Starting phenix.real_space_refine
on Sat Jan 18 18:30:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bgv_44524/01_2025/9bgv_44524.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bgv_44524/01_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_44524/01_2025/9bgv_44524.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bgv_44524/01_2025/9bgv_44524.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bgv_44524/01_2025/9bgv_44524.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bgv_44524/01_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.58, 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: 3.02
  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: 1.55
  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: 4.60

  Time building geometry restraints manager: 3.55 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: 0.07
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.280
  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:          0.470
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     30.760
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.890
-------------------------------------------------------------------------------
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      :  0.005   0.098  12858  Z= 0.296
  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 

*********************** 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  : 1.399 
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: 0.3036
  time to fit residues: 133.2894
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  : 1.313 
-------------------------------------------------------------------------------
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 = 0.178954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148856 restraints weight = 20641.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.153412 restraints weight = 11523.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.156511 restraints weight = 7611.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3995
-------------------------------------------------------------------------------
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  12858  Z= 0.284
  Angle     :  0.691  12.907  17450  Z= 0.347
  Chirality :  0.047   0.180   1930
  Planarity :  0.005   0.074   2270
  Dihedral  :  6.329  70.960   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 

*********************** 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  : 1.420 
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: 0.3888 (mtp) cc_final: 0.3631 (mtp)
REVERT: A  163 GLU cc_start: 0.7319 (mp0) cc_final: 0.7032 (mp0)
REVERT: A  185 SER cc_start: 0.7427 (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: 0.7839 (ttm)
REVERT: A  345 LYS cc_start: 0.8138 (OUTLIER) cc_final: 0.7875 (mttt)
REVERT: A  364 GLN cc_start: 0.7737 (pp30) cc_final: 0.7104 (tm-30)
REVERT: A  389 MET cc_start: 0.6995 (ttp) cc_final: 0.6632 (ttm)
REVERT: A  452 ASP cc_start: 0.7263 (t70) cc_final: 0.6890 (t0)
REVERT: A  502 SER cc_start: 0.7397 (t) cc_final: 0.7176 (t)
REVERT: A  525 ASP cc_start: 0.6172 (t70) cc_final: 0.5817 (t0)
REVERT: A  665 TRP cc_start: 0.5958 (m-90) cc_final: 0.5698 (m-90)
REVERT: A  678 GLU cc_start: 0.7470 (pm20) cc_final: 0.7244 (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: 0.7860 (mt)
REVERT: A  751 ILE cc_start: 0.5635 (OUTLIER) cc_final: 0.5326 (mp)
REVERT: A  778 CYS cc_start: 0.7843 (t) cc_final: 0.7557 (t)
REVERT: A  794 GLU cc_start: 0.7258 (mt-10) cc_final: 0.6966 (mt-10)
REVERT: B   98 GLU cc_start: 0.8297 (pm20) cc_final: 0.7978 (pm20)
REVERT: B  112 ARG cc_start: 0.7667 (mtp85) cc_final: 0.7376 (mtp85)
REVERT: B  139 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7402 (tp-100)
REVERT: B  141 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7504 (mm-30)
REVERT: B  177 PHE cc_start: 0.7536 (m-80) cc_final: 0.7105 (m-10)
REVERT: B  260 ARG cc_start: 0.7460 (ttm170) cc_final: 0.7226 (tpp80)
REVERT: B  279 PHE cc_start: 0.7464 (t80) cc_final: 0.7201 (t80)
REVERT: B  282 MET cc_start: 0.5360 (tpt) cc_final: 0.5113 (tpt)
REVERT: B  298 HIS cc_start: 0.7131 (t-90) cc_final: 0.6747 (t-90)
REVERT: B  311 HIS cc_start: 0.6777 (t-90) cc_final: 0.6527 (t-90)
REVERT: B  345 LYS cc_start: 0.7915 (ptpp) cc_final: 0.7066 (ptpp)
REVERT: B  493 ASP cc_start: 0.6740 (t0) cc_final: 0.6398 (t0)
REVERT: B  495 LYS cc_start: 0.7823 (ttmm) cc_final: 0.7374 (ttmm)
REVERT: B  529 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7625 (tmtt)
REVERT: B  590 HIS cc_start: 0.6648 (t70) cc_final: 0.6385 (t70)
REVERT: B  614 ASN cc_start: 0.7630 (m-40) cc_final: 0.7210 (m-40)
REVERT: B  689 PHE cc_start: 0.7672 (t80) cc_final: 0.7226 (t80)
REVERT: B  716 ARG cc_start: 0.7115 (mmm160) cc_final: 0.6724 (mmm160)
REVERT: B  726 LYS cc_start: 0.8323 (mttt) cc_final: 0.7867 (ttmt)
  outliers start: 24
  outliers final: 11
  residues processed: 308
  average time/residue: 0.3097
  time to fit residues: 129.8317
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  : 1.402 
-------------------------------------------------------------------------------
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:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    7.9990
   chunk 137 optimal weight:    0.1980
   chunk 31 optimal weight:    0.6980
   chunk 123 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.4246 r_free = 0.4246 target = 0.177725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.147024 restraints weight = 20704.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.151847 restraints weight = 11444.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.155049 restraints weight = 7508.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6601
moved from start:          0.1665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  12858  Z= 0.244
  Angle     :  0.660  11.693  17450  Z= 0.332
  Chirality :  0.046   0.179   1930
  Planarity :  0.005   0.058   2270
  Dihedral  :  6.276  73.314   1712
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.03 %
    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: -0.50 (0.22), residues: 1570
  helix:  0.61 (0.20), residues: 663
  sheet: -0.48 (0.28), residues: 321
  loop : -1.24 (0.27), residues: 586

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 231 
 HIS   0.007   0.001   HIS B  77 
 PHE   0.057   0.002   PHE A 445 
 TYR   0.032   0.002   TYR B  80 
 ARG   0.007   0.000   ARG A  71 

*********************** 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
  322 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 289
  time to evaluate  : 1.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   31 MET cc_start: 0.3612 (tpt) cc_final: 0.3353 (tpt)
REVERT: A  163 GLU cc_start: 0.7253 (mp0) cc_final: 0.6996 (mp0)
REVERT: A  279 PHE cc_start: 0.7177 (t80) cc_final: 0.6419 (t80)
REVERT: A  282 MET cc_start: 0.8215 (tpp) cc_final: 0.7794 (ttm)
REVERT: A  364 GLN cc_start: 0.7715 (pp30) cc_final: 0.7118 (tm-30)
REVERT: A  452 ASP cc_start: 0.7239 (t70) cc_final: 0.6842 (t0)
REVERT: A  457 ARG cc_start: 0.5916 (ttm-80) cc_final: 0.5625 (ttm-80)
REVERT: A  525 ASP cc_start: 0.6173 (t70) cc_final: 0.5804 (t0)
REVERT: A  611 GLU cc_start: 0.6820 (mp0) cc_final: 0.6429 (mp0)
REVERT: A  665 TRP cc_start: 0.5955 (m-90) cc_final: 0.5685 (m-90)
REVERT: A  745 LEU cc_start: 0.8193 (mt) cc_final: 0.7972 (mt)
REVERT: A  751 ILE cc_start: 0.5528 (OUTLIER) cc_final: 0.5230 (mp)
REVERT: A  776 ILE cc_start: 0.8373 (OUTLIER) cc_final: 0.7788 (pt)
REVERT: A  778 CYS cc_start: 0.7770 (t) cc_final: 0.6485 (m)
REVERT: A  794 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6925 (mt-10)
REVERT: B   77 HIS cc_start: 0.8233 (OUTLIER) cc_final: 0.7352 (m-70)
REVERT: B   98 GLU cc_start: 0.8331 (pm20) cc_final: 0.8002 (pm20)
REVERT: B  141 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7454 (mm-30)
REVERT: B  177 PHE cc_start: 0.7531 (m-80) cc_final: 0.7096 (m-10)
REVERT: B  260 ARG cc_start: 0.7454 (ttm170) cc_final: 0.7216 (tpp80)
REVERT: B  279 PHE cc_start: 0.7412 (t80) cc_final: 0.7162 (t80)
REVERT: B  282 MET cc_start: 0.5344 (tpt) cc_final: 0.5107 (tpt)
REVERT: B  298 HIS cc_start: 0.7152 (t-90) cc_final: 0.6747 (t-90)
REVERT: B  345 LYS cc_start: 0.7894 (ptpp) cc_final: 0.7021 (ptpp)
REVERT: B  407 ASP cc_start: 0.6684 (p0) cc_final: 0.6126 (p0)
REVERT: B  408 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7990 (mmpt)
REVERT: B  493 ASP cc_start: 0.6652 (t0) cc_final: 0.6447 (t0)
REVERT: B  495 LYS cc_start: 0.7795 (ttmm) cc_final: 0.7372 (ttmm)
REVERT: B  529 LYS cc_start: 0.8192 (tmtt) cc_final: 0.7612 (tmtt)
REVERT: B  590 HIS cc_start: 0.6676 (t70) cc_final: 0.6379 (t70)
REVERT: B  614 ASN cc_start: 0.7771 (m-40) cc_final: 0.7130 (m110)
REVERT: B  682 MET cc_start: 0.6777 (mtp) cc_final: 0.6300 (mtp)
REVERT: B  689 PHE cc_start: 0.7816 (t80) cc_final: 0.7544 (t80)
REVERT: B  726 LYS cc_start: 0.8367 (mttt) cc_final: 0.7853 (ttmt)
  outliers start: 33
  outliers final: 19
  residues processed: 302
  average time/residue: 0.2982
  time to fit residues: 122.8983
Evaluate side-chains
  301 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 279
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
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  545 MET
Chi-restraints excluded: chain A residue  549 ARG
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  656 ASN
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  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  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  729 LYS
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 140 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0010
   chunk 139 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   chunk 77 optimal weight:    0.3980
   chunk 138 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 118 optimal weight:    0.5980
   overall best weight:    0.3386

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.178975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.148620 restraints weight = 20447.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.153359 restraints weight = 11301.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.156579 restraints weight = 7411.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3991
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.1965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.076  12858  Z= 0.215
  Angle     :  0.649  11.485  17450  Z= 0.326
  Chirality :  0.045   0.176   1930
  Planarity :  0.005   0.065   2270
  Dihedral  :  6.176  73.629   1712
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 17.01 %
    Favored  : 80.43 %
  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:  0.63 (0.20), residues: 670
  sheet: -0.51 (0.28), residues: 331
  loop : -1.26 (0.27), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 618 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.064   0.002   PHE A 445 
 TYR   0.032   0.001   TYR B  80 
 ARG   0.006   0.000   ARG A  71 

*********************** 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
  324 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 289
  time to evaluate  : 1.336 
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  163 GLU cc_start: 0.7190 (mp0) cc_final: 0.6954 (mp0)
REVERT: A  279 PHE cc_start: 0.7051 (t80) cc_final: 0.6317 (t80)
REVERT: A  282 MET cc_start: 0.8124 (tpp) cc_final: 0.7667 (ttm)
REVERT: A  364 GLN cc_start: 0.7672 (pp30) cc_final: 0.7114 (tm-30)
REVERT: A  452 ASP cc_start: 0.7152 (t70) cc_final: 0.6869 (t0)
REVERT: A  457 ARG cc_start: 0.5765 (ttm-80) cc_final: 0.5522 (ttm-80)
REVERT: A  495 LYS cc_start: 0.8194 (mttm) cc_final: 0.7872 (mttm)
REVERT: A  525 ASP cc_start: 0.6154 (t70) cc_final: 0.5777 (t0)
REVERT: A  596 HIS cc_start: 0.4861 (t70) cc_final: 0.4547 (t70)
REVERT: A  598 PRO cc_start: 0.7921 (Cg_exo) cc_final: 0.7609 (Cg_endo)
REVERT: A  630 TRP cc_start: 0.7855 (m-10) cc_final: 0.7377 (m-10)
REVERT: A  665 TRP cc_start: 0.5972 (m-90) cc_final: 0.5697 (m-90)
REVERT: A  776 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7855 (pt)
REVERT: A  778 CYS cc_start: 0.7734 (t) cc_final: 0.6452 (m)
REVERT: A  794 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6953 (mt-10)
REVERT: B   77 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7387 (m-70)
REVERT: B   98 GLU cc_start: 0.8322 (pm20) cc_final: 0.8008 (pm20)
REVERT: B  118 VAL cc_start: 0.4175 (OUTLIER) cc_final: 0.3875 (t)
REVERT: B  141 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7437 (mm-30)
REVERT: B  177 PHE cc_start: 0.7382 (m-80) cc_final: 0.7012 (m-10)
REVERT: B  187 MET cc_start: 0.6136 (ttp) cc_final: 0.5879 (tmm)
REVERT: B  201 ASP cc_start: 0.6739 (p0) cc_final: 0.6162 (p0)
REVERT: B  220 PHE cc_start: 0.7626 (m-10) cc_final: 0.7175 (m-80)
REVERT: B  260 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7215 (tpp80)
REVERT: B  279 PHE cc_start: 0.7464 (t80) cc_final: 0.7170 (t80)
REVERT: B  282 MET cc_start: 0.5287 (tpt) cc_final: 0.5056 (tpt)
REVERT: B  298 HIS cc_start: 0.7139 (t-90) cc_final: 0.6766 (t-90)
REVERT: B  345 LYS cc_start: 0.7827 (ptpp) cc_final: 0.7077 (ptpp)
REVERT: B  357 GLU cc_start: 0.7383 (tp30) cc_final: 0.6863 (tp30)
REVERT: B  371 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7248 (mm)
REVERT: B  403 ASP cc_start: 0.6832 (p0) cc_final: 0.6606 (p0)
REVERT: B  495 LYS cc_start: 0.7748 (ttmm) cc_final: 0.7377 (ttmm)
REVERT: B  529 LYS cc_start: 0.8189 (tmtt) cc_final: 0.7612 (tmtt)
REVERT: B  590 HIS cc_start: 0.6742 (t70) cc_final: 0.6422 (t70)
REVERT: B  603 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7879 (mm)
REVERT: B  614 ASN cc_start: 0.7785 (m-40) cc_final: 0.7466 (m110)
REVERT: B  689 PHE cc_start: 0.7770 (t80) cc_final: 0.7477 (t80)
REVERT: B  726 LYS cc_start: 0.8312 (mttt) cc_final: 0.7893 (ttmt)
  outliers start: 35
  outliers final: 21
  residues processed: 310
  average time/residue: 0.2925
  time to fit residues: 125.2691
Evaluate side-chains
  305 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 279
  time to evaluate  : 1.349 
-------------------------------------------------------------------------------
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  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  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  371 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:    0.9990
   chunk 149 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 126 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 56 optimal weight:    0.4980
   chunk 112 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 58 optimal weight:    0.2980
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.179967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.149847 restraints weight = 20560.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.154659 restraints weight = 11381.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.157865 restraints weight = 7466.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6614
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.105  12858  Z= 0.313
  Angle     :  0.689  10.623  17450  Z= 0.348
  Chirality :  0.047   0.229   1930
  Planarity :  0.005   0.059   2270
  Dihedral  :  6.266  72.559   1712
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 17.52 %
    Favored  : 78.37 %
  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: -0.68 (0.21), residues: 1570
  helix:  0.47 (0.20), residues: 673
  sheet: -0.55 (0.28), residues: 315
  loop : -1.39 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 231 
 HIS   0.006   0.001   HIS A 365 
 PHE   0.027   0.002   PHE B 602 
 TYR   0.031   0.002   TYR B  80 
 ARG   0.008   0.000   ARG A  71 

*********************** 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
  347 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 291
  time to evaluate  : 1.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  163 GLU cc_start: 0.7294 (mp0) cc_final: 0.7027 (mp0)
REVERT: A  279 PHE cc_start: 0.7186 (t80) cc_final: 0.6388 (t80)
REVERT: A  282 MET cc_start: 0.8217 (tpp) cc_final: 0.7813 (ttm)
REVERT: A  364 GLN cc_start: 0.7713 (pp30) cc_final: 0.7220 (tm-30)
REVERT: A  452 ASP cc_start: 0.7156 (t70) cc_final: 0.6860 (t0)
REVERT: A  495 LYS cc_start: 0.8199 (mttm) cc_final: 0.7895 (mttm)
REVERT: A  525 ASP cc_start: 0.6147 (t70) cc_final: 0.5763 (t0)
REVERT: A  596 HIS cc_start: 0.4805 (t70) cc_final: 0.4515 (t70)
REVERT: A  598 PRO cc_start: 0.8015 (Cg_exo) cc_final: 0.7740 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.5990 (m-90) cc_final: 0.5754 (m-90)
REVERT: A  745 LEU cc_start: 0.8060 (mt) cc_final: 0.7654 (mp)
REVERT: A  751 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.5019 (pt)
REVERT: A  776 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7878 (pt)
REVERT: A  778 CYS cc_start: 0.7793 (t) cc_final: 0.6575 (m)
REVERT: A  794 GLU cc_start: 0.7229 (mt-10) cc_final: 0.6951 (mt-10)
REVERT: B   77 HIS cc_start: 0.8129 (OUTLIER) cc_final: 0.7374 (m-70)
REVERT: B   98 GLU cc_start: 0.8310 (pm20) cc_final: 0.8000 (pm20)
REVERT: B  118 VAL cc_start: 0.4190 (OUTLIER) cc_final: 0.3921 (t)
REVERT: B  141 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7441 (mm-30)
REVERT: B  177 PHE cc_start: 0.7422 (m-80) cc_final: 0.7035 (m-10)
REVERT: B  220 PHE cc_start: 0.7669 (m-10) cc_final: 0.7237 (m-80)
REVERT: B  260 ARG cc_start: 0.7439 (ttm170) cc_final: 0.7202 (tpp80)
REVERT: B  279 PHE cc_start: 0.7497 (t80) cc_final: 0.7201 (t80)
REVERT: B  298 HIS cc_start: 0.7146 (t-90) cc_final: 0.6743 (t-90)
REVERT: B  345 LYS cc_start: 0.7884 (ptpp) cc_final: 0.7081 (ptpp)
REVERT: B  357 GLU cc_start: 0.7338 (tp30) cc_final: 0.6876 (tp30)
REVERT: B  371 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7419 (mm)
REVERT: B  372 GLU cc_start: 0.6968 (tm-30) cc_final: 0.6690 (tm-30)
REVERT: B  495 LYS cc_start: 0.7804 (ttmm) cc_final: 0.7416 (ttmm)
REVERT: B  529 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7612 (tmtt)
REVERT: B  590 HIS cc_start: 0.6610 (t70) cc_final: 0.6357 (t70)
REVERT: B  614 ASN cc_start: 0.7764 (m-40) cc_final: 0.7470 (m110)
REVERT: B  689 PHE cc_start: 0.7742 (t80) cc_final: 0.7275 (t80)
REVERT: B  726 LYS cc_start: 0.8283 (mttt) cc_final: 0.7907 (ttmt)
  outliers start: 56
  outliers final: 33
  residues processed: 324
  average time/residue: 0.2920
  time to fit residues: 131.0775
Evaluate side-chains
  317 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 279
  time to evaluate  : 1.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  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  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  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  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  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  712 SER
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 145 optimal weight:    0.5980
   chunk 104 optimal weight:    0.4980
   chunk 35 optimal weight:    0.6980
   chunk 139 optimal weight:    0.0980
   chunk 51 optimal weight:    0.2980
   chunk 133 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4180

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.181403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.151478 restraints weight = 20664.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.156285 restraints weight = 11393.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.159472 restraints weight = 7485.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6584
moved from start:          0.2247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.081  12858  Z= 0.233
  Angle     :  0.661   9.774  17450  Z= 0.335
  Chirality :  0.046   0.190   1930
  Planarity :  0.005   0.048   2270
  Dihedral  :  6.231  72.753   1712
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.79 %
    Favored  : 76.98 %
  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: -0.61 (0.21), residues: 1570
  helix:  0.60 (0.20), residues: 673
  sheet: -0.71 (0.28), residues: 331
  loop : -1.33 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 618 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.062   0.002   PHE A 445 
 TYR   0.030   0.002   TYR B  80 
 ARG   0.009   0.000   ARG A 131 

*********************** 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
  335 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 291
  time to evaluate  : 1.618 
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  163 GLU cc_start: 0.7246 (mp0) cc_final: 0.6985 (mp0)
REVERT: A  279 PHE cc_start: 0.7041 (t80) cc_final: 0.6250 (t80)
REVERT: A  282 MET cc_start: 0.8056 (tpp) cc_final: 0.7656 (ttm)
REVERT: A  364 GLN cc_start: 0.7692 (pp30) cc_final: 0.7190 (tm-30)
REVERT: A  452 ASP cc_start: 0.7130 (t70) cc_final: 0.6843 (t0)
REVERT: A  495 LYS cc_start: 0.8175 (mttm) cc_final: 0.7881 (mttm)
REVERT: A  525 ASP cc_start: 0.6128 (t70) cc_final: 0.5756 (t0)
REVERT: A  596 HIS cc_start: 0.4949 (t70) cc_final: 0.4482 (t70)
REVERT: A  598 PRO cc_start: 0.7954 (Cg_exo) cc_final: 0.7665 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6156 (m-90) cc_final: 0.5864 (m-90)
REVERT: A  751 ILE cc_start: 0.5081 (OUTLIER) cc_final: 0.4837 (mp)
REVERT: A  776 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8081 (pt)
REVERT: A  778 CYS cc_start: 0.7793 (t) cc_final: 0.6579 (m)
REVERT: B   77 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7417 (m-70)
REVERT: B   98 GLU cc_start: 0.8300 (pm20) cc_final: 0.8079 (pm20)
REVERT: B  118 VAL cc_start: 0.4075 (OUTLIER) cc_final: 0.3782 (t)
REVERT: B  141 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7438 (mm-30)
REVERT: B  177 PHE cc_start: 0.7424 (m-80) cc_final: 0.7066 (m-10)
REVERT: B  187 MET cc_start: 0.6234 (ttp) cc_final: 0.5946 (tmm)
REVERT: B  220 PHE cc_start: 0.7679 (m-10) cc_final: 0.7184 (m-80)
REVERT: B  260 ARG cc_start: 0.7414 (ttm170) cc_final: 0.7185 (tpp80)
REVERT: B  279 PHE cc_start: 0.7501 (t80) cc_final: 0.7196 (t80)
REVERT: B  298 HIS cc_start: 0.7142 (t-90) cc_final: 0.6737 (t-90)
REVERT: B  345 LYS cc_start: 0.7864 (ptpp) cc_final: 0.7090 (ptpp)
REVERT: B  357 GLU cc_start: 0.7295 (tp30) cc_final: 0.6825 (tp30)
REVERT: B  371 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7416 (mm)
REVERT: B  372 GLU cc_start: 0.6993 (tm-30) cc_final: 0.6699 (tm-30)
REVERT: B  495 LYS cc_start: 0.7772 (ttmm) cc_final: 0.7412 (ttmm)
REVERT: B  529 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7599 (tmtt)
REVERT: B  590 HIS cc_start: 0.6627 (t70) cc_final: 0.6346 (t70)
REVERT: B  614 ASN cc_start: 0.7709 (m-40) cc_final: 0.7267 (m110)
REVERT: B  744 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7938 (tp)
  outliers start: 44
  outliers final: 27
  residues processed: 314
  average time/residue: 0.2927
  time to fit residues: 125.7941
Evaluate side-chains
  313 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 280
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  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  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  371 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  712 SER
Chi-restraints excluded: chain B residue  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Chi-restraints excluded: chain B residue  744 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 78 optimal weight:    3.9990
   chunk 102 optimal weight:    0.2980
   chunk 86 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 112 optimal weight:    0.5980
   chunk 131 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 123 optimal weight:    0.5980
   chunk 147 optimal weight:    0.2980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.4980

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.178638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.148339 restraints weight = 20656.937|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.153036 restraints weight = 11370.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.156183 restraints weight = 7416.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6594
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.088  12858  Z= 0.262
  Angle     :  0.689   9.580  17450  Z= 0.350
  Chirality :  0.046   0.175   1930
  Planarity :  0.005   0.057   2270
  Dihedral  :  6.268  74.379   1712
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.67 %
    Favored  : 94.33 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 20.23 %
    Favored  : 76.17 %
  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: -0.62 (0.21), residues: 1570
  helix:  0.59 (0.20), residues: 667
  sheet: -0.60 (0.28), residues: 319
  loop : -1.38 (0.26), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B 231 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.026   0.002   PHE B 602 
 TYR   0.031   0.002   TYR B  80 
 ARG   0.008   0.000   ARG A  71 

*********************** 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
  337 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 288
  time to evaluate  : 1.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.6509 (t0)
REVERT: A  158 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8148 (pt)
REVERT: A  279 PHE cc_start: 0.7090 (t80) cc_final: 0.6256 (t80)
REVERT: A  282 MET cc_start: 0.8203 (tpp) cc_final: 0.7777 (ttm)
REVERT: A  364 GLN cc_start: 0.7705 (pp30) cc_final: 0.7189 (tm-30)
REVERT: A  452 ASP cc_start: 0.7171 (t70) cc_final: 0.6885 (t0)
REVERT: A  495 LYS cc_start: 0.8214 (mttm) cc_final: 0.7878 (mttm)
REVERT: A  525 ASP cc_start: 0.6132 (t70) cc_final: 0.5752 (t0)
REVERT: A  596 HIS cc_start: 0.4889 (t70) cc_final: 0.4417 (t70)
REVERT: A  598 PRO cc_start: 0.7973 (Cg_exo) cc_final: 0.7673 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6204 (m-90) cc_final: 0.5879 (m-90)
REVERT: A  751 ILE cc_start: 0.5164 (OUTLIER) cc_final: 0.4927 (pt)
REVERT: A  776 ILE cc_start: 0.8465 (OUTLIER) cc_final: 0.8076 (pt)
REVERT: A  778 CYS cc_start: 0.7743 (t) cc_final: 0.6521 (m)
REVERT: A  794 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6962 (mt-10)
REVERT: B   77 HIS cc_start: 0.8123 (OUTLIER) cc_final: 0.7458 (m-70)
REVERT: B  118 VAL cc_start: 0.4076 (OUTLIER) cc_final: 0.3785 (t)
REVERT: B  141 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7509 (mm-30)
REVERT: B  177 PHE cc_start: 0.7352 (m-80) cc_final: 0.6969 (m-10)
REVERT: B  187 MET cc_start: 0.6276 (ttp) cc_final: 0.5963 (tmm)
REVERT: B  220 PHE cc_start: 0.7661 (m-10) cc_final: 0.7152 (m-80)
REVERT: B  260 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7220 (tpp80)
REVERT: B  279 PHE cc_start: 0.7462 (t80) cc_final: 0.7250 (t80)
REVERT: B  298 HIS cc_start: 0.7146 (t-90) cc_final: 0.6707 (t-90)
REVERT: B  345 LYS cc_start: 0.7874 (ptpp) cc_final: 0.7091 (ptpp)
REVERT: B  357 GLU cc_start: 0.7323 (tp30) cc_final: 0.6775 (tp30)
REVERT: B  371 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7277 (mm)
REVERT: B  495 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7243 (ttmm)
REVERT: B  529 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7605 (tmtt)
REVERT: B  536 GLN cc_start: 0.7030 (mm110) cc_final: 0.6826 (mm-40)
REVERT: B  614 ASN cc_start: 0.7796 (m-40) cc_final: 0.7226 (m110)
  outliers start: 49
  outliers final: 30
  residues processed: 312
  average time/residue: 0.3141
  time to fit residues: 136.4594
Evaluate side-chains
  319 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 282
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 LYS
Chi-restraints excluded: chain A residue   66 ASP
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  414 VAL
Chi-restraints excluded: chain A residue  485 VAL
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  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   43 MET
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  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  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:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 142 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 155 optimal weight:    0.5980
   chunk 114 optimal weight:    0.7980
   chunk 74 optimal weight:    0.3980
   chunk 58 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 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 = 0.4262 r_free = 0.4262 target = 0.178678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.148209 restraints weight = 20737.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.152924 restraints weight = 11396.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.156139 restraints weight = 7439.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.085  12858  Z= 0.252
  Angle     :  0.699   9.589  17450  Z= 0.355
  Chirality :  0.047   0.292   1930
  Planarity :  0.005   0.047   2270
  Dihedral  :  6.246  75.220   1712
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 10.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 21.48 %
    Favored  : 75.22 %
  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: -0.59 (0.21), residues: 1570
  helix:  0.60 (0.20), residues: 673
  sheet: -0.61 (0.28), residues: 319
  loop : -1.34 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 231 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.061   0.002   PHE A 445 
 TYR   0.031   0.002   TYR B  80 
 ARG   0.011   0.000   ARG A 131 

*********************** 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
  327 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 282
  time to evaluate  : 1.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   66 ASP cc_start: 0.6729 (OUTLIER) cc_final: 0.6513 (t0)
REVERT: A  131 ARG cc_start: 0.6572 (tpp80) cc_final: 0.6297 (tpp80)
REVERT: A  158 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.8111 (pt)
REVERT: A  279 PHE cc_start: 0.7071 (t80) cc_final: 0.6231 (t80)
REVERT: A  282 MET cc_start: 0.8186 (tpp) cc_final: 0.7747 (ttm)
REVERT: A  364 GLN cc_start: 0.7694 (pp30) cc_final: 0.7140 (tm-30)
REVERT: A  452 ASP cc_start: 0.7156 (t70) cc_final: 0.6909 (t0)
REVERT: A  495 LYS cc_start: 0.8205 (mttm) cc_final: 0.7875 (mttm)
REVERT: A  525 ASP cc_start: 0.6118 (t70) cc_final: 0.5734 (t0)
REVERT: A  596 HIS cc_start: 0.4918 (t70) cc_final: 0.4467 (t70)
REVERT: A  598 PRO cc_start: 0.7934 (Cg_exo) cc_final: 0.7655 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6205 (m-90) cc_final: 0.5880 (m-90)
REVERT: A  776 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.7982 (pt)
REVERT: A  778 CYS cc_start: 0.7729 (t) cc_final: 0.6643 (m)
REVERT: B   77 HIS cc_start: 0.8146 (OUTLIER) cc_final: 0.7470 (m-70)
REVERT: B   98 GLU cc_start: 0.8168 (pm20) cc_final: 0.7803 (pm20)
REVERT: B  118 VAL cc_start: 0.4047 (OUTLIER) cc_final: 0.3768 (t)
REVERT: B  141 GLU cc_start: 0.7830 (mm-30) cc_final: 0.7566 (mm-30)
REVERT: B  177 PHE cc_start: 0.7348 (m-80) cc_final: 0.6964 (m-10)
REVERT: B  187 MET cc_start: 0.6238 (ttp) cc_final: 0.5910 (tmm)
REVERT: B  220 PHE cc_start: 0.7649 (m-10) cc_final: 0.7153 (m-80)
REVERT: B  260 ARG cc_start: 0.7471 (ttm170) cc_final: 0.7237 (tpp80)
REVERT: B  279 PHE cc_start: 0.7423 (t80) cc_final: 0.7148 (t80)
REVERT: B  298 HIS cc_start: 0.7139 (t-90) cc_final: 0.6681 (t-90)
REVERT: B  345 LYS cc_start: 0.7882 (ptpp) cc_final: 0.7076 (ptpp)
REVERT: B  357 GLU cc_start: 0.7315 (tp30) cc_final: 0.6782 (tp30)
REVERT: B  371 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7336 (mm)
REVERT: B  372 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6744 (tm-30)
REVERT: B  495 LYS cc_start: 0.7557 (ttmm) cc_final: 0.7186 (ttmm)
REVERT: B  529 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7599 (tmtt)
REVERT: B  536 GLN cc_start: 0.7049 (mm110) cc_final: 0.6808 (mm-40)
REVERT: B  614 ASN cc_start: 0.7789 (m-40) cc_final: 0.7255 (m110)
REVERT: B  675 GLU cc_start: 0.6877 (mp0) cc_final: 0.6341 (mm-30)
  outliers start: 45
  outliers final: 27
  residues processed: 305
  average time/residue: 0.2939
  time to fit residues: 122.6841
Evaluate side-chains
  309 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 276
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
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  720 LEU
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  419 VAL
Chi-restraints excluded: chain B residue  458 ILE
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  718 VAL
Chi-restraints excluded: chain B residue  729 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0270
   chunk 136 optimal weight:    0.3980
   chunk 127 optimal weight:    0.0870
   chunk 104 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0980
   chunk 117 optimal weight:    0.0570
   chunk 0 optimal weight:    6.9990
   chunk 20 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9980
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.1334

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 248 ASN
B 365 HIS
B 397 ASN
B 564 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.180788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.151125 restraints weight = 20585.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.155687 restraints weight = 11405.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.158827 restraints weight = 7469.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6530
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12858  Z= 0.199
  Angle     :  0.689   9.698  17450  Z= 0.348
  Chirality :  0.045   0.249   1930
  Planarity :  0.004   0.047   2270
  Dihedral  :  6.138  76.450   1712
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.36 %
    Favored  : 74.93 %
  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: -0.39 (0.21), residues: 1570
  helix:  0.80 (0.21), residues: 665
  sheet: -0.46 (0.28), residues: 318
  loop : -1.29 (0.26), residues: 587

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 618 
 HIS   0.005   0.001   HIS B  77 
 PHE   0.020   0.002   PHE B 602 
 TYR   0.029   0.001   TYR B  80 
 ARG   0.008   0.000   ARG A  71 

*********************** 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
  312 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 275
  time to evaluate  : 1.404 
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: 0.1880 (tpt) cc_final: 0.0778 (tpt)
REVERT: A   66 ASP cc_start: 0.6651 (OUTLIER) cc_final: 0.6422 (t0)
REVERT: A  158 ILE cc_start: 0.8324 (pt) cc_final: 0.8098 (pt)
REVERT: A  210 LEU cc_start: 0.7871 (mp) cc_final: 0.7589 (tt)
REVERT: A  279 PHE cc_start: 0.6688 (t80) cc_final: 0.5853 (t80)
REVERT: A  282 MET cc_start: 0.7975 (tpp) cc_final: 0.7423 (ttt)
REVERT: A  364 GLN cc_start: 0.7586 (pp30) cc_final: 0.7034 (tm-30)
REVERT: A  374 GLU cc_start: 0.7823 (tp30) cc_final: 0.7351 (tp30)
REVERT: A  452 ASP cc_start: 0.7143 (t70) cc_final: 0.6820 (t70)
REVERT: A  495 LYS cc_start: 0.8154 (mttm) cc_final: 0.7813 (mttm)
REVERT: A  525 ASP cc_start: 0.6068 (t70) cc_final: 0.5703 (t0)
REVERT: A  596 HIS cc_start: 0.4847 (t70) cc_final: 0.4454 (t70)
REVERT: A  598 PRO cc_start: 0.7814 (Cg_exo) cc_final: 0.7509 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6179 (m-90) cc_final: 0.5820 (m-90)
REVERT: A  678 GLU cc_start: 0.7226 (pp20) cc_final: 0.6735 (tm-30)
REVERT: A  740 ARG cc_start: 0.5779 (mpp-170) cc_final: 0.4362 (mpp-170)
REVERT: A  776 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8023 (pt)
REVERT: A  778 CYS cc_start: 0.7556 (t) cc_final: 0.6928 (m)
REVERT: B   77 HIS cc_start: 0.8055 (OUTLIER) cc_final: 0.7443 (m-70)
REVERT: B   98 GLU cc_start: 0.8202 (pm20) cc_final: 0.7809 (pm20)
REVERT: B  118 VAL cc_start: 0.4155 (OUTLIER) cc_final: 0.3860 (t)
REVERT: B  187 MET cc_start: 0.6232 (ttp) cc_final: 0.5926 (tmm)
REVERT: B  220 PHE cc_start: 0.7574 (m-10) cc_final: 0.7106 (m-80)
REVERT: B  260 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7163 (tpp80)
REVERT: B  279 PHE cc_start: 0.7362 (t80) cc_final: 0.7138 (t80)
REVERT: B  298 HIS cc_start: 0.7147 (t-90) cc_final: 0.6675 (t-90)
REVERT: B  345 LYS cc_start: 0.7868 (ptpp) cc_final: 0.7052 (ptpp)
REVERT: B  357 GLU cc_start: 0.7294 (tp30) cc_final: 0.6775 (tp30)
REVERT: B  372 GLU cc_start: 0.7042 (tm-30) cc_final: 0.6676 (tm-30)
REVERT: B  495 LYS cc_start: 0.7459 (ttmm) cc_final: 0.7081 (ttmm)
REVERT: B  529 LYS cc_start: 0.8129 (tmtt) cc_final: 0.7528 (tmtt)
REVERT: B  590 HIS cc_start: 0.6745 (t-90) cc_final: 0.6425 (t70)
REVERT: B  614 ASN cc_start: 0.7731 (m-40) cc_final: 0.7297 (m110)
REVERT: B  675 GLU cc_start: 0.6756 (mp0) cc_final: 0.6286 (mm-30)
REVERT: B  786 PHE cc_start: 0.6610 (m-10) cc_final: 0.6215 (m-80)
  outliers start: 37
  outliers final: 22
  residues processed: 295
  average time/residue: 0.3083
  time to fit residues: 123.8929
Evaluate side-chains
  295 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 269
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  250 VAL
Chi-restraints excluded: chain A residue  383 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  545 MET
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  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  364 GLN
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0050
   chunk 137 optimal weight:    0.4980
   chunk 86 optimal weight:    0.2980
   chunk 9 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 69 optimal weight:    0.0040
   chunk 64 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.2806

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.179938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.149841 restraints weight = 20569.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.154487 restraints weight = 11364.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.157659 restraints weight = 7436.576|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  12858  Z= 0.222
  Angle     :  0.709  10.160  17450  Z= 0.361
  Chirality :  0.046   0.238   1930
  Planarity :  0.005   0.072   2270
  Dihedral  :  6.102  76.332   1712
  Min Nonbonded Distance : 2.220

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 23.68 %
    Favored  : 74.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.44 (0.21), residues: 1570
  helix:  0.74 (0.20), residues: 673
  sheet: -0.48 (0.28), residues: 319
  loop : -1.33 (0.26), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 630 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.022   0.002   PHE B 602 
 TYR   0.031   0.001   TYR B  80 
 ARG   0.009   0.000   ARG A  71 

********************** 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
  300 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 269
  time to evaluate  : 1.533 
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: 0.2422 (tpt) cc_final: 0.1525 (tpt)
REVERT: A  163 GLU cc_start: 0.7189 (mp0) cc_final: 0.6309 (mp0)
REVERT: A  210 LEU cc_start: 0.7879 (mp) cc_final: 0.7569 (tt)
REVERT: A  279 PHE cc_start: 0.6806 (t80) cc_final: 0.6080 (t80)
REVERT: A  282 MET cc_start: 0.7914 (tpp) cc_final: 0.7387 (ttt)
REVERT: A  364 GLN cc_start: 0.7577 (pp30) cc_final: 0.7076 (tm-30)
REVERT: A  448 LYS cc_start: 0.7906 (mmmm) cc_final: 0.7613 (ttmm)
REVERT: A  452 ASP cc_start: 0.7099 (t70) cc_final: 0.6819 (t70)
REVERT: A  495 LYS cc_start: 0.8174 (mttm) cc_final: 0.7872 (mttm)
REVERT: A  525 ASP cc_start: 0.6096 (t70) cc_final: 0.5695 (t0)
REVERT: A  596 HIS cc_start: 0.4849 (t70) cc_final: 0.4456 (t70)
REVERT: A  598 PRO cc_start: 0.7848 (Cg_exo) cc_final: 0.7542 (Cg_endo)
REVERT: A  665 TRP cc_start: 0.6206 (m-90) cc_final: 0.5840 (m-90)
REVERT: A  678 GLU cc_start: 0.7260 (pp20) cc_final: 0.6769 (tm-30)
REVERT: A  776 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8017 (pt)
REVERT: A  778 CYS cc_start: 0.7592 (t) cc_final: 0.6748 (m)
REVERT: B   77 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7527 (m-70)
REVERT: B   98 GLU cc_start: 0.8210 (pm20) cc_final: 0.7805 (pm20)
REVERT: B  118 VAL cc_start: 0.3882 (OUTLIER) cc_final: 0.3559 (t)
REVERT: B  141 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7522 (mm-30)
REVERT: B  187 MET cc_start: 0.6251 (ttp) cc_final: 0.5945 (tmm)
REVERT: B  220 PHE cc_start: 0.7585 (m-10) cc_final: 0.7158 (m-80)
REVERT: B  260 ARG cc_start: 0.7426 (ttm170) cc_final: 0.7206 (tpp80)
REVERT: B  279 PHE cc_start: 0.7406 (t80) cc_final: 0.7161 (t80)
REVERT: B  291 GLU cc_start: 0.7263 (tt0) cc_final: 0.6749 (mm-30)
REVERT: B  298 HIS cc_start: 0.7146 (t-90) cc_final: 0.6677 (t-90)
REVERT: B  345 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7059 (ptpp)
REVERT: B  357 GLU cc_start: 0.7338 (tp30) cc_final: 0.6788 (tp30)
REVERT: B  372 GLU cc_start: 0.7036 (tm-30) cc_final: 0.6688 (tm-30)
REVERT: B  408 LYS cc_start: 0.7967 (mmpt) cc_final: 0.7525 (mmpt)
REVERT: B  495 LYS cc_start: 0.7500 (ttmm) cc_final: 0.7117 (ttmm)
REVERT: B  529 LYS cc_start: 0.8171 (tmtt) cc_final: 0.7516 (tmtt)
REVERT: B  590 HIS cc_start: 0.6835 (t-90) cc_final: 0.6455 (t70)
REVERT: B  614 ASN cc_start: 0.7744 (m-40) cc_final: 0.7356 (m110)
REVERT: B  675 GLU cc_start: 0.6847 (mp0) cc_final: 0.6329 (mm-30)
  outliers start: 31
  outliers final: 21
  residues processed: 286
  average time/residue: 0.3356
  time to fit residues: 132.6883
Evaluate side-chains
  294 residues out of total 1364 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 270
  time to evaluate  : 1.436 
-------------------------------------------------------------------------------
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  485 VAL
Chi-restraints excluded: chain A residue  545 MET
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  704 VAL
Chi-restraints excluded: chain A residue  751 ILE
Chi-restraints excluded: chain A residue  776 ILE
Chi-restraints excluded: chain A residue  795 ILE
Chi-restraints excluded: chain B residue   60 VAL
Chi-restraints excluded: chain B residue   77 HIS
Chi-restraints excluded: chain B residue  118 VAL
Chi-restraints excluded: chain B residue  342 LEU
Chi-restraints excluded: chain B residue  364 GLN
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  487 SER
Chi-restraints excluded: chain B residue  503 ILE
Chi-restraints excluded: chain B residue  507 TYR
Chi-restraints excluded: chain B residue  509 LEU
Chi-restraints excluded: chain B residue  544 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 153 optimal weight:    0.0980
   chunk 32 optimal weight:    0.8980
   chunk 60 optimal weight:    0.3980
   chunk 144 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 123 optimal weight:    0.7980
   chunk 149 optimal weight:    0.0870
   chunk 37 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 108 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0570
   overall best weight:    0.2276

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.180468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.150265 restraints weight = 20777.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.154940 restraints weight = 11388.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.158141 restraints weight = 7436.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6540
moved from start:          0.2899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12858  Z= 0.213
  Angle     :  0.712  10.417  17450  Z= 0.362
  Chirality :  0.046   0.231   1930
  Planarity :  0.005   0.050   2270
  Dihedral  :  6.057  74.523   1712
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 23.75 %
    Favored  : 73.68 %
  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: -0.40 (0.21), residues: 1570
  helix:  0.82 (0.20), residues: 669
  sheet: -0.51 (0.28), residues: 325
  loop : -1.33 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 618 
 HIS   0.006   0.001   HIS B  77 
 PHE   0.021   0.002   PHE B 602 
 TYR   0.030   0.001   TYR B  80 
 ARG   0.009   0.000   ARG A  71 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4250.71 seconds
wall clock time: 77 minutes 38.90 seconds (4658.90 seconds total)