Starting phenix.real_space_refine
on Sat Aug 23 13:10:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9imz_60697/08_2025/9imz_60697_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9imz_60697/08_2025/9imz_60697.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9imz_60697/08_2025/9imz_60697_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9imz_60697/08_2025/9imz_60697_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9imz_60697/08_2025/9imz_60697.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9imz_60697/08_2025/9imz_60697.map"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.075
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      53      5.16       5
     C    7835      2.51       5
     N    2083      2.21       5
     O    2196      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 104 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12167
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4325
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4325
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 505}
          Chain breaks: 9
    Chain: "B"
      Number of atoms: 4122
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 516, 4122
          Classifications: {'peptide': 516}
          Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 484}
          Chain breaks: 7
    Chain: "C"
      Number of atoms: 1240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1240
          Classifications: {'peptide': 154}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 141}
    Chain: "D"
      Number of atoms: 1240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1240
          Classifications: {'peptide': 154}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 141}
    Chain: "E"
      Number of atoms: 1240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 154, 1240
          Classifications: {'peptide': 154}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 141}
  Time building chain proxies: 2.75, per 1000 atoms: 0.23
  Number of scatterers: 12167
  At special positions: 0
  Unit cell: (85.8, 122.1, 149.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      53     16.00
     O    2196      8.00
     N    2083      7.00
     C    7835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 522.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2882

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 8 sheets defined
      52.6% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 10
      removed outlier: 4.478A  pdb=" N   LEU A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 14 through 23
    Processing helix  chain 'A' and resid 34 through 41
    Processing helix  chain 'A' and resid 42 through 46
    Processing helix  chain 'A' and resid 48 through 62
    Processing helix  chain 'A' and resid 250 through 262
    Processing helix  chain 'A' and resid 292 through 296
      removed outlier: 4.071A  pdb=" N   ARG A 295 " --> pdb=" O   ASP A 292 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   VAL A 296 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 292 through 296'
    Processing helix  chain 'A' and resid 299 through 315
    Processing helix  chain 'A' and resid 320 through 332
      removed outlier: 3.875A  pdb=" N   GLU A 324 " --> pdb=" O   ASN A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 375
      removed outlier: 3.667A  pdb=" N   CYS A 366 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 382
    Processing helix  chain 'A' and resid 385 through 394
      removed outlier: 3.684A  pdb=" N   LEU A 389 " --> pdb=" O   ASP A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 401
    Processing helix  chain 'A' and resid 402 through 416
      removed outlier: 3.527A  pdb=" N   GLN A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 467
      removed outlier: 3.864A  pdb=" N   LYS A 454 " --> pdb=" O   HIS A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 482
      removed outlier: 3.668A  pdb=" N   GLY A 480 " --> pdb=" O   ASP A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 496
    Processing helix  chain 'A' and resid 497 through 515
      removed outlier: 3.883A  pdb=" N   PHE A 501 " --> pdb=" O   SER A 497 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   GLN A 514 " --> pdb=" O   LEU A 510 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   SER A 515 " --> pdb=" O   GLN A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 547
      removed outlier: 3.842A  pdb=" N   ARG A 544 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLU A 547 " --> pdb=" O   TRP A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 567
      No H-bonds generated for 'chain 'A' and resid 565 through 567'
    Processing helix  chain 'A' and resid 568 through 579
      removed outlier: 3.803A  pdb=" N   ARG A 572 " --> pdb=" O   GLN A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 600
      removed outlier: 3.876A  pdb=" N   ASN A 584 " --> pdb=" O   SER A 580 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLN A 585 " --> pdb=" O   PHE A 581 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   GLY A 600 " --> pdb=" O   GLN A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 645
      removed outlier: 3.791A  pdb=" N   VAL A 628 " --> pdb=" O   LYS A 624 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   LEU A 635 " --> pdb=" O   LEU A 631 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE A 645 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 649
      removed outlier: 3.586A  pdb=" N   ARG A 649 " --> pdb=" O   LEU A 646 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 646 through 649'
    Processing helix  chain 'A' and resid 659 through 669
      removed outlier: 3.922A  pdb=" N   ILE A 663 " --> pdb=" O   LEU A 659 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLN A 669 " --> pdb=" O   ALA A 665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 686
      removed outlier: 3.589A  pdb=" N   ALA A 686 " --> pdb=" O   ARG A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 700
      removed outlier: 3.739A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
      Proline residue:  A 694  - end of helix
    Processing helix  chain 'A' and resid 701 through 703
      No H-bonds generated for 'chain 'A' and resid 701 through 703'
    Processing helix  chain 'A' and resid 706 through 710
    Processing helix  chain 'A' and resid 711 through 727
      removed outlier: 4.463A  pdb=" N   ASP A 715 " --> pdb=" O   GLU A 711 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   ILE A 716 " --> pdb=" O   TYR A 712 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   SER A 726 " --> pdb=" O   ARG A 722 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU A 727 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 753
      removed outlier: 3.601A  pdb=" N   LEU A 752 " --> pdb=" O   VAL A 748 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   PHE A 753 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 766
      removed outlier: 3.549A  pdb=" N   GLU A 766 " --> pdb=" O   LEU A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 799
    Processing helix  chain 'A' and resid 800 through 802
      No H-bonds generated for 'chain 'A' and resid 800 through 802'
    Processing helix  chain 'A' and resid 803 through 815
      removed outlier: 3.604A  pdb=" N   LYS A 807 " --> pdb=" O   GLY A 803 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   VAL A 813 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 10
    Processing helix  chain 'B' and resid 14 through 24
    Processing helix  chain 'B' and resid 34 through 41
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 48 through 61
    Processing helix  chain 'B' and resid 292 through 296
      removed outlier: 4.123A  pdb=" N   VAL B 296 " --> pdb=" O   PRO B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 315
    Processing helix  chain 'B' and resid 320 through 333
      removed outlier: 3.639A  pdb=" N   THR B 333 " --> pdb=" O   PHE B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 362 through 375
      removed outlier: 3.510A  pdb=" N   CYS B 366 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 377 through 382
      removed outlier: 3.578A  pdb=" N   LEU B 381 " --> pdb=" O   HIS B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 395
      removed outlier: 3.583A  pdb=" N   GLU B 394 " --> pdb=" O   LYS B 390 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 402
      removed outlier: 4.163A  pdb=" N   LEU B 399 " --> pdb=" O   ASN B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 402 through 413
    Processing helix  chain 'B' and resid 450 through 470
      removed outlier: 3.751A  pdb=" N   LYS B 454 " --> pdb=" O   HIS B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 482
    Processing helix  chain 'B' and resid 483 through 496
    Processing helix  chain 'B' and resid 497 through 515
      removed outlier: 3.806A  pdb=" N   PHE B 501 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLN B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   SER B 515 " --> pdb=" O   GLN B 511 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 539 through 547
      removed outlier: 3.991A  pdb=" N   TRP B 543 " --> pdb=" O   LEU B 539 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   ARG B 544 " --> pdb=" O   GLY B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 551
    Processing helix  chain 'B' and resid 565 through 567
      No H-bonds generated for 'chain 'B' and resid 565 through 567'
    Processing helix  chain 'B' and resid 568 through 579
      removed outlier: 4.149A  pdb=" N   ARG B 572 " --> pdb=" O   GLN B 568 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASP B 573 " --> pdb=" O   GLY B 569 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   SER B 579 " --> pdb=" O   ILE B 575 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 599
    Processing helix  chain 'B' and resid 624 through 645
      removed outlier: 3.881A  pdb=" N   VAL B 628 " --> pdb=" O   LYS B 624 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   PHE B 645 " --> pdb=" O   GLY B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 657 through 668
      removed outlier: 4.330A  pdb=" N   ASP B 661 " --> pdb=" O   GLY B 657 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   SER B 662 " --> pdb=" O   GLU B 658 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ILE B 663 " --> pdb=" O   LEU B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 675 through 686
      removed outlier: 3.924A  pdb=" N   LEU B 679 " --> pdb=" O   ASP B 675 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA B 686 " --> pdb=" O   ARG B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 701
      removed outlier: 3.510A  pdb=" N   THR B 692 " --> pdb=" O   ARG B 688 " (cutoff:3.500A)
      Proline residue:  B 694  - end of helix
    Processing helix  chain 'B' and resid 705 through 710
      removed outlier: 4.359A  pdb=" N   LEU B 709 " --> pdb=" O   HIS B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 711 through 725
      removed outlier: 4.148A  pdb=" N   ASP B 715 " --> pdb=" O   GLU B 711 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ILE B 716 " --> pdb=" O   TYR B 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 731 through 736
      removed outlier: 3.603A  pdb=" N   LYS B 736 " --> pdb=" O   GLU B 732 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 738 through 753
      removed outlier: 3.792A  pdb=" N   PHE B 753 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 759 through 764
      removed outlier: 3.558A  pdb=" N   LEU B 762 " --> pdb=" O   PRO B 759 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   PHE B 763 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 791 through 799
    Processing helix  chain 'B' and resid 800 through 802
      No H-bonds generated for 'chain 'B' and resid 800 through 802'
    Processing helix  chain 'B' and resid 803 through 815
      removed outlier: 3.560A  pdb=" N   LYS B 807 " --> pdb=" O   GLY B 803 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TRP B 812 " --> pdb=" O   LEU B 808 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   VAL B 813 " --> pdb=" O   LEU B 809 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY B 815 " --> pdb=" O   SER B 811 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 52
      No H-bonds generated for 'chain 'C' and resid 50 through 52'
    Processing helix  chain 'C' and resid 119 through 125
    Processing helix  chain 'D' and resid 50 through 54
      removed outlier: 4.176A  pdb=" N   TYR D  53 " --> pdb=" O   SER D  50 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   ASP D  54 " --> pdb=" O   GLU D  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 50 through 54'
    Processing helix  chain 'D' and resid 80 through 84
      removed outlier: 3.762A  pdb=" N   LEU D  83 " --> pdb=" O   ASN D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 125
    Processing helix  chain 'E' and resid 85 through 90
      removed outlier: 3.766A  pdb=" N   VAL E  90 " --> pdb=" O   ASP E  86 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 119 through 125
      removed outlier: 3.774A  pdb=" N   ASN E 125 " --> pdb=" O   GLU E 121 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 195 through 197
      removed outlier: 3.736A  pdb=" N   ARG A 195 " --> pdb=" O   SER E  59 " (cutoff:3.500A)
      removed outlier: 7.207A  pdb=" N   ILE E  42 " --> pdb=" O   LEU E  57 " (cutoff:3.500A)
      removed outlier: 4.404A  pdb=" N   SER E  59 " --> pdb=" O   TRP E  40 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   TRP E  40 " --> pdb=" O   SER E  59 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   LEU E  61 " --> pdb=" O   LEU E  38 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   LEU E  38 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ILE E 107 " --> pdb=" O   CYS E  99 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   TYR E 101 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   GLU E 105 " --> pdb=" O   TYR E 101 " (cutoff:3.500A)
      removed outlier: 13.648A  pdb=" N   GLN E 104 " --> pdb=" O   ARG E 148 " (cutoff:3.500A)
      removed outlier: 12.128A  pdb=" N   ARG E 148 " --> pdb=" O   GLN E 104 " (cutoff:3.500A)
      removed outlier: 11.957A  pdb=" N   PHE E 106 " --> pdb=" O   VAL E 146 " (cutoff:3.500A)
      removed outlier: 10.412A  pdb=" N   VAL E 146 " --> pdb=" O   PHE E 106 " (cutoff:3.500A)
      removed outlier: 11.094A  pdb=" N   ARG E 108 " --> pdb=" O   PRO E 144 " (cutoff:3.500A)
      removed outlier: 11.305A  pdb=" N   GLY E 110 " --> pdb=" O   SER E 142 " (cutoff:3.500A)
      removed outlier: 8.538A  pdb=" N   SER E 142 " --> pdb=" O   GLY E 110 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   TYR E 112 " --> pdb=" O   LEU E 140 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   SER E  16 " --> pdb=" O   ARG E 137 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 826 through 827
      removed outlier: 7.307A  pdb=" N   ILE C  42 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   SER C  59 " --> pdb=" O   TRP C  40 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   TRP C  40 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LEU C  61 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU C  38 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   VAL C  94 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   GLY C  91 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ASN C 114 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR C  93 " --> pdb=" O   TYR C 112 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   TYR C 112 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL C  95 " --> pdb=" O   GLY C 110 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLY C 110 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ILE C  97 " --> pdb=" O   ARG C 108 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ARG C 108 " --> pdb=" O   ILE C  97 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   CYS C  99 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 826 through 827
      removed outlier: 7.307A  pdb=" N   ILE C  42 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   SER C  59 " --> pdb=" O   TRP C  40 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   TRP C  40 " --> pdb=" O   SER C  59 " (cutoff:3.500A)
      removed outlier: 4.576A  pdb=" N   LEU C  61 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   LEU C  38 " --> pdb=" O   LEU C  61 " (cutoff:3.500A)
      removed outlier: 4.842A  pdb=" N   VAL C  94 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
      removed outlier: 7.325A  pdb=" N   GLY C  91 " --> pdb=" O   ASN C 114 " (cutoff:3.500A)
      removed outlier: 4.912A  pdb=" N   ASN C 114 " --> pdb=" O   GLY C  91 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   THR C  93 " --> pdb=" O   TYR C 112 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   TYR C 112 " --> pdb=" O   THR C  93 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   VAL C  95 " --> pdb=" O   GLY C 110 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   GLY C 110 " --> pdb=" O   VAL C  95 " (cutoff:3.500A)
      removed outlier: 6.930A  pdb=" N   ILE C  97 " --> pdb=" O   ARG C 108 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   ARG C 108 " --> pdb=" O   ILE C  97 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   CYS C  99 " --> pdb=" O   PHE C 106 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 830 through 832
      removed outlier: 3.693A  pdb=" N   THR A 832 " --> pdb=" O   ARG C  69 " (cutoff:3.500A)
      removed outlier: 4.984A  pdb=" N   ARG C  69 " --> pdb=" O   THR A 832 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   GLN C  23 " --> pdb=" O   VAL C  11 " (cutoff:3.500A)
      removed outlier: 5.627A  pdb=" N   VAL C  11 " --> pdb=" O   GLN C  23 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   GLU C  25 " --> pdb=" O   VAL C   9 " (cutoff:3.500A)
      removed outlier: 4.629A  pdb=" N   VAL C   9 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 7.382A  pdb=" N   THR C  27 " --> pdb=" O   ASN C   7 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 4 through 11
      removed outlier: 6.677A  pdb=" N   THR D  27 " --> pdb=" O   ASN D   7 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL D   9 " --> pdb=" O   GLU D  25 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   GLU D  25 " --> pdb=" O   VAL D   9 " (cutoff:3.500A)
      removed outlier: 5.451A  pdb=" N   VAL D  11 " --> pdb=" O   GLN D  23 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   GLN D  23 " --> pdb=" O   VAL D  11 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ALA D  76 " --> pdb=" O   PHE D  22 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   PHE D  24 " --> pdb=" O   PHE D  74 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 16 through 17
      removed outlier: 3.647A  pdb=" N   ASN D 114 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
      removed outlier: 5.437A  pdb=" N   GLU D 105 " --> pdb=" O   TYR D 101 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   TYR D 101 " --> pdb=" O   GLU D 105 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ILE D 107 " --> pdb=" O   CYS D  99 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLY D  91 " --> pdb=" O   ASN D 115 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE D  42 " --> pdb=" O   ASP D  58 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   ASP D  58 " --> pdb=" O   ILE D  42 " (cutoff:3.500A)
      removed outlier: 7.507A  pdb=" N   TYR D  44 " --> pdb=" O   VAL D  56 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   VAL D  56 " --> pdb=" O   TYR D  44 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 16 through 17
      removed outlier: 3.647A  pdb=" N   ASN D 114 " --> pdb=" O   ASN D 138 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 4 through 12
      removed outlier: 5.605A  pdb=" N   VAL E   6 " --> pdb=" O   GLU E  29 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   GLU E  29 " --> pdb=" O   VAL E   6 " (cutoff:3.500A)
      removed outlier: 4.627A  pdb=" N   GLN E  23 " --> pdb=" O   LEU E  12 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ILE E  26 " --> pdb=" O   PHE E  72 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   PHE E  72 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)

    560 hydrogen bonds defined for protein.
    1590 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.49

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3853
        1.34 -     1.46: 1927
        1.46 -     1.58: 6595
        1.58 -     1.70: 0
        1.70 -     1.82: 78
  Bond restraints: 12453
  Sorted by residual:
  bond pdb=" CZ  ARG A 410 "
       pdb=" NH2 ARG A 410 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.46e+00
  bond pdb=" CZ  ARG A 336 "
       pdb=" NH2 ARG A 336 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.93e+00
  bond pdb=" CZ  ARG A  63 "
       pdb=" NH2 ARG A  63 "
    ideal  model  delta    sigma   weight residual
    1.330  1.296  0.034 1.30e-02 5.92e+03 6.91e+00
  bond pdb=" CZ  ARG B 725 "
       pdb=" NH2 ARG B 725 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.62e+00
  bond pdb=" CZ  ARG A 819 "
       pdb=" NH2 ARG A 819 "
    ideal  model  delta    sigma   weight residual
    1.330  1.297  0.033 1.30e-02 5.92e+03 6.52e+00
  ... (remaining 12448 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 16187
        1.86 -     3.72: 595
        3.72 -     5.58: 98
        5.58 -     7.44: 11
        7.44 -     9.30: 2
  Bond angle restraints: 16893
  Sorted by residual:
  angle pdb=" OE1 GLN B 754 "
        pdb=" CD  GLN B 754 "
        pdb=" NE2 GLN B 754 "
      ideal   model   delta    sigma   weight residual
     122.60  118.34    4.26 1.00e+00 1.00e+00 1.82e+01
  angle pdb=" C   ASN D  14 "
        pdb=" N   PRO D  15 "
        pdb=" CD  PRO D  15 "
      ideal   model   delta    sigma   weight residual
     120.60  129.90   -9.30 2.20e+00 2.07e-01 1.79e+01
  angle pdb=" OE1 GLN A 330 "
        pdb=" CD  GLN A 330 "
        pdb=" NE2 GLN A 330 "
      ideal   model   delta    sigma   weight residual
     122.60  118.65    3.95 1.00e+00 1.00e+00 1.56e+01
  angle pdb=" OE1 GLN A  67 "
        pdb=" CD  GLN A  67 "
        pdb=" NE2 GLN A  67 "
      ideal   model   delta    sigma   weight residual
     122.60  118.65    3.95 1.00e+00 1.00e+00 1.56e+01
  angle pdb=" CA  ASP C  86 "
        pdb=" CB  ASP C  86 "
        pdb=" CG  ASP C  86 "
      ideal   model   delta    sigma   weight residual
     112.60  116.49   -3.89 1.00e+00 1.00e+00 1.51e+01
  ... (remaining 16888 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.55: 6468
       17.55 -    35.10: 784
       35.10 -    52.65: 194
       52.65 -    70.19: 34
       70.19 -    87.74: 25
  Dihedral angle restraints: 7505
    sinusoidal: 3089
      harmonic: 4416
  Sorted by residual:
  dihedral pdb=" CA  PRO A 293 "
           pdb=" C   PRO A 293 "
           pdb=" N   ALA A 294 "
           pdb=" CA  ALA A 294 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.81  -20.19     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" CA  PRO C 130 "
           pdb=" C   PRO C 130 "
           pdb=" N   ASP C 131 "
           pdb=" CA  ASP C 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.21   17.79     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  ALA A 334 "
           pdb=" C   ALA A 334 "
           pdb=" N   ARG A 335 "
           pdb=" CA  ARG A 335 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.65  -17.35     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 7502 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 1543
       0.053 -    0.106: 260
       0.106 -    0.160: 71
       0.160 -    0.213: 8
       0.213 -    0.266: 3
  Chirality restraints: 1885
  Sorted by residual:
  chirality pdb=" CA  PHE A 360 "
            pdb=" N   PHE A 360 "
            pdb=" C   PHE A 360 "
            pdb=" CB  PHE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.77e+00
  chirality pdb=" CA  ASN B 316 "
            pdb=" N   ASN B 316 "
            pdb=" C   ASN B 316 "
            pdb=" CB  ASN B 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CA  PRO A 293 "
            pdb=" N   PRO A 293 "
            pdb=" C   PRO A 293 "
            pdb=" CB  PRO A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.50    0.22 2.00e-01 2.50e+01 1.22e+00
  ... (remaining 1882 not shown)

  Planarity restraints: 2192
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 812 "    0.067 2.00e-02 2.50e+03   4.34e-02 4.71e+01
        pdb=" CG  TRP A 812 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 812 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 812 "   -0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 812 "   -0.041 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 812 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 812 "   -0.076 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 812 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 812 "   -0.016 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 812 "    0.069 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 117 "   -0.049 2.00e-02 2.50e+03   2.67e-02 1.43e+01
        pdb=" CG  TYR C 117 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 117 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 117 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 117 "    0.017 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 117 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 117 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR C 117 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 801 "   -0.035 2.00e-02 2.50e+03   2.49e-02 1.24e+01
        pdb=" CG  TYR B 801 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 801 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 801 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 801 "    0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 801 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 801 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B 801 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 2189 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 89
        2.60 -     3.17: 9851
        3.17 -     3.75: 17529
        3.75 -     4.32: 21574
        4.32 -     4.90: 36564
  Nonbonded interactions: 85607
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 687 "
            pdb=" O   GLU A 781 "
     model   vdw
     2.021 3.120
  nonbonded pdb=" OH  TYR A 309 "
            pdb=" OE1 GLU A 324 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   GLU B 698 "
            pdb=" OG  SER B 701 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" O   ALA B   3 "
            pdb=" OG  SER B   7 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NE2 GLN A 669 "
            pdb=" OG  SER B 592 "
     model   vdw
     2.242 3.120
  ... (remaining 85602 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: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 67 or resid 287 through 515 or resid 538 through \ 
 832))
  selection = (chain 'B' and (resid 1 through 23 or resid 33 through 606 or resid 621 through  \ 
767 or resid 780 through 832))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.290
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
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   0.083  12453  Z= 0.277
  Angle     :  0.765   9.300  16893  Z= 0.457
  Chirality :  0.046   0.266   1885
  Planarity :  0.005   0.064   2192
  Dihedral  : 16.758  87.743   4623
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 23.23 %
    Favored  : 76.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.22), residues: 1476
  helix:  1.61 (0.21), residues: 629
  sheet:  1.23 (0.36), residues: 207
  loop : -0.34 (0.25), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 295 
 TYR   0.049   0.003   TYR C 117 
 PHE   0.030   0.002   PHE B 326 
 TRP   0.076   0.003   TRP A 812 
 HIS   0.003   0.000   HIS B 469 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (12453)
  covalent geometry    : angle       0.76543 (16893)
  hydrogen bonds       : bond        0.21357 (  541)
  hydrogen bonds       : angle       6.20791 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  488 MET cc_start: 0.8352 (ttp) cc_final: 0.8138 (tmm)
REVERT: A  791 ASP cc_start: 0.8250 (t0) cc_final: 0.8037 (t0)
REVERT: B    1 MET cc_start: 0.3669 (mpp) cc_final: 0.2019 (tpt)
REVERT: B   22 ILE cc_start: 0.8173 (mm) cc_final: 0.7925 (mt)
REVERT: B   45 LEU cc_start: 0.8561 (mt) cc_final: 0.8348 (pp)
REVERT: B  371 VAL cc_start: 0.9464 (t) cc_final: 0.9232 (m)
REVERT: B  488 MET cc_start: 0.8636 (ttp) cc_final: 0.8419 (ttt)
REVERT: B  512 MET cc_start: 0.8311 (ttt) cc_final: 0.8037 (ttm)
REVERT: B  801 TYR cc_start: 0.8538 (p90) cc_final: 0.8154 (p90)
REVERT: C  143 ASN cc_start: 0.8644 (m110) cc_final: 0.8325 (p0)
REVERT: D   30 CYS cc_start: 0.8427 (m) cc_final: 0.7684 (t)
REVERT: D   33 ASP cc_start: 0.7255 (m-30) cc_final: 0.7020 (t0)
REVERT: D   88 ASP cc_start: 0.7898 (m-30) cc_final: 0.7058 (t0)
REVERT: D  107 ILE cc_start: 0.9071 (tt) cc_final: 0.8835 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0956
  time to fit residues: 28.3524
Evaluate side-chains
  113 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 316 ASN
A 508 GLN
A 705 HIS
B  55 ASN
B  67 GLN
B 508 GLN
C  20 ASN
E   5 GLN
E 136 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.117052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.088913 restraints weight = 34457.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.088968 restraints weight = 33839.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.089411 restraints weight = 32106.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.089497 restraints weight = 22493.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.090571 restraints weight = 19751.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12453  Z= 0.140
  Angle     :  0.615  11.072  16893  Z= 0.309
  Chirality :  0.042   0.179   1885
  Planarity :  0.005   0.055   2192
  Dihedral  :  4.090  18.838   1637
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 22.86 %
    Favored  : 73.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.17 (0.22), residues: 1476
  helix:  1.73 (0.20), residues: 650
  sheet:  1.12 (0.36), residues: 216
  loop : -0.36 (0.25), residues: 610

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 464 
 TYR   0.012   0.001   TYR C 101 
 PHE   0.017   0.001   PHE B 505 
 TRP   0.018   0.001   TRP E  40 
 HIS   0.003   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (12453)
  covalent geometry    : angle       0.61487 (16893)
  hydrogen bonds       : bond        0.04987 (  541)
  hydrogen bonds       : angle       4.73799 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 119
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: B   22 ILE cc_start: 0.8717 (mm) cc_final: 0.8435 (mt)
REVERT: B  385 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (p0)
REVERT: B  719 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8695 (tt)
REVERT: B  801 TYR cc_start: 0.8437 (p90) cc_final: 0.7752 (p90)
REVERT: C    8 ASN cc_start: 0.7714 (t0) cc_final: 0.7476 (t0)
REVERT: C   43 ILE cc_start: 0.8897 (mm) cc_final: 0.8647 (mt)
REVERT: D   88 ASP cc_start: 0.7868 (m-30) cc_final: 0.7064 (t0)
REVERT: E   99 CYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7289 (p)
REVERT: E  132 PHE cc_start: 0.7108 (m-80) cc_final: 0.6747 (m-80)
REVERT: E  139 ILE cc_start: 0.9264 (mp) cc_final: 0.8818 (mm)
  outliers start: 43
  outliers final: 17
  residues processed: 149
  average time/residue: 0.0786
  time to fit residues: 17.9628
Evaluate side-chains
  121 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  316 ASN
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  567 CYS
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue   26 ILE
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain E residue   10 VAL
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue   99 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 126 optimal weight:    0.0050
   chunk 1 optimal weight:    0.0040
   chunk 129 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 45 optimal weight:    7.9990
   chunk 92 optimal weight:    0.7980
   chunk 117 optimal weight:   10.0000
   chunk 141 optimal weight:   30.0000
   chunk 24 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   overall best weight:    3.1610

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
B 469 HIS
** C  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 136 GLN
E  23 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.113385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.082253 restraints weight = 34851.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.080139 restraints weight = 25314.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.080642 restraints weight = 28772.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.081102 restraints weight = 21241.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.081257 restraints weight = 19420.450|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7981
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042  12453  Z= 0.231
  Angle     :  0.656   9.323  16893  Z= 0.329
  Chirality :  0.045   0.208   1885
  Planarity :  0.005   0.049   2192
  Dihedral  :  4.287  18.681   1637
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 21.00 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.22), residues: 1476
  helix:  1.55 (0.20), residues: 640
  sheet:  0.82 (0.36), residues: 216
  loop : -0.53 (0.25), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 108 
 TYR   0.017   0.002   TYR B 801 
 PHE   0.032   0.002   PHE B 505 
 TRP   0.029   0.002   TRP E  40 
 HIS   0.006   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00559 (12453)
  covalent geometry    : angle       0.65594 (16893)
  hydrogen bonds       : bond        0.05936 (  541)
  hydrogen bonds       : angle       4.60918 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 106
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9201 (OUTLIER) cc_final: 0.8637 (m-10)
REVERT: B    1 MET cc_start: 0.3909 (mmm) cc_final: 0.3542 (mmm)
REVERT: B   22 ILE cc_start: 0.8778 (mm) cc_final: 0.8521 (mt)
REVERT: B  385 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8510 (p0)
REVERT: B  512 MET cc_start: 0.8533 (ttm) cc_final: 0.8329 (ttm)
REVERT: B  719 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8714 (tt)
REVERT: B  801 TYR cc_start: 0.8448 (p90) cc_final: 0.8039 (p90)
REVERT: C  131 ASP cc_start: 0.7828 (t0) cc_final: 0.6903 (t0)
REVERT: D   88 ASP cc_start: 0.8032 (m-30) cc_final: 0.7401 (t0)
REVERT: E   99 CYS cc_start: 0.8175 (t) cc_final: 0.7911 (p)
REVERT: E  132 PHE cc_start: 0.7217 (m-80) cc_final: 0.6744 (m-80)
REVERT: E  139 ILE cc_start: 0.9316 (mp) cc_final: 0.8898 (mm)
REVERT: E  145 ARG cc_start: 0.7694 (ttp80) cc_final: 0.7278 (tpt90)
  outliers start: 55
  outliers final: 33
  residues processed: 156
  average time/residue: 0.0798
  time to fit residues: 19.1661
Evaluate side-chains
  130 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 94
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  312 CYS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  573 ASP
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  592 SER
Chi-restraints excluded: chain B residue  643 VAL
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain B residue  782 HIS
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  120 THR
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  108 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 57 optimal weight:    7.9990
   chunk 75 optimal weight:    0.8980
   chunk 131 optimal weight:    9.9990
   chunk 3 optimal weight:    9.9990
   chunk 148 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 0 optimal weight:   30.0000
   chunk 30 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 80 optimal weight:    7.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
E   5 GLN
E  23 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.114505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.083148 restraints weight = 34557.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.081076 restraints weight = 24278.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.081643 restraints weight = 27288.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.082023 restraints weight = 20390.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.082244 restraints weight = 18829.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12453  Z= 0.151
  Angle     :  0.560   8.642  16893  Z= 0.280
  Chirality :  0.041   0.173   1885
  Planarity :  0.004   0.051   2192
  Dihedral  :  4.104  16.378   1637
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 22.26 %
    Favored  : 74.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.22), residues: 1476
  helix:  1.75 (0.20), residues: 643
  sheet:  0.54 (0.35), residues: 234
  loop : -0.50 (0.25), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 464 
 TYR   0.011   0.001   TYR B 309 
 PHE   0.020   0.002   PHE B 505 
 TRP   0.031   0.001   TRP E  40 
 HIS   0.003   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12453)
  covalent geometry    : angle       0.55995 (16893)
  hydrogen bonds       : bond        0.04473 (  541)
  hydrogen bonds       : angle       4.26218 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 101
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9301 (OUTLIER) cc_final: 0.8681 (m-10)
REVERT: A  479 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8330 (tptt)
REVERT: B  385 ASP cc_start: 0.8728 (OUTLIER) cc_final: 0.8460 (p0)
REVERT: B  553 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6601 (tm-30)
REVERT: B  709 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9112 (mm)
REVERT: B  719 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8708 (tt)
REVERT: B  801 TYR cc_start: 0.8250 (p90) cc_final: 0.7834 (p90)
REVERT: C  134 LYS cc_start: 0.9144 (mmtm) cc_final: 0.8882 (mmtp)
REVERT: D   69 ARG cc_start: 0.8469 (ptp90) cc_final: 0.8037 (ptm-80)
REVERT: D   88 ASP cc_start: 0.7918 (m-30) cc_final: 0.7276 (t0)
REVERT: E  132 PHE cc_start: 0.7273 (m-80) cc_final: 0.6799 (m-80)
REVERT: E  145 ARG cc_start: 0.7643 (ttp80) cc_final: 0.7185 (tpt90)
  outliers start: 44
  outliers final: 24
  residues processed: 141
  average time/residue: 0.0793
  time to fit residues: 17.4417
Evaluate side-chains
  125 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  706 VAL
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   57 LEU
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  108 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 149 optimal weight:   20.0000
   chunk 71 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 113 optimal weight:   20.0000
   chunk 60 optimal weight:    4.9990
   chunk 41 optimal weight:    0.6980
   chunk 53 optimal weight:    8.9990
   chunk 19 optimal weight:    6.9990
   overall best weight:    2.2784

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
** C  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   5 GLN
E  23 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.113565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.081685 restraints weight = 34545.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.079292 restraints weight = 23836.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.079845 restraints weight = 30393.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.080057 restraints weight = 22134.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.080401 restraints weight = 20139.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.3389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12453  Z= 0.174
  Angle     :  0.588  11.229  16893  Z= 0.292
  Chirality :  0.042   0.230   1885
  Planarity :  0.004   0.051   2192
  Dihedral  :  4.116  15.822   1637
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 20.77 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.22), residues: 1476
  helix:  1.69 (0.20), residues: 648
  sheet:  0.39 (0.34), residues: 234
  loop : -0.53 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 464 
 TYR   0.017   0.001   TYR E 101 
 PHE   0.024   0.002   PHE B 505 
 TRP   0.039   0.002   TRP E  40 
 HIS   0.004   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (12453)
  covalent geometry    : angle       0.58756 (16893)
  hydrogen bonds       : bond        0.04960 (  541)
  hydrogen bonds       : angle       4.25360 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 98
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8611 (m-10)
REVERT: A  479 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8233 (tptt)
REVERT: B  385 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8520 (p0)
REVERT: B  553 GLN cc_start: 0.7746 (OUTLIER) cc_final: 0.6549 (tm-30)
REVERT: B  719 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8707 (tt)
REVERT: B  801 TYR cc_start: 0.8311 (p90) cc_final: 0.7822 (p90)
REVERT: C  131 ASP cc_start: 0.7744 (t0) cc_final: 0.7493 (t0)
REVERT: C  134 LYS cc_start: 0.9285 (mmtm) cc_final: 0.8804 (mmtp)
REVERT: D   62 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.6947 (p)
REVERT: D   69 ARG cc_start: 0.8464 (ptp90) cc_final: 0.8005 (ptm-80)
REVERT: D   88 ASP cc_start: 0.8041 (m-30) cc_final: 0.7389 (t0)
REVERT: E  112 TYR cc_start: 0.7634 (m-80) cc_final: 0.7284 (m-80)
REVERT: E  132 PHE cc_start: 0.7332 (m-80) cc_final: 0.6571 (m-80)
REVERT: E  145 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7154 (tpt90)
  outliers start: 59
  outliers final: 37
  residues processed: 152
  average time/residue: 0.0815
  time to fit residues: 19.1322
Evaluate side-chains
  137 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 94
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  462 VAL
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  639 PHE
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  592 SER
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  706 VAL
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  107 ILE
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue   62 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  142 SER
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue  108 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 78 optimal weight:    8.9990
   chunk 144 optimal weight:    6.9990
   chunk 132 optimal weight:    9.9990
   chunk 137 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 116 optimal weight:    9.9990
   chunk 82 optimal weight:    0.4980
   chunk 37 optimal weight:    8.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
E  23 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.114726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.082651 restraints weight = 34165.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.080390 restraints weight = 23079.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.080921 restraints weight = 26021.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.081632 restraints weight = 20256.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.081685 restraints weight = 18358.802|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12453  Z= 0.123
  Angle     :  0.542  10.336  16893  Z= 0.267
  Chirality :  0.041   0.178   1885
  Planarity :  0.004   0.051   2192
  Dihedral  :  3.948  14.194   1637
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.11 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.07 (0.22), residues: 1476
  helix:  1.91 (0.20), residues: 649
  sheet:  0.37 (0.35), residues: 234
  loop : -0.47 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 667 
 TYR   0.008   0.001   TYR B 309 
 PHE   0.015   0.001   PHE B 505 
 TRP   0.034   0.001   TRP E  40 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12453)
  covalent geometry    : angle       0.54187 (16893)
  hydrogen bonds       : bond        0.03996 (  541)
  hydrogen bonds       : angle       4.09395 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 99
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  479 LYS cc_start: 0.8732 (OUTLIER) cc_final: 0.8257 (tptt)
REVERT: B  385 ASP cc_start: 0.8731 (OUTLIER) cc_final: 0.8459 (p0)
REVERT: B  553 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.6481 (tm-30)
REVERT: B  709 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9117 (mm)
REVERT: B  719 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8690 (tt)
REVERT: B  801 TYR cc_start: 0.8175 (p90) cc_final: 0.7750 (p90)
REVERT: C    1 MET cc_start: 0.7333 (tpp) cc_final: 0.7121 (ptm)
REVERT: C  131 ASP cc_start: 0.7576 (t0) cc_final: 0.7366 (t0)
REVERT: C  134 LYS cc_start: 0.9299 (mmtm) cc_final: 0.8889 (mmtp)
REVERT: D   69 ARG cc_start: 0.8497 (ptp90) cc_final: 0.8034 (ptm-80)
REVERT: D   88 ASP cc_start: 0.8049 (m-30) cc_final: 0.7372 (t0)
REVERT: E  132 PHE cc_start: 0.7312 (m-80) cc_final: 0.6804 (m-80)
REVERT: E  145 ARG cc_start: 0.7568 (ttp80) cc_final: 0.7344 (tpt90)
  outliers start: 45
  outliers final: 29
  residues processed: 142
  average time/residue: 0.0841
  time to fit residues: 18.3568
Evaluate side-chains
  128 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 94
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  639 PHE
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  592 SER
Chi-restraints excluded: chain B residue  706 VAL
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain B residue  746 LEU
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue   99 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 60 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 120 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 141 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.114809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.082409 restraints weight = 34131.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.080299 restraints weight = 22815.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.080941 restraints weight = 24346.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.081199 restraints weight = 19396.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.081507 restraints weight = 18418.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12453  Z= 0.121
  Angle     :  0.552  10.735  16893  Z= 0.268
  Chirality :  0.041   0.174   1885
  Planarity :  0.004   0.048   2192
  Dihedral  :  3.831  13.859   1637
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 22.04 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.22), residues: 1476
  helix:  2.00 (0.20), residues: 652
  sheet:  0.36 (0.35), residues: 234
  loop : -0.40 (0.26), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 667 
 TYR   0.018   0.001   TYR E 101 
 PHE   0.016   0.001   PHE B 505 
 TRP   0.030   0.001   TRP E  40 
 HIS   0.004   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (12453)
  covalent geometry    : angle       0.55245 (16893)
  hydrogen bonds       : bond        0.03940 (  541)
  hydrogen bonds       : angle       3.98696 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 99
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8582 (m-10)
REVERT: A  479 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8278 (tptt)
REVERT: B  385 ASP cc_start: 0.8747 (OUTLIER) cc_final: 0.8456 (p0)
REVERT: B  553 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.6384 (tm-30)
REVERT: B  709 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9121 (mm)
REVERT: B  719 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8677 (tt)
REVERT: B  801 TYR cc_start: 0.8194 (p90) cc_final: 0.7760 (p90)
REVERT: C  134 LYS cc_start: 0.9369 (mmtm) cc_final: 0.8983 (mmtp)
REVERT: D   69 ARG cc_start: 0.8465 (ptp90) cc_final: 0.8003 (ptm-80)
REVERT: D   88 ASP cc_start: 0.8065 (m-30) cc_final: 0.7163 (t0)
REVERT: E   40 TRP cc_start: 0.9042 (m100) cc_final: 0.8398 (m100)
REVERT: E  112 TYR cc_start: 0.7611 (m-80) cc_final: 0.7227 (m-80)
REVERT: E  132 PHE cc_start: 0.7320 (m-80) cc_final: 0.6594 (m-80)
REVERT: E  145 ARG cc_start: 0.7554 (ttp80) cc_final: 0.7145 (tpt90)
  outliers start: 46
  outliers final: 36
  residues processed: 142
  average time/residue: 0.0792
  time to fit residues: 17.7753
Evaluate side-chains
  137 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 95
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  312 CYS
Chi-restraints excluded: chain A residue  313 ILE
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  396 GLU
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  509 LEU
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  755 ILE
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  389 LEU
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  502 VAL
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  592 SER
Chi-restraints excluded: chain B residue  635 LEU
Chi-restraints excluded: chain B residue  706 VAL
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  710 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain D residue   92 VAL
Chi-restraints excluded: chain D residue  100 THR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   98 THR
Chi-restraints excluded: chain E residue   99 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0270
   chunk 81 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9990
   chunk 23 optimal weight:    0.1980
   chunk 22 optimal weight:    0.0020
   chunk 0 optimal weight:   30.0000
   chunk 63 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0670
   chunk 118 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    0.1984

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.117018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.082613 restraints weight = 33941.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.081592 restraints weight = 25784.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.081401 restraints weight = 21863.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.081686 restraints weight = 20711.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.081845 restraints weight = 19491.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.3771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12453  Z= 0.096
  Angle     :  0.548  11.391  16893  Z= 0.263
  Chirality :  0.040   0.175   1885
  Planarity :  0.004   0.047   2192
  Dihedral  :  3.656  14.449   1637
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 23.83 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.23), residues: 1476
  helix:  2.15 (0.20), residues: 653
  sheet:  0.53 (0.36), residues: 234
  loop : -0.34 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 137 
 TYR   0.009   0.001   TYR B 801 
 PHE   0.025   0.001   PHE D  72 
 TRP   0.021   0.001   TRP E  40 
 HIS   0.003   0.000   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (12453)
  covalent geometry    : angle       0.54809 (16893)
  hydrogen bonds       : bond        0.02947 (  541)
  hydrogen bonds       : angle       3.87198 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9224 (OUTLIER) cc_final: 0.8471 (m-10)
REVERT: B  385 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8378 (p0)
REVERT: B  553 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6343 (tm-30)
REVERT: B  801 TYR cc_start: 0.8015 (p90) cc_final: 0.7591 (p90)
REVERT: C   43 ILE cc_start: 0.8859 (mm) cc_final: 0.8599 (mt)
REVERT: C  134 LYS cc_start: 0.9434 (mmtm) cc_final: 0.9049 (mmtp)
REVERT: D   27 THR cc_start: 0.9119 (p) cc_final: 0.8866 (t)
REVERT: D   69 ARG cc_start: 0.8333 (ptp90) cc_final: 0.7858 (ptm-80)
REVERT: D   74 PHE cc_start: 0.7620 (t80) cc_final: 0.7354 (t80)
REVERT: D   88 ASP cc_start: 0.8187 (m-30) cc_final: 0.7053 (t0)
REVERT: E   40 TRP cc_start: 0.9103 (m100) cc_final: 0.8587 (m100)
REVERT: E   96 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.7977 (tt)
REVERT: E  112 TYR cc_start: 0.7869 (m-80) cc_final: 0.7475 (m-80)
REVERT: E  132 PHE cc_start: 0.7461 (m-80) cc_final: 0.6753 (m-80)
REVERT: E  145 ARG cc_start: 0.7234 (ttp80) cc_final: 0.6920 (tpt90)
  outliers start: 27
  outliers final: 19
  residues processed: 124
  average time/residue: 0.0840
  time to fit residues: 16.5852
Evaluate side-chains
  116 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  312 CYS
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  146 VAL
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  135 LEU
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   96 LEU
Chi-restraints excluded: chain E residue   99 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 94 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    9.9990
   chunk 103 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 142 optimal weight:    8.9990
   chunk 115 optimal weight:    0.2980
   chunk 113 optimal weight:    5.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
B 782 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.116540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.080090 restraints weight = 34048.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.080521 restraints weight = 25193.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.081260 restraints weight = 19680.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.081650 restraints weight = 17785.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.081593 restraints weight = 16526.279|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  12453  Z= 0.096
  Angle     :  0.539   9.533  16893  Z= 0.261
  Chirality :  0.040   0.170   1885
  Planarity :  0.004   0.046   2192
  Dihedral  :  3.615  16.527   1637
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.75 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.40 (0.23), residues: 1476
  helix:  2.18 (0.20), residues: 649
  sheet:  0.55 (0.36), residues: 234
  loop : -0.30 (0.26), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 137 
 TYR   0.017   0.001   TYR E 101 
 PHE   0.016   0.001   PHE B  52 
 TRP   0.019   0.001   TRP E  40 
 HIS   0.003   0.000   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (12453)
  covalent geometry    : angle       0.53946 (16893)
  hydrogen bonds       : bond        0.03125 (  541)
  hydrogen bonds       : angle       3.81990 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 93
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9208 (OUTLIER) cc_final: 0.8459 (m-10)
REVERT: A  479 LYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8318 (tptt)
REVERT: B  385 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8385 (p0)
REVERT: B  553 GLN cc_start: 0.7400 (OUTLIER) cc_final: 0.6292 (tm-30)
REVERT: B  801 TYR cc_start: 0.7984 (p90) cc_final: 0.7537 (p90)
REVERT: C   43 ILE cc_start: 0.8864 (mm) cc_final: 0.8615 (mt)
REVERT: C  134 LYS cc_start: 0.9403 (mmtm) cc_final: 0.9033 (mmtp)
REVERT: D   27 THR cc_start: 0.9107 (p) cc_final: 0.8816 (t)
REVERT: D   69 ARG cc_start: 0.8390 (ptp90) cc_final: 0.7812 (ptm-80)
REVERT: D   74 PHE cc_start: 0.7590 (t80) cc_final: 0.7307 (t80)
REVERT: D   88 ASP cc_start: 0.8078 (m-30) cc_final: 0.6951 (t0)
REVERT: E   40 TRP cc_start: 0.9119 (m100) cc_final: 0.8601 (m100)
REVERT: E   96 LEU cc_start: 0.8754 (pp) cc_final: 0.7902 (tt)
REVERT: E  111 TYR cc_start: 0.8920 (OUTLIER) cc_final: 0.8484 (t80)
REVERT: E  132 PHE cc_start: 0.7481 (m-80) cc_final: 0.6748 (m-80)
REVERT: E  145 ARG cc_start: 0.7203 (ttp80) cc_final: 0.6703 (tpt90)
  outliers start: 30
  outliers final: 21
  residues processed: 120
  average time/residue: 0.0746
  time to fit residues: 13.9693
Evaluate side-chains
  117 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 91
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain B residue  738 CYS
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  111 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 144 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 62 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0970
   chunk 58 optimal weight:    0.0970
   chunk 149 optimal weight:    8.9990
   chunk 32 optimal weight:    0.6980
   chunk 78 optimal weight:    9.9990
   chunk 74 optimal weight:    3.9990
   chunk 76 optimal weight:    0.6980
   overall best weight:    1.1178

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

Flipped N/Q/H residues before XYZ refinement:
B  55 ASN
B 782 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.115458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.083036 restraints weight = 33831.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.081180 restraints weight = 21217.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.081618 restraints weight = 23933.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.082231 restraints weight = 18989.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.082394 restraints weight = 17132.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  12453  Z= 0.110
  Angle     :  0.546   9.428  16893  Z= 0.264
  Chirality :  0.041   0.165   1885
  Planarity :  0.004   0.047   2192
  Dihedral  :  3.623  15.032   1637
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 23.68 %
    Favored  : 74.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.23), residues: 1476
  helix:  2.22 (0.20), residues: 648
  sheet:  0.51 (0.36), residues: 234
  loop : -0.30 (0.26), residues: 594

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 145 
 TYR   0.014   0.001   TYR E 111 
 PHE   0.019   0.001   PHE E  72 
 TRP   0.018   0.001   TRP E  40 
 HIS   0.003   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (12453)
  covalent geometry    : angle       0.54584 (16893)
  hydrogen bonds       : bond        0.03588 (  541)
  hydrogen bonds       : angle       3.82242 ( 1590)

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

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

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2952 Ramachandran restraints generated.
    1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 97
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  460 TYR cc_start: 0.9233 (OUTLIER) cc_final: 0.8491 (m-10)
REVERT: A  479 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8345 (tptt)
REVERT: B  385 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8427 (p0)
REVERT: B  553 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6295 (tm-30)
REVERT: B  801 TYR cc_start: 0.8012 (p90) cc_final: 0.7618 (p90)
REVERT: C  134 LYS cc_start: 0.9343 (mmtm) cc_final: 0.8979 (mmtp)
REVERT: D   27 THR cc_start: 0.9133 (p) cc_final: 0.8847 (t)
REVERT: D   69 ARG cc_start: 0.8482 (ptp90) cc_final: 0.7983 (ptm-80)
REVERT: D   88 ASP cc_start: 0.7910 (m-30) cc_final: 0.6722 (t0)
REVERT: E   74 PHE cc_start: 0.7528 (t80) cc_final: 0.7214 (m-80)
REVERT: E   96 LEU cc_start: 0.8674 (pp) cc_final: 0.7910 (tt)
REVERT: E  111 TYR cc_start: 0.8679 (OUTLIER) cc_final: 0.8260 (t80)
REVERT: E  112 TYR cc_start: 0.7647 (m-80) cc_final: 0.7286 (m-80)
REVERT: E  132 PHE cc_start: 0.7349 (m-80) cc_final: 0.6575 (m-80)
REVERT: E  145 ARG cc_start: 0.7371 (ttp80) cc_final: 0.6865 (tpt90)
  outliers start: 30
  outliers final: 21
  residues processed: 122
  average time/residue: 0.0768
  time to fit residues: 14.7368
Evaluate side-chains
  119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  325 LEU
Chi-restraints excluded: chain A residue  388 THR
Chi-restraints excluded: chain A residue  460 TYR
Chi-restraints excluded: chain A residue  479 LYS
Chi-restraints excluded: chain A residue  577 SER
Chi-restraints excluded: chain A residue  633 LEU
Chi-restraints excluded: chain A residue  697 VAL
Chi-restraints excluded: chain A residue  709 LEU
Chi-restraints excluded: chain A residue  720 LEU
Chi-restraints excluded: chain B residue  313 ILE
Chi-restraints excluded: chain B residue  385 ASP
Chi-restraints excluded: chain B residue  470 HIS
Chi-restraints excluded: chain B residue  553 GLN
Chi-restraints excluded: chain B residue  592 SER
Chi-restraints excluded: chain B residue  709 LEU
Chi-restraints excluded: chain B residue  719 LEU
Chi-restraints excluded: chain C residue   30 CYS
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  118 THR
Chi-restraints excluded: chain D residue  104 GLN
Chi-restraints excluded: chain D residue  118 THR
Chi-restraints excluded: chain D residue  148 ARG
Chi-restraints excluded: chain E residue   99 CYS
Chi-restraints excluded: chain E residue  111 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 150
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 142 optimal weight:   10.0000
   chunk 121 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 37 optimal weight:    8.9990
   chunk 79 optimal weight:    9.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    1.9588

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

Flipped N/Q/H residues before XYZ refinement:
B 782 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.114199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.081941 restraints weight = 34220.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.079437 restraints weight = 23119.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.080022 restraints weight = 25812.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.080797 restraints weight = 20300.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.080822 restraints weight = 18348.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12453  Z= 0.155
  Angle     :  0.590   9.586  16893  Z= 0.288
  Chirality :  0.042   0.171   1885
  Planarity :  0.004   0.048   2192
  Dihedral  :  3.804  14.869   1637
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 23.98 %
    Favored  : 74.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.10 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.23), residues: 1476
  helix:  2.12 (0.21), residues: 646
  sheet:  0.52 (0.35), residues: 231
  loop : -0.38 (0.26), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 667 
 TYR   0.018   0.001   TYR E 101 
 PHE   0.021   0.002   PHE B 505 
 TRP   0.020   0.001   TRP E  40 
 HIS   0.004   0.001   HIS D  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (12453)
  covalent geometry    : angle       0.58966 (16893)
  hydrogen bonds       : bond        0.04426 (  541)
  hydrogen bonds       : angle       3.97285 ( 1590)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1600.68 seconds
wall clock time: 28 minutes 18.42 seconds (1698.42 seconds total)