc_final: 0.7988 (pm20)
REVERT: B  141 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: B  177 PHE cc_start: 0.7426 (m-80) cc_final: 0.7084 (m-10)
REVERT: B  201 ASP cc_start: 0.6915 (p0) cc_final: 0.6347 (p0)
REVERT: B  260 ARG cc_start: 0.7424 (ttm170) cc_final: 0.7196 (tpp80)
REVERT: B  279 PHE cc_start: 0.7522 (t80) cc_final: 0.7255 (t80)
REVERT: B  282 MET cc_start: 0.5280 (tpt) cc_final: 0.5042 (tpt)
REVERT: B  298 HIS cc_start: 0.7133 (t-90) cc_final: 0.6736 (t-90)
REVERT: B  345 LYS cc_start: 0.7896 (ptpp) cc_final: 0.7024 (ptpp)
REVERT: B  357 GLU cc_start: 0.7446 (tp30) cc_final: 0.6886 (tp30)
REVERT: B  407 ASP cc_start: 0.6542 (p0) cc_final: 0.6186 (p0)
REVERT: B  417 ILE cc_start: 0.7882 (tp) cc_final: 0.7674 (tp)
REVERT: B  495 LYS cc_start: 0.7763 (ttmm) cc_final: 0.7397 (ttmm)
REVERT: B  529 LYS cc_start: 0.8148 (tmtt) cc_final: 0.7600 (tmtt)
REVERT: B  590 HIS cc_start: 0.6674 (t70) cc_final: 0.6409 (t70)
REVERT: B  614 ASN cc_start: 0.7679 (m-40) cc_final: 0.6780 (m110)
REVERT: B  675 GLU cc_start: 0.6624 (mp0) cc_final: 0.6339 (mm-30)
REVERT: B  689 PHE cc_start: 0.7725 (t80) cc_final: 0.7471 (t80)
  outliers start: 27
  outliers final: 17
  residues processed: 309
  average time/residue: 0.2832
  time to fit residues: 119.9483
Evaluate side-chains
  308 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 289
  time to evaluate  : 1.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  640 LEU
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  700 VAL
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  342 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  509 LEU
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 27 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9990
   chunk 139 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 112 optimal weight:    0.0970
   chunk 77 optimal weight:    0.0770
   chunk 138 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.3336

-------------------------------------------------------------------------------
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 562 ASN
B 564 GLN
B 626 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.181992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.152420 restraints weight = 20338.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.157201 restraints weight = 11222.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.160339 restraints weight = 7354.445|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6568
moved from start:          0.2010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  12859  Z= 0.138
  Angle     :  0.646  12.719  17450  Z= 0.325
  Chirality :  0.045   0.175   1930
  Planarity :  0.005   0.048   2270
  Dihedral  :  6.175  75.183   1712
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 17.45 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.21), residues: 1570
  helix:  0.65 (0.20), residues: 673
  sheet: -0.51 (0.28), residues: 331
  loop : -1.24 (0.27), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 618 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.063   0.002   PHE A 445 
 TYR   0.032   0.001   TYR B  80 
 ARG   0.007   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03889 (  623)
  hydrogen bonds       : angle       4.92839 ( 1800)
  covalent geometry    : bond        0.00326 (12858)
  covalent geometry    : angle       0.64636 (17450)
  Misc. bond           : bond        0.00234 (    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
  331 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 293
  time to evaluate  : 1.224 
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  279 PHE cc_start: 0.6990 (t80) cc_final: 0.6265 (t80)
REVERT: A  282 MET cc_start: 0.8001 (tpp) cc_final: 0.7584 (ttm)
REVERT: A  364 GLN cc_start: 0.7675 (pp30) cc_final: 0.7126 (tm-30)
REVERT: A  452 ASP cc_start: 0.7094 (t70) cc_final: 0.6835 (t0)
REVERT: A  457 ARG cc_start: 0.5731 (ttm-80) cc_final: 0.5521 (ttm-80)
REVERT: A  495 LYS cc_start: 0.8170 (mttm) cc_final: 0.7847 (mttm)
REVERT: A  525 ASP cc_start: 0.6135 (t70) cc_final: 0.5768 (t0)
REVERT: A  596 HIS cc_start: 0.4858 (t70) cc_final: 0.4508 (t70)
REVERT: A  665 TRP cc_start: 0.5963 (m-90) cc_final: 0.5727 (m-90)
REVERT: A  729 LYS cc_start: 0.7429 (tptt) cc_final: 0.6935 (tptt)
REVERT: A  745 LEU cc_start: 0.8041 (mt) cc_final: 0.7813 (mp)
REVERT: A  751 ILE cc_start: 0.5184 (OUTLIER) cc_final: 0.4874 (mp)
REVERT: A  762 GLU cc_start: 0.6548 (tm-30) cc_final: 0.6311 (tm-30)
REVERT: A  776 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7820 (pt)
REVERT: A  778 CYS cc_start: 0.7708 (t) cc_final: 0.6453 (m)
REVERT: A  794 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6892 (mt-10)
REVERT: B   77 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7469 (m-70)
REVERT: B   98 GLU cc_start: 0.8310 (pm20) cc_final: 0.8003 (pm20)
REVERT: B  112 ARG cc_start: 0.7645 (mtp85) cc_final: 0.7323 (mtp85)
REVERT: B  118 VAL cc_start: 0.4132 (OUTLIER) cc_final: 0.3854 (t)
REVERT: B  141 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7402 (mm-30)
REVERT: B  220 PHE cc_start: 0.7598 (m-10) cc_final: 0.7234 (m-80)
REVERT: B  260 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7184 (tpp80)
REVERT: B  263 ARG cc_start: 0.6942 (mtp-110) cc_final: 0.6654 (mtp85)
REVERT: B  279 PHE cc_start: 0.7584 (t80) cc_final: 0.7317 (t80)
REVERT: B  282 MET cc_start: 0.5215 (tpt) cc_final: 0.5013 (tpt)
REVERT: B  298 HIS cc_start: 0.7134 (t-90) cc_final: 0.6761 (t-90)
REVERT: B  345 LYS cc_start: 0.7850 (ptpp) cc_final: 0.7110 (ptpp)
REVERT: B  357 GLU cc_start: 0.7329 (tp30) cc_final: 0.6821 (tp30)
REVERT: B  495 LYS cc_start: 0.7760 (ttmm) cc_final: 0.7385 (ttmm)
REVERT: B  529 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7603 (tmtt)
REVERT: B  590 HIS cc_start: 0.6626 (t70) cc_final: 0.6377 (t70)
REVERT: B  603 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.8010 (mm)
REVERT: B  614 ASN cc_start: 0.7805 (m-40) cc_final: 0.7260 (m110)
REVERT: B  675 GLU cc_start: 0.6678 (mp0) cc_final: 0.6347 (mm-30)
REVERT: B  744 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7935 (tp)
  outliers start: 38
  outliers final: 21
  residues processed: 313
  average time/residue: 0.2875
  time to fit residues: 123.9517
Evaluate side-chains
  314 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 287
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  414 VAL
Chi-restraints excluded: chain A residue  545 MET
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  636 HIS
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  676 ILE
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  730 SER
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  342 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  603 ILE
Chi-restraints excluded: chain B residue  642 VAL
Chi-restraints excluded: chain B residue  712 SER
Chi-restraints excluded: chain B residue  718 VAL
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 68 optimal weight:    1.9990
   chunk 149 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 112 optimal weight:    0.1980
   chunk 60 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 58 optimal weight:    0.0970
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 562 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 = 0.4296 r_free = 0.4296 target = 0.181400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.151403 restraints weight = 20440.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156161 restraints weight = 11233.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.159272 restraints weight = 7371.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6591
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.092  12859  Z= 0.171
  Angle     :  0.666  10.045  17450  Z= 0.336
  Chirality :  0.046   0.236   1930
  Planarity :  0.005   0.070   2270
  Dihedral  :  6.225  74.681   1712
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.62 %
    Favored  : 77.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.21), residues: 1570
  helix:  0.56 (0.20), residues: 668
  sheet: -0.56 (0.28), residues: 331
  loop : -1.31 (0.26), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 618 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.026   0.002   PHE B 602 
 TYR   0.032   0.002   TYR B  80 
 ARG   0.007   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04080 (  623)
  hydrogen bonds       : angle       5.03448 ( 1800)
  covalent geometry    : bond        0.00404 (12858)
  covalent geometry    : angle       0.66552 (17450)
  Misc. bond           : bond        0.00179 (    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
  346 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 296
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8134 (pt)
REVERT: A  279 PHE cc_start: 0.7113 (t80) cc_final: 0.6329 (t80)
REVERT: A  282 MET cc_start: 0.8230 (tpp) cc_final: 0.7860 (ttm)
REVERT: A  364 GLN cc_start: 0.7682 (pp30) cc_final: 0.7172 (tm-30)
REVERT: A  452 ASP cc_start: 0.7122 (t70) cc_final: 0.6842 (t0)
REVERT: A  495 LYS cc_start: 0.8197 (mttm) cc_final: 0.7898 (mttm)
REVERT: A  525 ASP cc_start: 0.6137 (t70) cc_final: 0.5752 (t0)
REVERT: A  596 HIS cc_start: 0.4787 (t70) cc_final: 0.4503 (t70)
REVERT: A  598 PRO cc_start: 0.7993 (Cg_exo) cc_final: 0.7697 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.5989 (m-90) cc_final: 0.5751 (m-90)
REVERT: A  729 LYS cc_start: 0.7487 (tptt) cc_final: 0.7003 (tptt)
REVERT: A  734 ARG cc_start: 0.6853 (ttm110) cc_final: 0.6578 (ttm110)
REVERT: A  745 LEU cc_start: 0.8054 (mt) cc_final: 0.7708 (mp)
REVERT: A  751 ILE cc_start: 0.5104 (OUTLIER) cc_final: 0.4836 (pt)
REVERT: A  762 GLU cc_start: 0.6589 (tm-30) cc_final: 0.6345 (tm-30)
REVERT: A  776 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8008 (pt)
REVERT: A  778 CYS cc_start: 0.7727 (t) cc_final: 0.6540 (m)
REVERT: A  794 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6923 (mt-10)
REVERT: B   77 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7436 (m-70)
REVERT: B   98 GLU cc_start: 0.8292 (pm20) cc_final: 0.8072 (pm20)
REVERT: B  118 VAL cc_start: 0.4148 (OUTLIER) cc_final: 0.3873 (t)
REVERT: B  141 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7439 (mm-30)
REVERT: B  177 PHE cc_start: 0.7424 (m-80) cc_final: 0.7073 (m-10)
REVERT: B  220 PHE cc_start: 0.7629 (m-10) cc_final: 0.7210 (m-80)
REVERT: B  260 ARG cc_start: 0.7425 (ttm170) cc_final: 0.7188 (tpp80)
REVERT: B  279 PHE cc_start: 0.7556 (t80) cc_final: 0.7262 (t80)
REVERT: B  298 HIS cc_start: 0.7142 (t-90) cc_final: 0.6726 (t-90)
REVERT: B  345 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7080 (ptpp)
REVERT: B  371 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7389 (mm)
REVERT: B  372 GLU cc_start: 0.6975 (tm-30) cc_final: 0.6701 (tm-30)
REVERT: B  495 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7389 (ttmm)
REVERT: B  529 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7608 (tmtt)
REVERT: B  590 HIS cc_start: 0.6664 (t70) cc_final: 0.6383 (t70)
REVERT: B  614 ASN cc_start: 0.7747 (m-40) cc_final: 0.7444 (m110)
REVERT: B  675 GLU cc_start: 0.6783 (mp0) cc_final: 0.6347 (mm-30)
REVERT: B  744 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7954 (tp)
  outliers start: 50
  outliers final: 28
  residues processed: 326
  average time/residue: 0.2861
  time to fit residues: 130.1167
Evaluate side-chains
  326 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 291
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  158 ILE
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  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  568 VAL
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  704 VAL
Chi-restraints excluded: chain A residue  720 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   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  288 ARG
Chi-restraints excluded: chain B residue  342 LEU
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  503 ILE
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  692 ILE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 145 optimal weight:    0.9980
   chunk 104 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 139 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 133 optimal weight:    0.5980
   chunk 91 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   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 562 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 = 0.4280 r_free = 0.4280 target = 0.179920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.149635 restraints weight = 20719.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.154373 restraints weight = 11475.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.157613 restraints weight = 7571.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6626
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.105  12859  Z= 0.213
  Angle     :  0.708  10.343  17450  Z= 0.359
  Chirality :  0.047   0.180   1930
  Planarity :  0.005   0.062   2270
  Dihedral  :  6.349  74.911   1712
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 19.13 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.21), residues: 1570
  helix:  0.41 (0.20), residues: 670
  sheet: -0.74 (0.28), residues: 325
  loop : -1.40 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 231 
 HIS   0.006   0.001   HIS A 365 
 PHE   0.063   0.002   PHE A 445 
 TYR   0.031   0.002   TYR B  80 
 ARG   0.009   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04398 (  623)
  hydrogen bonds       : angle       5.17358 ( 1800)
  covalent geometry    : bond        0.00500 (12858)
  covalent geometry    : angle       0.70769 (17450)
  Misc. bond           : bond        0.00156 (    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
  354 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 294
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 ILE cc_start: 0.8444 (OUTLIER) cc_final: 0.8187 (pt)
REVERT: A  279 PHE cc_start: 0.7198 (t80) cc_final: 0.6369 (t80)
REVERT: A  282 MET cc_start: 0.8159 (tpp) cc_final: 0.7788 (ttm)
REVERT: A  364 GLN cc_start: 0.7733 (pp30) cc_final: 0.7257 (tm-30)
REVERT: A  452 ASP cc_start: 0.7117 (t70) cc_final: 0.6889 (t0)
REVERT: A  495 LYS cc_start: 0.8179 (mttm) cc_final: 0.7874 (mttm)
REVERT: A  525 ASP cc_start: 0.6133 (t70) cc_final: 0.5768 (t0)
REVERT: A  596 HIS cc_start: 0.4856 (t70) cc_final: 0.4391 (t70)
REVERT: A  598 PRO cc_start: 0.8059 (Cg_exo) cc_final: 0.7781 (Cg_endo)
REVERT: A  630 TRP cc_start: 0.7884 (m-10) cc_final: 0.7319 (m-10)
REVERT: A  665 TRP cc_start: 0.6167 (m-90) cc_final: 0.5918 (m-90)
REVERT: A  729 LYS cc_start: 0.7432 (tptt) cc_final: 0.7082 (tptp)
REVERT: A  745 LEU cc_start: 0.8041 (mt) cc_final: 0.7662 (mp)
REVERT: A  746 GLU cc_start: 0.6943 (pp20) cc_final: 0.6639 (tm-30)
REVERT: A  776 ILE cc_start: 0.8458 (OUTLIER) cc_final: 0.8028 (pt)
REVERT: A  778 CYS cc_start: 0.7821 (t) cc_final: 0.6666 (m)
REVERT: A  794 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6915 (mt-10)
REVERT: B   77 HIS cc_start: 0.8099 (OUTLIER) cc_final: 0.7414 (m-70)
REVERT: B  118 VAL cc_start: 0.4118 (OUTLIER) cc_final: 0.3833 (t)
REVERT: B  141 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7451 (mm-30)
REVERT: B  177 PHE cc_start: 0.7443 (m-80) cc_final: 0.7148 (m-10)
REVERT: B  201 ASP cc_start: 0.6983 (p0) cc_final: 0.6366 (p0)
REVERT: B  220 PHE cc_start: 0.7622 (m-10) cc_final: 0.7139 (m-80)
REVERT: B  260 ARG cc_start: 0.7279 (ttm170) cc_final: 0.7048 (tpp80)
REVERT: B  279 PHE cc_start: 0.7497 (t80) cc_final: 0.7265 (t80)
REVERT: B  298 HIS cc_start: 0.7114 (t-90) cc_final: 0.6721 (t-90)
REVERT: B  345 LYS cc_start: 0.7889 (ptpp) cc_final: 0.7088 (ptpp)
REVERT: B  371 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7507 (mm)
REVERT: B  372 GLU cc_start: 0.6948 (tm-30) cc_final: 0.6717 (tm-30)
REVERT: B  468 LEU cc_start: 0.6207 (OUTLIER) cc_final: 0.5955 (mm)
REVERT: B  495 LYS cc_start: 0.7803 (ttmm) cc_final: 0.7450 (ttmm)
REVERT: B  529 LYS cc_start: 0.8150 (tmtt) cc_final: 0.7599 (tmtt)
REVERT: B  614 ASN cc_start: 0.7538 (m-40) cc_final: 0.7273 (m110)
REVERT: B  675 GLU cc_start: 0.6691 (mp0) cc_final: 0.6134 (mp0)
  outliers start: 60
  outliers final: 37
  residues processed: 323
  average time/residue: 0.2722
  time to fit residues: 121.7762
Evaluate side-chains
  334 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 291
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  158 ILE
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  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  568 VAL
Chi-restraints excluded: chain A residue  580 LEU
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   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  288 ARG
Chi-restraints excluded: chain B residue  310 ILE
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  468 LEU
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  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  692 ILE
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 101 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 102 optimal weight:    0.6980
   chunk 86 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 112 optimal weight:    0.5980
   chunk 131 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 123 optimal weight:    0.8980
   chunk 147 optimal weight:    0.0980
   chunk 70 optimal weight:    0.0980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.178082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.147688 restraints weight = 20557.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.152435 restraints weight = 11296.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.155557 restraints weight = 7383.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.3988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6604
moved from start:          0.2387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  12859  Z= 0.165
  Angle     :  0.697  10.417  17450  Z= 0.352
  Chirality :  0.046   0.185   1930
  Planarity :  0.005   0.054   2270
  Dihedral  :  6.307  74.957   1712
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 20.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.21), residues: 1570
  helix:  0.48 (0.20), residues: 675
  sheet: -0.64 (0.28), residues: 325
  loop : -1.37 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 618 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.026   0.002   PHE B 602 
 TYR   0.030   0.002   TYR B  80 
 ARG   0.010   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04114 (  623)
  hydrogen bonds       : angle       5.07408 ( 1800)
  covalent geometry    : bond        0.00393 (12858)
  covalent geometry    : angle       0.69730 (17450)
  Misc. bond           : bond        0.00160 (    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
  347 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 291
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  132 ASP cc_start: 0.6603 (p0) cc_final: 0.6045 (p0)
REVERT: A  158 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8150 (pt)
REVERT: A  279 PHE cc_start: 0.7088 (t80) cc_final: 0.6264 (t80)
REVERT: A  282 MET cc_start: 0.8175 (tpp) cc_final: 0.7785 (ttm)
REVERT: A  364 GLN cc_start: 0.7726 (pp30) cc_final: 0.7210 (tm-30)
REVERT: A  452 ASP cc_start: 0.7150 (t70) cc_final: 0.6906 (t0)
REVERT: A  495 LYS cc_start: 0.8176 (mttm) cc_final: 0.7859 (mttm)
REVERT: A  525 ASP cc_start: 0.6121 (t70) cc_final: 0.5758 (t0)
REVERT: A  596 HIS cc_start: 0.4853 (t70) cc_final: 0.4381 (t70)
REVERT: A  598 PRO cc_start: 0.8019 (Cg_exo) cc_final: 0.7725 (Cg_endo)
REVERT: A  630 TRP cc_start: 0.7781 (m-10) cc_final: 0.7320 (m-10)
REVERT: A  665 TRP cc_start: 0.6187 (m-90) cc_final: 0.5904 (m-90)
REVERT: A  745 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7706 (mp)
REVERT: A  751 ILE cc_start: 0.5143 (OUTLIER) cc_final: 0.4582 (mm)
REVERT: A  776 ILE cc_start: 0.8438 (OUTLIER) cc_final: 0.8036 (pt)
REVERT: A  778 CYS cc_start: 0.7785 (t) cc_final: 0.6583 (m)
REVERT: B   77 HIS cc_start: 0.8089 (OUTLIER) cc_final: 0.7381 (m-70)
REVERT: B  118 VAL cc_start: 0.4089 (OUTLIER) cc_final: 0.3801 (t)
REVERT: B  141 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7525 (mm-30)
REVERT: B  177 PHE cc_start: 0.7390 (m-80) cc_final: 0.7020 (m-10)
REVERT: B  220 PHE cc_start: 0.7616 (m-10) cc_final: 0.7159 (m-80)
REVERT: B  260 ARG cc_start: 0.7443 (ttm170) cc_final: 0.7210 (tpp80)
REVERT: B  279 PHE cc_start: 0.7528 (t80) cc_final: 0.7310 (t80)
REVERT: B  298 HIS cc_start: 0.7112 (t-90) cc_final: 0.6676 (t-90)
REVERT: B  345 LYS cc_start: 0.7890 (ptpp) cc_final: 0.7086 (ptpp)
REVERT: B  371 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7483 (mm)
REVERT: B  372 GLU cc_start: 0.6983 (tm-30) cc_final: 0.6728 (tm-30)
REVERT: B  468 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5907 (mm)
REVERT: B  495 LYS cc_start: 0.7783 (ttmm) cc_final: 0.7432 (ttmm)
REVERT: B  529 LYS cc_start: 0.8159 (tmtt) cc_final: 0.7591 (tmtt)
REVERT: B  536 GLN cc_start: 0.7017 (mm110) cc_final: 0.6814 (mm-40)
REVERT: B  590 HIS cc_start: 0.6825 (t-90) cc_final: 0.6450 (t70)
REVERT: B  614 ASN cc_start: 0.7584 (m-40) cc_final: 0.7306 (m110)
REVERT: B  675 GLU cc_start: 0.6703 (mp0) cc_final: 0.6291 (mm-30)
REVERT: B  689 PHE cc_start: 0.7740 (t80) cc_final: 0.7331 (t80)
  outliers start: 56
  outliers final: 34
  residues processed: 316
  average time/residue: 0.2925
  time to fit residues: 127.3080
Evaluate side-chains
  327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 285
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ILE
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  485 VAL
Chi-restraints excluded: chain A residue  545 MET
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  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  745 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  288 ARG
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  468 LEU
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  507 TYR
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  692 ILE
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 34 optimal weight:    0.3980
   chunk 142 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 155 optimal weight:    0.6980
   chunk 114 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0670
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.178454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148420 restraints weight = 20763.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.153207 restraints weight = 11385.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.156476 restraints weight = 7392.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6595
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  12859  Z= 0.165
  Angle     :  0.711   9.691  17450  Z= 0.358
  Chirality :  0.046   0.286   1930
  Planarity :  0.005   0.048   2270
  Dihedral  :  6.270  75.633   1712
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.89 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.21), residues: 1570
  helix:  0.51 (0.20), residues: 674
  sheet: -0.67 (0.28), residues: 323
  loop : -1.30 (0.26), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 618 
 HIS   0.006   0.001   HIS B 590 
 PHE   0.058   0.002   PHE A 445 
 TYR   0.030   0.002   TYR B  80 
 ARG   0.009   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  623)
  hydrogen bonds       : angle       5.01185 ( 1800)
  covalent geometry    : bond        0.00393 (12858)
  covalent geometry    : angle       0.71058 (17450)
  Misc. bond           : bond        0.00160 (    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
  336 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 284
  time to evaluate  : 1.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8154 (pt)
REVERT: A  279 PHE cc_start: 0.7075 (t80) cc_final: 0.6244 (t80)
REVERT: A  282 MET cc_start: 0.8152 (tpp) cc_final: 0.7749 (ttm)
REVERT: A  364 GLN cc_start: 0.7709 (pp30) cc_final: 0.7166 (tm-30)
REVERT: A  452 ASP cc_start: 0.7136 (t70) cc_final: 0.6916 (t0)
REVERT: A  495 LYS cc_start: 0.8150 (mttm) cc_final: 0.7821 (mttm)
REVERT: A  525 ASP cc_start: 0.6112 (t70) cc_final: 0.5752 (t0)
REVERT: A  596 HIS cc_start: 0.4866 (t70) cc_final: 0.4430 (t70)
REVERT: A  598 PRO cc_start: 0.8012 (Cg_exo) cc_final: 0.7717 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6192 (m-90) cc_final: 0.5865 (m-90)
REVERT: A  745 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7765 (mp)
REVERT: A  751 ILE cc_start: 0.5119 (OUTLIER) cc_final: 0.4790 (pt)
REVERT: A  776 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8066 (pt)
REVERT: A  778 CYS cc_start: 0.7717 (t) cc_final: 0.6603 (m)
REVERT: B   77 HIS cc_start: 0.8060 (OUTLIER) cc_final: 0.7415 (m-70)
REVERT: B  118 VAL cc_start: 0.4220 (OUTLIER) cc_final: 0.3922 (t)
REVERT: B  141 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7541 (mm-30)
REVERT: B  177 PHE cc_start: 0.7376 (m-80) cc_final: 0.7025 (m-10)
REVERT: B  220 PHE cc_start: 0.7568 (m-10) cc_final: 0.7165 (m-80)
REVERT: B  260 ARG cc_start: 0.7314 (ttm170) cc_final: 0.7094 (tpp80)
REVERT: B  279 PHE cc_start: 0.7478 (t80) cc_final: 0.7212 (t80)
REVERT: B  298 HIS cc_start: 0.7082 (t-90) cc_final: 0.6640 (t-90)
REVERT: B  345 LYS cc_start: 0.7900 (ptpp) cc_final: 0.7087 (ptpp)
REVERT: B  371 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7457 (mm)
REVERT: B  372 GLU cc_start: 0.7011 (tm-30) cc_final: 0.6734 (tm-30)
REVERT: B  468 LEU cc_start: 0.6190 (OUTLIER) cc_final: 0.5978 (mm)
REVERT: B  495 LYS cc_start: 0.7789 (ttmm) cc_final: 0.7413 (ttmm)
REVERT: B  529 LYS cc_start: 0.8164 (tmtt) cc_final: 0.7587 (tmtt)
REVERT: B  590 HIS cc_start: 0.6935 (t-90) cc_final: 0.6522 (t70)
REVERT: B  614 ASN cc_start: 0.7608 (m-40) cc_final: 0.7335 (m110)
REVERT: B  675 GLU cc_start: 0.6685 (mp0) cc_final: 0.6292 (mm-30)
REVERT: B  689 PHE cc_start: 0.7756 (t80) cc_final: 0.7364 (t80)
  outliers start: 52
  outliers final: 36
  residues processed: 310
  average time/residue: 0.3476
  time to fit residues: 150.2355
Evaluate side-chains
  322 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 278
  time to evaluate  : 2.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  158 ILE
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  545 MET
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  568 VAL
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  730 SER
Chi-restraints excluded: chain A residue  744 LEU
Chi-restraints excluded: chain A residue  745 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  288 ARG
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  417 ILE
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  468 LEU
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  507 TYR
Chi-restraints excluded: chain B residue  509 LEU
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  692 ILE
Chi-restraints excluded: chain B residue  718 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 136 optimal weight:    0.5980
   chunk 127 optimal weight:    0.5980
   chunk 104 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0170
   chunk 117 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 78 optimal weight:    0.7980
   chunk 92 optimal weight:    0.0170
   overall best weight:    0.3256

-------------------------------------------------------------------------------
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 564 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.179089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.149059 restraints weight = 20535.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.153787 restraints weight = 11244.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.156952 restraints weight = 7299.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6572
moved from start:          0.2628

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= 0.145
  Angle     :  0.718  11.510  17450  Z= 0.363
  Chirality :  0.046   0.267   1930
  Planarity :  0.005   0.071   2270
  Dihedral  :  6.207  74.219   1712
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 22.29 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.21), residues: 1570
  helix:  0.65 (0.20), residues: 667
  sheet: -0.60 (0.28), residues: 323
  loop : -1.26 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 231 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.023   0.002   PHE B 602 
 TYR   0.030   0.001   TYR B  80 
 ARG   0.010   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  623)
  hydrogen bonds       : angle       4.91829 ( 1800)
  covalent geometry    : bond        0.00347 (12858)
  covalent geometry    : angle       0.71823 (17450)
  Misc. bond           : bond        0.00185 (    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
  325 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 280
  time to evaluate  : 1.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.5031 (mmm) cc_final: 0.2472 (tpt)
REVERT: A  210 LEU cc_start: 0.7884 (mp) cc_final: 0.7636 (tt)
REVERT: A  279 PHE cc_start: 0.6932 (t80) cc_final: 0.6122 (t80)
REVERT: A  282 MET cc_start: 0.7988 (tpp) cc_final: 0.7516 (ttm)
REVERT: A  364 GLN cc_start: 0.7662 (pp30) cc_final: 0.7120 (tm-30)
REVERT: A  452 ASP cc_start: 0.7131 (t70) cc_final: 0.6902 (t0)
REVERT: A  495 LYS cc_start: 0.8149 (mttm) cc_final: 0.7859 (mttm)
REVERT: A  525 ASP cc_start: 0.6092 (t70) cc_final: 0.5731 (t0)
REVERT: A  596 HIS cc_start: 0.4814 (t70) cc_final: 0.4405 (t70)
REVERT: A  598 PRO cc_start: 0.7925 (Cg_exo) cc_final: 0.7628 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6182 (m-90) cc_final: 0.5861 (m-90)
REVERT: A  678 GLU cc_start: 0.7287 (pp20) cc_final: 0.6779 (tm-30)
REVERT: A  745 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7694 (mp)
REVERT: A  751 ILE cc_start: 0.4839 (OUTLIER) cc_final: 0.4242 (mm)
REVERT: A  776 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8012 (pt)
REVERT: A  778 CYS cc_start: 0.7655 (t) cc_final: 0.6698 (m)
REVERT: B   77 HIS cc_start: 0.8014 (OUTLIER) cc_final: 0.7483 (m-70)
REVERT: B  118 VAL cc_start: 0.3840 (OUTLIER) cc_final: 0.3525 (t)
REVERT: B  141 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7528 (mm-30)
REVERT: B  177 PHE cc_start: 0.7379 (m-80) cc_final: 0.7043 (m-10)
REVERT: B  220 PHE cc_start: 0.7540 (m-10) cc_final: 0.7143 (m-80)
REVERT: B  260 ARG cc_start: 0.7421 (ttm170) cc_final: 0.7210 (tpp80)
REVERT: B  279 PHE cc_start: 0.7491 (t80) cc_final: 0.7253 (t80)
REVERT: B  298 HIS cc_start: 0.7088 (t-90) cc_final: 0.6633 (t-90)
REVERT: B  345 LYS cc_start: 0.7899 (ptpp) cc_final: 0.7058 (ptpp)
REVERT: B  371 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7421 (mm)
REVERT: B  372 GLU cc_start: 0.7014 (tm-30) cc_final: 0.6725 (tm-30)
REVERT: B  495 LYS cc_start: 0.7761 (ttmm) cc_final: 0.7405 (ttmm)
REVERT: B  529 LYS cc_start: 0.8155 (tmtt) cc_final: 0.7559 (tmtt)
REVERT: B  614 ASN cc_start: 0.7606 (m-40) cc_final: 0.7335 (m110)
REVERT: B  675 GLU cc_start: 0.6684 (mp0) cc_final: 0.6310 (mm-30)
REVERT: B  689 PHE cc_start: 0.7759 (t80) cc_final: 0.7384 (t80)
  outliers start: 45
  outliers final: 29
  residues processed: 306
  average time/residue: 0.3532
  time to fit residues: 149.1083
Evaluate side-chains
  310 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 275
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
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  545 MET
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  568 VAL
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  745 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  288 ARG
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  507 TYR
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  692 ILE
Chi-restraints excluded: chain B residue  718 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9980
   chunk 137 optimal weight:    0.0030
   chunk 86 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0870
   chunk 69 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.4168

-------------------------------------------------------------------------------
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 168 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.178931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.149079 restraints weight = 20554.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.153756 restraints weight = 11231.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.156924 restraints weight = 7303.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6578
moved from start:          0.2719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  12859  Z= 0.162
  Angle     :  0.738  11.878  17450  Z= 0.375
  Chirality :  0.046   0.239   1930
  Planarity :  0.005   0.121   2270
  Dihedral  :  6.224  74.398   1712
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 22.29 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.21), residues: 1570
  helix:  0.70 (0.20), residues: 667
  sheet: -0.62 (0.28), residues: 323
  loop : -1.28 (0.26), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 231 
 HIS   0.008   0.001   HIS B 590 
 PHE   0.024   0.002   PHE B 602 
 TYR   0.030   0.001   TYR B  80 
 ARG   0.009   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04007 (  623)
  hydrogen bonds       : angle       4.98281 ( 1800)
  covalent geometry    : bond        0.00386 (12858)
  covalent geometry    : angle       0.73751 (17450)
  Misc. bond           : bond        0.00237 (    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
  319 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 278
  time to evaluate  : 1.403 
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   30 MET cc_start: 0.6126 (ppp) cc_final: 0.5868 (ppp)
REVERT: A  279 PHE cc_start: 0.6993 (t80) cc_final: 0.6157 (t80)
REVERT: A  282 MET cc_start: 0.7934 (tpp) cc_final: 0.7529 (ttm)
REVERT: A  364 GLN cc_start: 0.7637 (pp30) cc_final: 0.7142 (tm-30)
REVERT: A  452 ASP cc_start: 0.7123 (t70) cc_final: 0.6894 (t0)
REVERT: A  495 LYS cc_start: 0.8157 (mttm) cc_final: 0.7830 (mttm)
REVERT: A  525 ASP cc_start: 0.6093 (t70) cc_final: 0.5729 (t0)
REVERT: A  596 HIS cc_start: 0.4804 (t70) cc_final: 0.4401 (t70)
REVERT: A  598 PRO cc_start: 0.7944 (Cg_exo) cc_final: 0.7654 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6205 (m-90) cc_final: 0.5879 (m-90)
REVERT: A  745 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7703 (mp)
REVERT: A  751 ILE cc_start: 0.4986 (OUTLIER) cc_final: 0.4368 (mm)
REVERT: A  776 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8061 (pt)
REVERT: A  778 CYS cc_start: 0.7676 (t) cc_final: 0.6741 (m)
REVERT: B   77 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7553 (m-70)
REVERT: B  118 VAL cc_start: 0.3830 (OUTLIER) cc_final: 0.3516 (t)
REVERT: B  141 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7542 (mm-30)
REVERT: B  220 PHE cc_start: 0.7537 (m-10) cc_final: 0.7182 (m-80)
REVERT: B  260 ARG cc_start: 0.7290 (ttm170) cc_final: 0.7063 (tpp80)
REVERT: B  279 PHE cc_start: 0.7514 (t80) cc_final: 0.7277 (t80)
REVERT: B  298 HIS cc_start: 0.7075 (t-90) cc_final: 0.6623 (t-90)
REVERT: B  345 LYS cc_start: 0.7901 (ptpp) cc_final: 0.7069 (ptpp)
REVERT: B  365 HIS cc_start: 0.5950 (m170) cc_final: 0.4683 (m170)
REVERT: B  371 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7435 (mm)
REVERT: B  495 LYS cc_start: 0.7562 (ttmm) cc_final: 0.7213 (ttmm)
REVERT: B  529 LYS cc_start: 0.8158 (tmtt) cc_final: 0.7691 (tmtt)
REVERT: B  590 HIS cc_start: 0.6815 (t-90) cc_final: 0.6463 (t70)
REVERT: B  614 ASN cc_start: 0.7609 (m-40) cc_final: 0.7345 (m110)
REVERT: B  675 GLU cc_start: 0.6708 (mp0) cc_final: 0.6308 (mm-30)
REVERT: B  689 PHE cc_start: 0.7760 (t80) cc_final: 0.7393 (t80)
  outliers start: 41
  outliers final: 30
  residues processed: 300
  average time/residue: 0.3206
  time to fit residues: 133.9194
Evaluate side-chains
  310 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 274
  time to evaluate  : 1.458 
-------------------------------------------------------------------------------
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  545 MET
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  557 LYS
Chi-restraints excluded: chain A residue  568 VAL
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  730 SER
Chi-restraints excluded: chain A residue  745 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   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  288 ARG
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  416 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  692 ILE
Chi-restraints excluded: chain B residue  718 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 153 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 144 optimal weight:    2.9990
   chunk 51 optimal weight:    0.3980
   chunk 123 optimal weight:    0.9990
   chunk 149 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 108 optimal weight:    3.9990
   chunk 42 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.177237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.147025 restraints weight = 20728.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.151692 restraints weight = 11349.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.154849 restraints weight = 7419.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6608
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095  12859  Z= 0.197
  Angle     :  0.773  11.440  17450  Z= 0.393
  Chirality :  0.047   0.236   1930
  Planarity :  0.005   0.055   2270
  Dihedral  :  6.315  75.908   1712
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.95 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.21), residues: 1570
  helix:  0.52 (0.20), residues: 672
  sheet: -0.71 (0.28), residues: 323
  loop : -1.30 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP B 231 
 HIS   0.007   0.001   HIS B 590 
 PHE   0.025   0.002   PHE B 602 
 TYR   0.030   0.002   TYR B  80 
 ARG   0.010   0.001   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04304 (  623)
  hydrogen bonds       : angle       5.10630 ( 1800)
  covalent geometry    : bond        0.00464 (12858)
  covalent geometry    : angle       0.77271 (17450)
  Misc. bond           : bond        0.00249 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4860.69 seconds
wall clock time: 86 minutes 44.86 seconds (5204.86 seconds total)