Starting phenix.real_space_refine
on Sat Aug 23 23:49:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uid_42293/08_2025/8uid_42293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uid_42293/08_2025/8uid_42293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uid_42293/08_2025/8uid_42293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uid_42293/08_2025/8uid_42293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uid_42293/08_2025/8uid_42293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uid_42293/08_2025/8uid_42293.cif"
  }
  resolution = 2.81
  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=  -0.002 sd=   0.276
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      44      5.16       5
     C   10098      2.51       5
     N    2628      2.21       5
     O    2868      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 76 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: 15638
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 738, 5968
          Classifications: {'peptide': 738}
          Link IDs: {'CIS': 1, 'PTRANS': 35, 'TRANS': 701}
    Chain: "B"
      Number of atoms: 1851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 227, 1851
          Classifications: {'peptide': 227}
          Link IDs: {'PTRANS': 14, 'TRANS': 212}
  Restraints were copied for chains:
    C, D
  Time building chain proxies: 4.41, per 1000 atoms: 0.28
  Number of scatterers: 15638
  At special positions: 0
  Unit cell: (105.78, 128.14, 86.86, 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      44     16.00
     O    2868      8.00
     N    2628      7.00
     C   10098      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: 1.06
  Conformation dependent library (CDL) restraints added in 539.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3540

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 28 sheets defined
      20.3% alpha, 31.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 16
      No H-bonds generated for 'chain 'A' and resid 14 through 16'
    Processing helix  chain 'A' and resid 17 through 28
    Processing helix  chain 'A' and resid 38 through 43
    Processing helix  chain 'A' and resid 67 through 78
    Processing helix  chain 'A' and resid 94 through 99
    Processing helix  chain 'A' and resid 102 through 107
      removed outlier: 3.785A  pdb=" N   LYS A 106 " --> pdb=" O   TRP A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 138
      removed outlier: 3.504A  pdb=" N   LYS A 119 " --> pdb=" O   PRO A 115 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS A 120 " --> pdb=" O   GLY A 116 " (cutoff:3.500A)
      Proline residue:  A 134  - end of helix
    Processing helix  chain 'A' and resid 154 through 169
      removed outlier: 3.660A  pdb=" N   ILE A 158 " --> pdb=" O   ASN A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 211
      removed outlier: 3.559A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 258
      removed outlier: 3.547A  pdb=" N   THR A 247 " --> pdb=" O   PRO A 243 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU A 248 " --> pdb=" O   PRO A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 314
      removed outlier: 3.588A  pdb=" N   TYR A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 320
      removed outlier: 3.541A  pdb=" N   SER A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 489
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 619 through 625
    Processing helix  chain 'A' and resid 722 through 729
    Processing helix  chain 'A' and resid 731 through 738
      removed outlier: 3.981A  pdb=" N   LYS A 735 " --> pdb=" O   GLU A 731 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 804 through 807
      removed outlier: 3.524A  pdb=" N   LEU B 807 " --> pdb=" O   THR B 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 804 through 807'
    Processing helix  chain 'B' and resid 844 through 849
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 868 through 871
    Processing helix  chain 'C' and resid 14 through 16
      No H-bonds generated for 'chain 'C' and resid 14 through 16'
    Processing helix  chain 'C' and resid 17 through 28
    Processing helix  chain 'C' and resid 38 through 43
    Processing helix  chain 'C' and resid 67 through 78
    Processing helix  chain 'C' and resid 94 through 99
    Processing helix  chain 'C' and resid 102 through 107
      removed outlier: 3.785A  pdb=" N   LYS C 106 " --> pdb=" O   TRP C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 114 through 138
      removed outlier: 3.504A  pdb=" N   LYS C 119 " --> pdb=" O   PRO C 115 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   HIS C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      Proline residue:  C 134  - end of helix
    Processing helix  chain 'C' and resid 154 through 169
      removed outlier: 3.660A  pdb=" N   ILE C 158 " --> pdb=" O   ASN C 154 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 197 through 211
      removed outlier: 3.561A  pdb=" N   PHE C 201 " --> pdb=" O   ASP C 197 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 243 through 258
      removed outlier: 3.547A  pdb=" N   THR C 247 " --> pdb=" O   PRO C 243 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLU C 248 " --> pdb=" O   PRO C 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 298 through 314
      removed outlier: 3.588A  pdb=" N   TYR C 302 " --> pdb=" O   SER C 298 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 314 through 320
      removed outlier: 3.542A  pdb=" N   SER C 320 " --> pdb=" O   GLU C 316 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 489
    Processing helix  chain 'C' and resid 598 through 603
    Processing helix  chain 'C' and resid 619 through 625
    Processing helix  chain 'C' and resid 722 through 729
    Processing helix  chain 'C' and resid 731 through 738
      removed outlier: 3.981A  pdb=" N   LYS C 735 " --> pdb=" O   GLU C 731 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 804 through 807
      removed outlier: 3.523A  pdb=" N   LEU D 807 " --> pdb=" O   THR D 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 804 through 807'
    Processing helix  chain 'D' and resid 844 through 849
    Processing helix  chain 'D' and resid 850 through 855
    Processing helix  chain 'D' and resid 868 through 871
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 175
      removed outlier: 3.788A  pdb=" N   LEU A 173 " --> pdb=" O   ILE A 142 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A  82 " --> pdb=" O   GLY A 143 " (cutoff:3.500A)
      removed outlier: 8.118A  pdb=" N   GLN A 145 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA A  84 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   VAL A  33 " --> pdb=" O   ILE A  83 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   ARG A  85 " --> pdb=" O   VAL A  33 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   THR A  35 " --> pdb=" O   ARG A  85 " (cutoff:3.500A)
      removed outlier: 5.897A  pdb=" N   LEU A   4 " --> pdb=" O   CYS A  32 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   SER A  34 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   GLY A   6 " --> pdb=" O   SER A  34 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   TYR A  36 " --> pdb=" O   GLY A   6 " (cutoff:3.500A)
      removed outlier: 5.736A  pdb=" N   GLU A   7 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET A 266 " --> pdb=" O   GLU A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 328 through 329
    Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 340
      removed outlier: 3.879A  pdb=" N   LEU A 385 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL A 398 " --> pdb=" O   ASP A 387 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   VAL A 389 " --> pdb=" O   LYS A 396 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LYS A 396 " --> pdb=" O   VAL A 389 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA A 429 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   THR A 400 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU A 427 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 359
    Processing sheet with id=AA5, first strand: chain 'A' and resid 403 through 410
      removed outlier: 5.635A  pdb=" N   ALA A 404 " --> pdb=" O   TYR A 419 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR A 419 " --> pdb=" O   ALA A 404 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU A 406 " --> pdb=" O   ILE A 417 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL A 414 " --> pdb=" O   LEU A 478 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE A 480 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET A 416 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 7.553A  pdb=" N   THR A 482 " --> pdb=" O   MET A 416 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ILE A 418 " --> pdb=" O   THR A 482 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP A 438 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 490 through 494
      removed outlier: 6.435A  pdb=" N   LEU A 497 " --> pdb=" O   VAL A 493 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 510
      removed outlier: 3.541A  pdb=" N   ALA A 540 " --> pdb=" O   LYS B 971 " (cutoff:3.500A)
      removed outlier: 4.491A  pdb=" N   ILE A 541 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 574
    Processing sheet with id=AA9, first strand: chain 'A' and resid 573 through 574
      removed outlier: 5.151A  pdb=" N   ILE B 952 " --> pdb=" O   TRP B 900 " (cutoff:3.500A)
      removed outlier: 6.982A  pdb=" N   TRP B 900 " --> pdb=" O   ILE B 952 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL B 893 " --> pdb=" O   VAL B 927 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 859 through 861
      removed outlier: 4.194A  pdb=" N   TYR A 579 " --> pdb=" O   ALA B 861 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   GLY B 914 " --> pdb=" O   VAL B 906 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL B 908 " --> pdb=" O   PHE B 912 " (cutoff:3.500A)
      removed outlier: 5.391A  pdb=" N   PHE B 912 " --> pdb=" O   VAL B 908 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 591 through 593
      removed outlier: 3.924A  pdb=" N   TRP B 838 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU B 837 " --> pdb=" O   ARG A 615 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE A 644 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   TYR A 648 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 659
      removed outlier: 6.926A  pdb=" N   PHE A 636 " --> pdb=" O   TYR A 692 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   TYR A 692 " --> pdb=" O   PHE A 636 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR B 832 " --> pdb=" O   LEU A 697 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704
      removed outlier: 3.514A  pdb=" N   GLY A 701 " --> pdb=" O   VAL B 829 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 710
      removed outlier: 6.219A  pdb=" N   VAL B 789 " --> pdb=" O   TYR B 793 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   TYR B 793 " --> pdb=" O   VAL B 789 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 173 through 175
      removed outlier: 3.787A  pdb=" N   LEU C 173 " --> pdb=" O   ILE C 142 " (cutoff:3.500A)
      removed outlier: 6.895A  pdb=" N   VAL C  82 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   GLN C 145 " --> pdb=" O   VAL C  82 " (cutoff:3.500A)
      removed outlier: 7.039A  pdb=" N   ALA C  84 " --> pdb=" O   GLN C 145 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   VAL C  33 " --> pdb=" O   ILE C  83 " (cutoff:3.500A)
      removed outlier: 7.308A  pdb=" N   ARG C  85 " --> pdb=" O   VAL C  33 " (cutoff:3.500A)
      removed outlier: 6.840A  pdb=" N   THR C  35 " --> pdb=" O   ARG C  85 " (cutoff:3.500A)
      removed outlier: 5.898A  pdb=" N   LEU C   4 " --> pdb=" O   CYS C  32 " (cutoff:3.500A)
      removed outlier: 7.137A  pdb=" N   SER C  34 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 6.485A  pdb=" N   GLY C   6 " --> pdb=" O   SER C  34 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   TYR C  36 " --> pdb=" O   GLY C   6 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   GLU C   7 " --> pdb=" O   ILE C 264 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   MET C 266 " --> pdb=" O   GLU C   7 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 328 through 329
    Processing sheet with id=AB8, first strand: chain 'C' and resid 335 through 340
      removed outlier: 3.880A  pdb=" N   LEU C 385 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
      removed outlier: 5.955A  pdb=" N   VAL C 398 " --> pdb=" O   ASP C 387 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   VAL C 389 " --> pdb=" O   LYS C 396 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   LYS C 396 " --> pdb=" O   VAL C 389 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ALA C 429 " --> pdb=" O   VAL C 398 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   THR C 400 " --> pdb=" O   GLU C 427 " (cutoff:3.500A)
      removed outlier: 6.834A  pdb=" N   GLU C 427 " --> pdb=" O   THR C 400 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 357 through 359
    Processing sheet with id=AC1, first strand: chain 'C' and resid 403 through 410
      removed outlier: 5.635A  pdb=" N   ALA C 404 " --> pdb=" O   TYR C 419 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   TYR C 419 " --> pdb=" O   ALA C 404 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU C 406 " --> pdb=" O   ILE C 417 " (cutoff:3.500A)
      removed outlier: 6.304A  pdb=" N   VAL C 414 " --> pdb=" O   LEU C 478 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   ILE C 480 " --> pdb=" O   VAL C 414 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   MET C 416 " --> pdb=" O   ILE C 480 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   THR C 482 " --> pdb=" O   MET C 416 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ILE C 418 " --> pdb=" O   THR C 482 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP C 438 " --> pdb=" O   LYS C 470 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 490 through 494
      removed outlier: 6.435A  pdb=" N   LEU C 497 " --> pdb=" O   VAL C 493 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   VAL C 557 " --> pdb=" O   LEU C 553 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 509 through 510
      removed outlier: 3.542A  pdb=" N   ALA C 540 " --> pdb=" O   LYS D 971 " (cutoff:3.500A)
      removed outlier: 4.490A  pdb=" N   ILE C 541 " --> pdb=" O   LEU C 548 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 573 through 574
    Processing sheet with id=AC5, first strand: chain 'C' and resid 573 through 574
      removed outlier: 5.150A  pdb=" N   ILE D 952 " --> pdb=" O   TRP D 900 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   TRP D 900 " --> pdb=" O   ILE D 952 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL D 893 " --> pdb=" O   VAL D 927 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'D' and resid 859 through 861
      removed outlier: 4.194A  pdb=" N   TYR C 579 " --> pdb=" O   ALA D 861 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLY D 914 " --> pdb=" O   VAL D 906 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   VAL D 908 " --> pdb=" O   PHE D 912 " (cutoff:3.500A)
      removed outlier: 5.390A  pdb=" N   PHE D 912 " --> pdb=" O   VAL D 908 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 591 through 593
      removed outlier: 3.924A  pdb=" N   TRP D 838 " --> pdb=" O   ILE C 593 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLU D 837 " --> pdb=" O   ARG C 615 " (cutoff:3.500A)
      removed outlier: 5.802A  pdb=" N   ILE C 644 " --> pdb=" O   TYR C 648 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   TYR C 648 " --> pdb=" O   ILE C 644 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 655 through 659
      removed outlier: 6.927A  pdb=" N   PHE C 636 " --> pdb=" O   TYR C 692 " (cutoff:3.500A)
      removed outlier: 6.430A  pdb=" N   TYR C 692 " --> pdb=" O   PHE C 636 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR D 832 " --> pdb=" O   LEU C 697 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 701 through 704
      removed outlier: 3.515A  pdb=" N   GLY C 701 " --> pdb=" O   VAL D 829 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 709 through 710
      removed outlier: 6.219A  pdb=" N   VAL D 789 " --> pdb=" O   TYR D 793 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   TYR D 793 " --> pdb=" O   VAL D 789 " (cutoff:3.500A)

    600 hydrogen bonds defined for protein.
    1584 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: 3.13

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3902
        1.33 -     1.45: 3313
        1.45 -     1.58: 8763
        1.58 -     1.70: 0
        1.70 -     1.82: 66
  Bond restraints: 16044
  Sorted by residual:
  bond pdb=" CZ  ARG C 111 "
       pdb=" NH2 ARG C 111 "
    ideal  model  delta    sigma   weight residual
    1.330  1.284  0.046 1.30e-02 5.92e+03 1.23e+01
  bond pdb=" CA  LYS A 322 "
       pdb=" C   LYS A 322 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 9.60e-03 1.09e+04 1.20e+01
  bond pdb=" CA  LYS C 322 "
       pdb=" C   LYS C 322 "
    ideal  model  delta    sigma   weight residual
    1.518  1.551 -0.033 9.60e-03 1.09e+04 1.18e+01
  bond pdb=" CZ  ARG A 111 "
       pdb=" NH2 ARG A 111 "
    ideal  model  delta    sigma   weight residual
    1.330  1.285  0.045 1.30e-02 5.92e+03 1.18e+01
  bond pdb=" CZ  ARG C 300 "
       pdb=" NH2 ARG C 300 "
    ideal  model  delta    sigma   weight residual
    1.330  1.286  0.044 1.30e-02 5.92e+03 1.16e+01
  ... (remaining 16039 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 17838
        2.46 -     4.92: 3660
        4.92 -     7.37: 285
        7.37 -     9.83: 29
        9.83 -    12.29: 2
  Bond angle restraints: 21814
  Sorted by residual:
  angle pdb=" CA  LYS C 322 "
        pdb=" C   LYS C 322 "
        pdb=" N   PRO C 323 "
      ideal   model   delta    sigma   weight residual
     117.68  123.08   -5.40 7.10e-01 1.98e+00 5.79e+01
  angle pdb=" CA  LYS A 322 "
        pdb=" C   LYS A 322 "
        pdb=" N   PRO A 323 "
      ideal   model   delta    sigma   weight residual
     117.68  123.06   -5.38 7.10e-01 1.98e+00 5.74e+01
  angle pdb=" CA  ARG A 239 "
        pdb=" C   ARG A 239 "
        pdb=" N   LEU A 240 "
      ideal   model   delta    sigma   weight residual
     118.38  127.40   -9.02 1.30e+00 5.92e-01 4.82e+01
  angle pdb=" CA  ARG C 239 "
        pdb=" C   ARG C 239 "
        pdb=" N   LEU C 240 "
      ideal   model   delta    sigma   weight residual
     118.38  127.40   -9.02 1.30e+00 5.92e-01 4.81e+01
  angle pdb=" C   ARG A 239 "
        pdb=" N   LEU A 240 "
        pdb=" CA  LEU A 240 "
      ideal   model   delta    sigma   weight residual
     121.70  133.99  -12.29 1.80e+00 3.09e-01 4.66e+01
  ... (remaining 21809 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 8309
       15.98 -    31.96: 851
       31.96 -    47.94: 196
       47.94 -    63.92: 70
       63.92 -    79.90: 30
  Dihedral angle restraints: 9456
    sinusoidal: 3866
      harmonic: 5590
  Sorted by residual:
  dihedral pdb=" C   ASP A 638 "
           pdb=" N   ASP A 638 "
           pdb=" CA  ASP A 638 "
           pdb=" CB  ASP A 638 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.65   17.05     0      2.50e+00 1.60e-01 4.65e+01
  dihedral pdb=" C   ASP C 638 "
           pdb=" N   ASP C 638 "
           pdb=" CA  ASP C 638 "
           pdb=" CB  ASP C 638 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -139.62   17.02     0      2.50e+00 1.60e-01 4.63e+01
  dihedral pdb=" CA  ASN C 148 "
           pdb=" C   ASN C 148 "
           pdb=" N   GLU C 149 "
           pdb=" CA  GLU C 149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.63   29.37     0      5.00e+00 4.00e-02 3.45e+01
  ... (remaining 9453 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 2017
       0.148 -    0.296: 332
       0.296 -    0.444: 25
       0.444 -    0.592: 4
       0.592 -    0.740: 2
  Chirality restraints: 2380
  Sorted by residual:
  chirality pdb=" CA  ASP A 638 "
            pdb=" N   ASP A 638 "
            pdb=" C   ASP A 638 "
            pdb=" CB  ASP A 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CA  ASP C 638 "
            pdb=" N   ASP C 638 "
            pdb=" C   ASP C 638 "
            pdb=" CB  ASP C 638 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.77    0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CB  ILE D 939 "
            pdb=" CA  ILE D 939 "
            pdb=" CG1 ILE D 939 "
            pdb=" CG2 ILE D 939 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.12    0.52 2.00e-01 2.50e+01 6.78e+00
  ... (remaining 2377 not shown)

  Planarity restraints: 2780
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 196 "    0.182 2.00e-02 2.50e+03   9.21e-02 2.12e+02
        pdb=" CG  TRP C 196 "   -0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 196 "   -0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 196 "   -0.092 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 196 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 196 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 196 "   -0.127 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 196 "    0.100 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 196 "   -0.031 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 196 "    0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 196 "   -0.182 2.00e-02 2.50e+03   9.20e-02 2.12e+02
        pdb=" CG  TRP A 196 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 196 "    0.044 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 196 "    0.092 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 196 "    0.049 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 196 "    0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 196 "    0.127 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 196 "   -0.099 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 196 "    0.030 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 196 "   -0.103 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  10 "    0.173 2.00e-02 2.50e+03   1.01e-01 2.03e+02
        pdb=" CG  TYR C  10 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  10 "   -0.081 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  10 "   -0.084 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  10 "   -0.075 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  10 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  10 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR C  10 "    0.164 2.00e-02 2.50e+03
  ... (remaining 2777 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.38: 10
        2.38 -     3.01: 7893
        3.01 -     3.64: 23349
        3.64 -     4.27: 41477
        4.27 -     4.90: 67466
  Nonbonded interactions: 140195
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN B 824 "
            pdb=" NH2 ARG C 360 "
     model   vdw
     1.749 3.200
  nonbonded pdb=" NH2 ARG A 360 "
            pdb=" ND2 ASN D 824 "
     model   vdw
     1.785 3.200
  nonbonded pdb=" OG  SER B 749 "
            pdb=" O   ALA C 330 "
     model   vdw
     1.895 3.040
  nonbonded pdb=" O   ALA A 330 "
            pdb=" OG  SER D 749 "
     model   vdw
     1.896 3.040
  nonbonded pdb=" NH2 ARG A 375 "
            pdb=" O   ARG C 231 "
     model   vdw
     2.133 3.120
  ... (remaining 140190 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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 individual isotropic
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:             0.910
  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:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     14.910
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:5.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
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      :  0.013   0.046  16044  Z= 0.764
  Angle     :  1.898  12.291  21814  Z= 1.249
  Chirality :  0.110   0.740   2380
  Planarity :  0.018   0.169   2780
  Dihedral  : 15.024  79.899   5916
  Min Nonbonded Distance : 1.749

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  :  6.82 %
    Favored  : 89.13 %
  Cbeta Deviations :  1.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -1.38 (0.17), residues: 1922
  helix: -1.81 (0.23), residues: 310
  sheet:  0.40 (0.24), residues: 404
  loop : -1.16 (0.17), residues: 1208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.002   ARG C  66 
 TYR   0.187   0.026   TYR A 235 
 PHE   0.082   0.019   PHE A 310 
 TRP   0.182   0.024   TRP A 196 
 HIS   0.018   0.005   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.01261 (16044)
  covalent geometry    : angle       1.89847 (21814)
  hydrogen bonds       : bond        0.13956 (  596)
  hydrogen bonds       : angle       7.47140 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  388 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 319
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  194 SER cc_start: 0.8370 (m) cc_final: 0.7983 (t)
REVERT: A  218 MET cc_start: 0.8503 (ttt) cc_final: 0.8151 (ttp)
REVERT: A  355 ASN cc_start: 0.7681 (m-40) cc_final: 0.7434 (m110)
REVERT: B  840 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8060 (pp)
REVERT: B  885 LYS cc_start: 0.8184 (ptmm) cc_final: 0.7946 (ptmt)
REVERT: C  194 SER cc_start: 0.8380 (m) cc_final: 0.8010 (t)
REVERT: C  218 MET cc_start: 0.8511 (ttt) cc_final: 0.8155 (ttp)
REVERT: C  355 ASN cc_start: 0.7723 (m-40) cc_final: 0.7466 (m110)
REVERT: D  840 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8048 (pp)
REVERT: D  885 LYS cc_start: 0.8187 (ptmm) cc_final: 0.7961 (ptmt)
  outliers start: 69
  outliers final: 12
  residues processed: 375
  average time/residue: 0.6075
  time to fit residues: 248.5417
Evaluate side-chains
  181 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 167
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 VAL
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  840 ILE
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   33 VAL
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  552 ARG
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  840 ILE
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 130 optimal weight:    0.7980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 149 optimal weight:    9.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 145 GLN
A 272 ASN
A 460 HIS
C  59 HIS
C 145 GLN
C 272 ASN
C 460 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.152526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.127732 restraints weight = 17539.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 1.82
r_work: 0.3417 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3278 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  16044  Z= 0.145
  Angle     :  0.675   9.441  21814  Z= 0.363
  Chirality :  0.050   0.221   2380
  Planarity :  0.005   0.043   2780
  Dihedral  :  7.303  58.092   2202
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.22 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.59 (0.19), residues: 1922
  helix: -0.20 (0.28), residues: 304
  sheet:  0.43 (0.24), residues: 474
  loop : -0.80 (0.18), residues: 1144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 948 
 TYR   0.028   0.002   TYR D 832 
 PHE   0.016   0.002   PHE D 788 
 TRP   0.024   0.002   TRP A 152 
 HIS   0.005   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (16044)
  covalent geometry    : angle       0.67528 (21814)
  hydrogen bonds       : bond        0.04108 (  596)
  hydrogen bonds       : angle       5.76550 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 216
  time to evaluate  : 0.627 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8190 (t70) cc_final: 0.7758 (m-30)
REVERT: A  168 LYS cc_start: 0.7492 (OUTLIER) cc_final: 0.7243 (mtpp)
REVERT: A  199 ARG cc_start: 0.7106 (mmp-170) cc_final: 0.6764 (mpp-170)
REVERT: A  218 MET cc_start: 0.8989 (ttt) cc_final: 0.8694 (ttp)
REVERT: A  299 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7425 (tp30)
REVERT: A  338 GLN cc_start: 0.8196 (tt0) cc_final: 0.7872 (pt0)
REVERT: A  355 ASN cc_start: 0.8518 (m-40) cc_final: 0.7688 (p0)
REVERT: A  452 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7488 (mt-10)
REVERT: A  524 GLU cc_start: 0.7686 (pm20) cc_final: 0.6758 (pt0)
REVERT: B  759 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7503 (mm-30)
REVERT: B  927 VAL cc_start: 0.8113 (OUTLIER) cc_final: 0.7863 (t)
REVERT: B  939 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.7796 (mt)
REVERT: C   20 ASP cc_start: 0.8188 (t70) cc_final: 0.7750 (m-30)
REVERT: C  168 LYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7288 (mtpp)
REVERT: C  199 ARG cc_start: 0.7170 (mmp-170) cc_final: 0.6803 (mpp-170)
REVERT: C  218 MET cc_start: 0.9004 (ttt) cc_final: 0.8711 (ttp)
REVERT: C  299 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7400 (tp30)
REVERT: C  338 GLN cc_start: 0.8206 (tt0) cc_final: 0.7895 (pt0)
REVERT: C  355 ASN cc_start: 0.8500 (m-40) cc_final: 0.7581 (p0)
REVERT: C  446 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.7682 (mt)
REVERT: C  524 GLU cc_start: 0.7670 (pm20) cc_final: 0.6766 (pt0)
REVERT: D  759 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7586 (mp0)
REVERT: D  859 GLU cc_start: 0.7633 (mm-30) cc_final: 0.6399 (mp0)
REVERT: D  939 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7796 (mt)
  outliers start: 65
  outliers final: 13
  residues processed: 260
  average time/residue: 0.5784
  time to fit residues: 165.7043
Evaluate side-chains
  179 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 156
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  331 SER
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 120 optimal weight:    3.9990
   chunk 187 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 144 optimal weight:    5.9990
   chunk 70 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 137 optimal weight:    7.9990
   chunk 164 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 263 ASN
A 312 ASN
A 422 HIS
** C 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 263 ASN
C 312 ASN
** C 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 422 HIS
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.141639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115162 restraints weight = 17813.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.90
r_work: 0.3237 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3097 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3097
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  16044  Z= 0.223
  Angle     :  0.697   9.234  21814  Z= 0.367
  Chirality :  0.052   0.254   2380
  Planarity :  0.005   0.040   2780
  Dihedral  :  6.836  59.707   2188
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 15.92 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.57 (0.19), residues: 1922
  helix: -0.01 (0.29), residues: 304
  sheet:  0.27 (0.24), residues: 470
  loop : -0.73 (0.18), residues: 1148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 948 
 TYR   0.017   0.002   TYR C 639 
 PHE   0.014   0.002   PHE A 216 
 TRP   0.022   0.002   TRP A 152 
 HIS   0.007   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 (16044)
  covalent geometry    : angle       0.69731 (21814)
  hydrogen bonds       : bond        0.04236 (  596)
  hydrogen bonds       : angle       5.48224 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 162
  time to evaluate  : 0.636 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8251 (t70) cc_final: 0.7712 (m-30)
REVERT: A  108 MET cc_start: 0.7514 (OUTLIER) cc_final: 0.6184 (mmt)
REVERT: A  119 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7762 (ptpt)
REVERT: A  168 LYS cc_start: 0.7482 (OUTLIER) cc_final: 0.7188 (mtpp)
REVERT: A  199 ARG cc_start: 0.6987 (mmp-170) cc_final: 0.6562 (tpp80)
REVERT: A  299 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7314 (tp30)
REVERT: A  325 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5823 (mp0)
REVERT: A  338 GLN cc_start: 0.8126 (tt0) cc_final: 0.7695 (pt0)
REVERT: A  355 ASN cc_start: 0.8622 (m-40) cc_final: 0.8297 (m-40)
REVERT: A  446 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8275 (tt)
REVERT: A  452 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7428 (mt-10)
REVERT: A  524 GLU cc_start: 0.7647 (pm20) cc_final: 0.7403 (mp0)
REVERT: A  539 GLU cc_start: 0.7642 (tp30) cc_final: 0.7407 (mt-10)
REVERT: A  675 GLU cc_start: 0.8522 (tt0) cc_final: 0.8199 (tt0)
REVERT: B  939 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7787 (mt)
REVERT: C   20 ASP cc_start: 0.8219 (t70) cc_final: 0.7696 (m-30)
REVERT: C  119 LYS cc_start: 0.8022 (ttmt) cc_final: 0.7772 (ptpt)
REVERT: C  168 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7150 (mtpp)
REVERT: C  199 ARG cc_start: 0.7005 (mmp-170) cc_final: 0.6573 (tpp80)
REVERT: C  299 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7308 (tp30)
REVERT: C  325 GLU cc_start: 0.6346 (OUTLIER) cc_final: 0.5852 (mp0)
REVERT: C  338 GLN cc_start: 0.8095 (tt0) cc_final: 0.7714 (pt0)
REVERT: C  355 ASN cc_start: 0.8607 (m-40) cc_final: 0.8288 (m-40)
REVERT: C  446 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8276 (tt)
REVERT: C  494 ASP cc_start: 0.6930 (t0) cc_final: 0.6646 (t0)
REVERT: C  524 GLU cc_start: 0.7616 (pm20) cc_final: 0.7376 (mp0)
REVERT: C  539 GLU cc_start: 0.7669 (tp30) cc_final: 0.7364 (mt-10)
REVERT: D  859 GLU cc_start: 0.7650 (mm-30) cc_final: 0.6330 (mp0)
REVERT: D  939 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7787 (mt)
  outliers start: 80
  outliers final: 27
  residues processed: 222
  average time/residue: 0.6041
  time to fit residues: 146.9206
Evaluate side-chains
  182 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 144
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  210 SER
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  281 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  385 LEU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 183 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 82 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   chunk 155 optimal weight:    5.9990
   chunk 118 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 154 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 100 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
C 177 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.143025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.116690 restraints weight = 17792.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 1.91
r_work: 0.3261 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3122 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  16044  Z= 0.166
  Angle     :  0.626   8.908  21814  Z= 0.329
  Chirality :  0.049   0.204   2380
  Planarity :  0.005   0.043   2780
  Dihedral  :  6.519  58.867   2188
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 18.10 %
    Favored  : 77.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.54 (0.19), residues: 1922
  helix:  0.22 (0.29), residues: 304
  sheet:  0.21 (0.24), residues: 476
  loop : -0.75 (0.18), residues: 1142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 853 
 TYR   0.014   0.002   TYR A 639 
 PHE   0.012   0.002   PHE D 788 
 TRP   0.021   0.002   TRP C 152 
 HIS   0.003   0.001   HIS C 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (16044)
  covalent geometry    : angle       0.62583 (21814)
  hydrogen bonds       : bond        0.03766 (  596)
  hydrogen bonds       : angle       5.33120 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 161
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8106 (t70) cc_final: 0.7637 (m-30)
REVERT: A  108 MET cc_start: 0.7494 (OUTLIER) cc_final: 0.6171 (mmt)
REVERT: A  168 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7163 (mtpp)
REVERT: A  199 ARG cc_start: 0.7067 (mmp-170) cc_final: 0.6596 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7275 (tp30)
REVERT: A  325 GLU cc_start: 0.6222 (OUTLIER) cc_final: 0.5774 (mp0)
REVERT: A  338 GLN cc_start: 0.8113 (tt0) cc_final: 0.7742 (pt0)
REVERT: A  452 GLU cc_start: 0.7722 (mt-10) cc_final: 0.7362 (mt-10)
REVERT: A  494 ASP cc_start: 0.6997 (t0) cc_final: 0.6652 (t0)
REVERT: A  524 GLU cc_start: 0.7569 (pm20) cc_final: 0.7272 (mp0)
REVERT: A  535 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8191 (p)
REVERT: A  539 GLU cc_start: 0.7639 (tp30) cc_final: 0.7071 (mp0)
REVERT: A  568 ARG cc_start: 0.5599 (mmt180) cc_final: 0.5399 (mmt-90)
REVERT: B  759 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7614 (mm-30)
REVERT: B  808 LYS cc_start: 0.8149 (pttp) cc_final: 0.7872 (pptt)
REVERT: B  819 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7876 (mp0)
REVERT: B  859 GLU cc_start: 0.7651 (mm-30) cc_final: 0.6323 (mp0)
REVERT: B  939 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7772 (mt)
REVERT: C   20 ASP cc_start: 0.8115 (t70) cc_final: 0.7637 (m-30)
REVERT: C   77 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6832 (tp30)
REVERT: C  108 MET cc_start: 0.7636 (mpp) cc_final: 0.6340 (mmt)
REVERT: C  119 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7767 (mtpt)
REVERT: C  135 TYR cc_start: 0.8282 (m-80) cc_final: 0.7680 (m-80)
REVERT: C  168 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7125 (mtpp)
REVERT: C  199 ARG cc_start: 0.7127 (mmp-170) cc_final: 0.6626 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7266 (tp30)
REVERT: C  325 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5763 (mp0)
REVERT: C  338 GLN cc_start: 0.8084 (tt0) cc_final: 0.7843 (pt0)
REVERT: C  494 ASP cc_start: 0.6989 (t0) cc_final: 0.6606 (t0)
REVERT: C  524 GLU cc_start: 0.7528 (pm20) cc_final: 0.7235 (mp0)
REVERT: D  759 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7446 (mm-30)
REVERT: D  808 LYS cc_start: 0.8173 (pttp) cc_final: 0.7911 (pptt)
REVERT: D  859 GLU cc_start: 0.7675 (mm-30) cc_final: 0.6349 (mp0)
REVERT: D  939 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7781 (mt)
  outliers start: 67
  outliers final: 19
  residues processed: 212
  average time/residue: 0.5495
  time to fit residues: 129.0082
Evaluate side-chains
  173 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 141
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  819 GLU
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 128 optimal weight:    0.5980
   chunk 130 optimal weight:    3.9990
   chunk 9 optimal weight:    0.6980
   chunk 39 optimal weight:    6.9990
   chunk 148 optimal weight:    6.9990
   chunk 67 optimal weight:   10.0000
   chunk 164 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 106 optimal weight:    4.9990
   chunk 152 optimal weight:    4.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 476 ASN
C 476 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.143617 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117321 restraints weight = 17685.043|
|-----------------------------------------------------------------------------|
r_work (start): 0.3380 rms_B_bonded: 1.91
r_work: 0.3269 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16044  Z= 0.154
  Angle     :  0.599   8.713  21814  Z= 0.316
  Chirality :  0.048   0.255   2380
  Planarity :  0.004   0.039   2780
  Dihedral  :  6.287  58.666   2188
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 18.27 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.50 (0.19), residues: 1922
  helix:  0.41 (0.30), residues: 304
  sheet:  0.10 (0.23), residues: 486
  loop : -0.71 (0.19), residues: 1132

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 853 
 TYR   0.014   0.002   TYR C 639 
 PHE   0.012   0.002   PHE B 788 
 TRP   0.020   0.001   TRP A 152 
 HIS   0.003   0.001   HIS C 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (16044)
  covalent geometry    : angle       0.59899 (21814)
  hydrogen bonds       : bond        0.03655 (  596)
  hydrogen bonds       : angle       5.23790 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 158
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.8023 (t70) cc_final: 0.7559 (m-30)
REVERT: A   77 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6801 (tp30)
REVERT: A  108 MET cc_start: 0.7497 (mpp) cc_final: 0.6180 (mmt)
REVERT: A  109 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7795 (ptp-170)
REVERT: A  168 LYS cc_start: 0.7446 (OUTLIER) cc_final: 0.7117 (mtpp)
REVERT: A  199 ARG cc_start: 0.7093 (mmp-170) cc_final: 0.6613 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7237 (tp30)
REVERT: A  325 GLU cc_start: 0.6172 (OUTLIER) cc_final: 0.5671 (mp0)
REVERT: A  338 GLN cc_start: 0.8092 (tt0) cc_final: 0.7841 (pt0)
REVERT: A  446 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7540 (mt)
REVERT: A  452 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7375 (mt-10)
REVERT: A  494 ASP cc_start: 0.7067 (t0) cc_final: 0.6671 (t0)
REVERT: A  524 GLU cc_start: 0.7456 (pm20) cc_final: 0.7167 (mp0)
REVERT: A  535 SER cc_start: 0.8414 (OUTLIER) cc_final: 0.8178 (p)
REVERT: A  615 ARG cc_start: 0.7304 (mtt-85) cc_final: 0.6920 (mtt-85)
REVERT: A  669 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7183 (mm-30)
REVERT: B  759 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7631 (mm-30)
REVERT: B  808 LYS cc_start: 0.8136 (pttp) cc_final: 0.7847 (pptt)
REVERT: B  813 GLU cc_start: 0.8211 (tt0) cc_final: 0.7961 (tt0)
REVERT: B  859 GLU cc_start: 0.7665 (mm-30) cc_final: 0.6355 (mp0)
REVERT: C   20 ASP cc_start: 0.8025 (t70) cc_final: 0.7558 (m-30)
REVERT: C   77 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6858 (tp30)
REVERT: C  108 MET cc_start: 0.7592 (mpp) cc_final: 0.6293 (mmt)
REVERT: C  119 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7687 (mtpt)
REVERT: C  135 TYR cc_start: 0.8290 (m-80) cc_final: 0.7621 (m-80)
REVERT: C  168 LYS cc_start: 0.7443 (OUTLIER) cc_final: 0.7094 (mtpp)
REVERT: C  199 ARG cc_start: 0.7123 (mmp-170) cc_final: 0.6612 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7230 (tp30)
REVERT: C  325 GLU cc_start: 0.6221 (OUTLIER) cc_final: 0.5756 (mp0)
REVERT: C  427 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7790 (tt0)
REVERT: C  446 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8159 (tt)
REVERT: C  494 ASP cc_start: 0.7128 (t0) cc_final: 0.6787 (t0)
REVERT: C  524 GLU cc_start: 0.7502 (pm20) cc_final: 0.7214 (mp0)
REVERT: C  539 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7481 (mp0)
REVERT: C  615 ARG cc_start: 0.7291 (mtt-85) cc_final: 0.6901 (mtt-85)
REVERT: C  669 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7165 (mm-30)
REVERT: D  808 LYS cc_start: 0.8167 (pttp) cc_final: 0.7895 (pptt)
REVERT: D  859 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6395 (mp0)
  outliers start: 73
  outliers final: 27
  residues processed: 213
  average time/residue: 0.5594
  time to fit residues: 132.1031
Evaluate side-chains
  183 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 142
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  109 ARG
Chi-restraints excluded: chain A residue  168 LYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  325 GLU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  535 SER
Chi-restraints excluded: chain A residue  591 THR
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  669 GLU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  848 ILE
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  325 GLU
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  531 LEU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  591 THR
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  669 GLU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  848 ILE
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 166 optimal weight:    0.5980
   chunk 17 optimal weight:    0.0570
   chunk 93 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 72 optimal weight:    4.9990
   chunk 125 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 116 optimal weight:    0.9990
   chunk 64 optimal weight:    6.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
A 588 HIS
C 588 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.120385 restraints weight = 17527.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 1.90
r_work: 0.3314 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.3885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16044  Z= 0.114
  Angle     :  0.554   8.369  21814  Z= 0.293
  Chirality :  0.047   0.215   2380
  Planarity :  0.004   0.038   2780
  Dihedral  :  5.815  57.759   2184
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.39 %
    Favored  : 76.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.37 (0.19), residues: 1922
  helix:  0.58 (0.30), residues: 300
  sheet:  0.30 (0.23), residues: 468
  loop : -0.69 (0.19), residues: 1154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 853 
 TYR   0.013   0.001   TYR A 639 
 PHE   0.013   0.001   PHE B 788 
 TRP   0.019   0.001   TRP C 152 
 HIS   0.002   0.001   HIS C 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (16044)
  covalent geometry    : angle       0.55385 (21814)
  hydrogen bonds       : bond        0.03323 (  596)
  hydrogen bonds       : angle       5.13353 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 156
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7979 (t70) cc_final: 0.7539 (m-30)
REVERT: A   77 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6828 (tp30)
REVERT: A  108 MET cc_start: 0.7519 (mpp) cc_final: 0.6140 (mmt)
REVERT: A  135 TYR cc_start: 0.8283 (m-80) cc_final: 0.7669 (m-80)
REVERT: A  199 ARG cc_start: 0.7112 (mmp-170) cc_final: 0.6623 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7100 (tp30)
REVERT: A  355 ASN cc_start: 0.8463 (m-40) cc_final: 0.7626 (p0)
REVERT: A  446 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7579 (mt)
REVERT: A  447 ILE cc_start: 0.7641 (OUTLIER) cc_final: 0.7373 (mp)
REVERT: A  452 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7324 (mt-10)
REVERT: A  494 ASP cc_start: 0.7197 (t0) cc_final: 0.6838 (t0)
REVERT: A  524 GLU cc_start: 0.7536 (pm20) cc_final: 0.7254 (mp0)
REVERT: A  539 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7390 (mp0)
REVERT: A  735 LYS cc_start: 0.7022 (mmtp) cc_final: 0.6097 (mptt)
REVERT: B  759 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7612 (mp0)
REVERT: B  808 LYS cc_start: 0.8081 (pttp) cc_final: 0.7813 (pptt)
REVERT: B  813 GLU cc_start: 0.8202 (tt0) cc_final: 0.7938 (tt0)
REVERT: B  859 GLU cc_start: 0.7708 (mm-30) cc_final: 0.6410 (mp0)
REVERT: C   20 ASP cc_start: 0.7974 (t70) cc_final: 0.7529 (m-30)
REVERT: C   77 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6873 (tp30)
REVERT: C  105 THR cc_start: 0.8548 (p) cc_final: 0.8173 (t)
REVERT: C  108 MET cc_start: 0.7624 (mpp) cc_final: 0.6327 (mmt)
REVERT: C  119 LYS cc_start: 0.7965 (ttmt) cc_final: 0.7694 (mtpt)
REVERT: C  135 TYR cc_start: 0.8292 (m-80) cc_final: 0.7701 (m-80)
REVERT: C  168 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7177 (mtpp)
REVERT: C  199 ARG cc_start: 0.7115 (mmp-170) cc_final: 0.6611 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7102 (tp30)
REVERT: C  316 GLU cc_start: 0.7900 (tt0) cc_final: 0.7602 (pm20)
REVERT: C  355 ASN cc_start: 0.8502 (m-40) cc_final: 0.7641 (p0)
REVERT: C  446 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7580 (mt)
REVERT: C  447 ILE cc_start: 0.7631 (OUTLIER) cc_final: 0.7350 (mp)
REVERT: C  494 ASP cc_start: 0.7202 (t0) cc_final: 0.6826 (t0)
REVERT: C  524 GLU cc_start: 0.7481 (pm20) cc_final: 0.7231 (mp0)
REVERT: C  539 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7456 (mp0)
REVERT: C  735 LYS cc_start: 0.6927 (mmtp) cc_final: 0.6057 (mppt)
REVERT: D  759 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7289 (mm-30)
REVERT: D  808 LYS cc_start: 0.8097 (pttp) cc_final: 0.7831 (pptt)
REVERT: D  859 GLU cc_start: 0.7689 (mm-30) cc_final: 0.6430 (mp0)
  outliers start: 66
  outliers final: 16
  residues processed: 204
  average time/residue: 0.5633
  time to fit residues: 127.4743
Evaluate side-chains
  162 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 137
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain B residue  759 GLU
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  447 ILE
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain D residue  759 GLU
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 136 optimal weight:    6.9990
   chunk 82 optimal weight:    0.9990
   chunk 110 optimal weight:    0.5980
   chunk 157 optimal weight:    8.9990
   chunk 42 optimal weight:    8.9990
   chunk 183 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   overall best weight:    0.8586

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
C 145 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.146173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.120040 restraints weight = 17449.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 1.91
r_work: 0.3308 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.4008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16044  Z= 0.119
  Angle     :  0.551   8.224  21814  Z= 0.291
  Chirality :  0.047   0.200   2380
  Planarity :  0.004   0.038   2780
  Dihedral  :  5.761  57.959   2184
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.74 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.28 (0.19), residues: 1922
  helix:  0.76 (0.30), residues: 304
  sheet:  0.36 (0.23), residues: 468
  loop : -0.67 (0.19), residues: 1150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 853 
 TYR   0.013   0.001   TYR A 639 
 PHE   0.013   0.001   PHE B 788 
 TRP   0.019   0.001   TRP A 152 
 HIS   0.002   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (16044)
  covalent geometry    : angle       0.55074 (21814)
  hydrogen bonds       : bond        0.03318 (  596)
  hydrogen bonds       : angle       5.04829 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 152
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7992 (t70) cc_final: 0.7546 (m-30)
REVERT: A   77 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6893 (tp30)
REVERT: A  108 MET cc_start: 0.7484 (mpp) cc_final: 0.6155 (mmt)
REVERT: A  135 TYR cc_start: 0.8308 (m-80) cc_final: 0.7708 (m-80)
REVERT: A  299 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7116 (tp30)
REVERT: A  355 ASN cc_start: 0.8480 (m-40) cc_final: 0.7629 (p0)
REVERT: A  446 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7601 (mt)
REVERT: A  447 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7399 (mp)
REVERT: A  452 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7330 (mt-10)
REVERT: A  494 ASP cc_start: 0.7381 (t0) cc_final: 0.6948 (t0)
REVERT: A  524 GLU cc_start: 0.7505 (pm20) cc_final: 0.7233 (mp0)
REVERT: A  539 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7433 (mp0)
REVERT: A  735 LYS cc_start: 0.6867 (mmtp) cc_final: 0.5930 (mptm)
REVERT: B  808 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7808 (pptt)
REVERT: B  859 GLU cc_start: 0.7685 (mm-30) cc_final: 0.6426 (mp0)
REVERT: C   20 ASP cc_start: 0.7986 (t70) cc_final: 0.7545 (m-30)
REVERT: C   77 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6880 (tp30)
REVERT: C  105 THR cc_start: 0.8508 (p) cc_final: 0.8151 (t)
REVERT: C  108 MET cc_start: 0.7611 (mpp) cc_final: 0.6317 (mmt)
REVERT: C  119 LYS cc_start: 0.7950 (ttmt) cc_final: 0.7671 (mtpt)
REVERT: C  135 TYR cc_start: 0.8282 (m-80) cc_final: 0.7675 (m-80)
REVERT: C  168 LYS cc_start: 0.7399 (OUTLIER) cc_final: 0.7186 (mtpp)
REVERT: C  299 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7103 (tp30)
REVERT: C  316 GLU cc_start: 0.7889 (tt0) cc_final: 0.7583 (pm20)
REVERT: C  355 ASN cc_start: 0.8513 (m-40) cc_final: 0.7639 (p0)
REVERT: C  446 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.7572 (mt)
REVERT: C  447 ILE cc_start: 0.7602 (OUTLIER) cc_final: 0.7343 (mp)
REVERT: C  494 ASP cc_start: 0.7322 (t0) cc_final: 0.6872 (t0)
REVERT: C  524 GLU cc_start: 0.7510 (pm20) cc_final: 0.7262 (mp0)
REVERT: C  539 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7423 (mp0)
REVERT: D  808 LYS cc_start: 0.8109 (pttp) cc_final: 0.7857 (pptt)
REVERT: D  859 GLU cc_start: 0.7720 (mm-30) cc_final: 0.6450 (mp0)
  outliers start: 62
  outliers final: 25
  residues processed: 204
  average time/residue: 0.5678
  time to fit residues: 127.7218
Evaluate side-chains
  170 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  808 LYS
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  147 GLU
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  447 ILE
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   chunk 171 optimal weight:    3.9990
   chunk 26 optimal weight:    0.1980
   chunk 23 optimal weight:    0.4980
   chunk 81 optimal weight:    7.9990
   chunk 175 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 159 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   overall best weight:    2.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.141831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115156 restraints weight = 17672.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3354 rms_B_bonded: 1.92
r_work: 0.3242 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.3939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  16044  Z= 0.194
  Angle     :  0.623   8.851  21814  Z= 0.327
  Chirality :  0.049   0.202   2380
  Planarity :  0.004   0.038   2780
  Dihedral  :  6.067  59.060   2184
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 19.62 %
    Favored  : 76.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.46 (0.19), residues: 1922
  helix:  0.56 (0.30), residues: 306
  sheet:  0.23 (0.23), residues: 468
  loop : -0.76 (0.19), residues: 1148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 364 
 TYR   0.015   0.002   TYR A 234 
 PHE   0.014   0.002   PHE A 587 
 TRP   0.018   0.002   TRP A 152 
 HIS   0.004   0.001   HIS A 460 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 (16044)
  covalent geometry    : angle       0.62308 (21814)
  hydrogen bonds       : bond        0.03762 (  596)
  hydrogen bonds       : angle       5.20680 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 144
  time to evaluate  : 0.440 
Fit side-chains
REVERT: A   20 ASP cc_start: 0.8016 (t70) cc_final: 0.7538 (m-30)
REVERT: A   77 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6762 (tp30)
REVERT: A  108 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6232 (mmt)
REVERT: A  199 ARG cc_start: 0.7335 (tpm-80) cc_final: 0.6634 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7239 (tp30)
REVERT: A  316 GLU cc_start: 0.7985 (tt0) cc_final: 0.7636 (pm20)
REVERT: A  355 ASN cc_start: 0.8651 (m-40) cc_final: 0.8351 (m-40)
REVERT: A  446 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.7624 (mt)
REVERT: A  447 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7713 (mp)
REVERT: A  452 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7273 (mt-10)
REVERT: A  494 ASP cc_start: 0.7385 (t0) cc_final: 0.6936 (t0)
REVERT: A  524 GLU cc_start: 0.7562 (pm20) cc_final: 0.7333 (mp0)
REVERT: A  539 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7500 (mp0)
REVERT: A  735 LYS cc_start: 0.6967 (mmtp) cc_final: 0.6005 (mptm)
REVERT: B  813 GLU cc_start: 0.8265 (tt0) cc_final: 0.7983 (tt0)
REVERT: B  859 GLU cc_start: 0.7653 (mm-30) cc_final: 0.6367 (mp0)
REVERT: C   20 ASP cc_start: 0.8032 (t70) cc_final: 0.7557 (m-30)
REVERT: C   77 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6817 (tp30)
REVERT: C  108 MET cc_start: 0.7573 (mpp) cc_final: 0.6268 (mmt)
REVERT: C  119 LYS cc_start: 0.7999 (ttmt) cc_final: 0.7770 (ptpt)
REVERT: C  168 LYS cc_start: 0.7428 (OUTLIER) cc_final: 0.6781 (ttmt)
REVERT: C  199 ARG cc_start: 0.7354 (tpm-80) cc_final: 0.6639 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7240 (tp30)
REVERT: C  316 GLU cc_start: 0.7958 (tt0) cc_final: 0.7637 (pm20)
REVERT: C  355 ASN cc_start: 0.8639 (m-40) cc_final: 0.8347 (m-40)
REVERT: C  446 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7608 (mt)
REVERT: C  447 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7606 (mp)
REVERT: C  494 ASP cc_start: 0.7410 (t0) cc_final: 0.6940 (t0)
REVERT: C  524 GLU cc_start: 0.7515 (pm20) cc_final: 0.7269 (mp0)
REVERT: C  539 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7562 (mp0)
REVERT: C  735 LYS cc_start: 0.6865 (mmtp) cc_final: 0.5950 (mptm)
REVERT: D  859 GLU cc_start: 0.7687 (mm-30) cc_final: 0.6416 (mp0)
  outliers start: 66
  outliers final: 25
  residues processed: 199
  average time/residue: 0.5653
  time to fit residues: 124.2850
Evaluate side-chains
  168 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 135
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  447 ILE
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 161 optimal weight:   20.0000
   chunk 18 optimal weight:    3.9990
   chunk 90 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 12 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9980
   chunk 159 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 145 GLN
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.146925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.120953 restraints weight = 17554.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 1.88
r_work: 0.3318 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3181 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  16044  Z= 0.130
  Angle     :  0.566   8.311  21814  Z= 0.298
  Chirality :  0.047   0.187   2380
  Planarity :  0.004   0.041   2780
  Dihedral  :  5.835  57.901   2184
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 20.51 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.19), residues: 1922
  helix:  0.71 (0.30), residues: 306
  sheet:  0.30 (0.23), residues: 464
  loop : -0.78 (0.19), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 934 
 TYR   0.016   0.001   TYR A 639 
 PHE   0.024   0.002   PHE C 587 
 TRP   0.020   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (16044)
  covalent geometry    : angle       0.56558 (21814)
  hydrogen bonds       : bond        0.03378 (  596)
  hydrogen bonds       : angle       5.11775 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 143
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7958 (t70) cc_final: 0.7558 (m-30)
REVERT: A   77 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6933 (tp30)
REVERT: A  108 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.6266 (mmt)
REVERT: A  135 TYR cc_start: 0.8326 (m-80) cc_final: 0.7756 (m-80)
REVERT: A  199 ARG cc_start: 0.7433 (tpm-80) cc_final: 0.6724 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7185 (tp30)
REVERT: A  446 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7580 (mt)
REVERT: A  447 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7643 (mp)
REVERT: A  452 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7284 (mt-10)
REVERT: A  494 ASP cc_start: 0.7287 (t0) cc_final: 0.6904 (t0)
REVERT: A  524 GLU cc_start: 0.7501 (pm20) cc_final: 0.7234 (mp0)
REVERT: A  539 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7432 (mp0)
REVERT: B  808 LYS cc_start: 0.7960 (pttp) cc_final: 0.7693 (pptt)
REVERT: B  813 GLU cc_start: 0.8233 (tt0) cc_final: 0.7959 (tt0)
REVERT: B  859 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6400 (mp0)
REVERT: C   20 ASP cc_start: 0.7962 (t70) cc_final: 0.7569 (m-30)
REVERT: C   77 GLU cc_start: 0.7322 (mt-10) cc_final: 0.7070 (tp30)
REVERT: C  105 THR cc_start: 0.8524 (p) cc_final: 0.8186 (t)
REVERT: C  108 MET cc_start: 0.7672 (mpp) cc_final: 0.6357 (mmt)
REVERT: C  135 TYR cc_start: 0.8314 (m-80) cc_final: 0.7738 (m-80)
REVERT: C  168 LYS cc_start: 0.7467 (OUTLIER) cc_final: 0.7237 (mtpp)
REVERT: C  199 ARG cc_start: 0.7414 (tpm-80) cc_final: 0.6720 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7187 (tp30)
REVERT: C  316 GLU cc_start: 0.7913 (tt0) cc_final: 0.7606 (pm20)
REVERT: C  427 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.7295 (tm-30)
REVERT: C  446 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.7591 (mt)
REVERT: C  447 ILE cc_start: 0.7763 (OUTLIER) cc_final: 0.7547 (mp)
REVERT: C  452 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7258 (mt-10)
REVERT: C  494 ASP cc_start: 0.7380 (t0) cc_final: 0.6930 (t0)
REVERT: C  524 GLU cc_start: 0.7491 (pm20) cc_final: 0.7226 (mp0)
REVERT: C  539 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7467 (mp0)
REVERT: C  613 ARG cc_start: 0.8378 (tpp80) cc_final: 0.8125 (ttm170)
REVERT: D  808 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7861 (pptt)
REVERT: D  859 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6459 (mp0)
  outliers start: 52
  outliers final: 26
  residues processed: 184
  average time/residue: 0.5850
  time to fit residues: 118.7621
Evaluate side-chains
  171 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  447 ILE
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  805 ARG
Chi-restraints excluded: chain D residue  808 LYS
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 153 optimal weight:    8.9990
   chunk 182 optimal weight:    4.9990
   chunk 151 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 141 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 54 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 149 optimal weight:    5.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.144038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.118124 restraints weight = 17620.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 1.86
r_work: 0.3290 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.00 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8325
moved from start:          0.4034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  16044  Z= 0.170
  Angle     :  0.605   8.764  21814  Z= 0.317
  Chirality :  0.048   0.191   2380
  Planarity :  0.005   0.042   2780
  Dihedral  :  5.989  58.764   2184
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 21.39 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.47 (0.19), residues: 1922
  helix:  0.65 (0.30), residues: 306
  sheet:  0.29 (0.23), residues: 464
  loop : -0.84 (0.19), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 364 
 TYR   0.018   0.002   TYR A 639 
 PHE   0.028   0.002   PHE A 587 
 TRP   0.019   0.001   TRP C 152 
 HIS   0.004   0.001   HIS C 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (16044)
  covalent geometry    : angle       0.60471 (21814)
  hydrogen bonds       : bond        0.03599 (  596)
  hydrogen bonds       : angle       5.15136 ( 1584)

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

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

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3844 Ramachandran restraints generated.
    1922 Oldfield, 0 Emsley, 1922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 144
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 ASP cc_start: 0.7970 (t70) cc_final: 0.7560 (m-30)
REVERT: A   77 GLU cc_start: 0.7251 (mt-10) cc_final: 0.7004 (tp30)
REVERT: A  108 MET cc_start: 0.7548 (OUTLIER) cc_final: 0.6242 (mmt)
REVERT: A  199 ARG cc_start: 0.7462 (tpm-80) cc_final: 0.6784 (mpp-170)
REVERT: A  299 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7269 (tp30)
REVERT: A  316 GLU cc_start: 0.7984 (tt0) cc_final: 0.7628 (pm20)
REVERT: A  412 ASP cc_start: 0.7454 (p0) cc_final: 0.6270 (m-30)
REVERT: A  446 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7574 (mt)
REVERT: A  452 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7312 (mt-10)
REVERT: A  494 ASP cc_start: 0.7326 (t0) cc_final: 0.6961 (t0)
REVERT: A  524 GLU cc_start: 0.7500 (pm20) cc_final: 0.7275 (mp0)
REVERT: A  539 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7476 (mp0)
REVERT: A  583 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7110 (tp30)
REVERT: A  735 LYS cc_start: 0.6812 (mmtp) cc_final: 0.5909 (mptm)
REVERT: B  813 GLU cc_start: 0.8265 (tt0) cc_final: 0.7970 (tt0)
REVERT: B  859 GLU cc_start: 0.7661 (mm-30) cc_final: 0.6423 (mp0)
REVERT: C   20 ASP cc_start: 0.7955 (t70) cc_final: 0.7564 (m-30)
REVERT: C   77 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7022 (tp30)
REVERT: C  105 THR cc_start: 0.8572 (p) cc_final: 0.8236 (t)
REVERT: C  108 MET cc_start: 0.7696 (mpp) cc_final: 0.6378 (mmt)
REVERT: C  168 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.6803 (ttmt)
REVERT: C  199 ARG cc_start: 0.7445 (tpm-80) cc_final: 0.6773 (mpp-170)
REVERT: C  299 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7257 (tp30)
REVERT: C  316 GLU cc_start: 0.7947 (tt0) cc_final: 0.7635 (pm20)
REVERT: C  412 ASP cc_start: 0.7430 (p0) cc_final: 0.6239 (m-30)
REVERT: C  427 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.7294 (tm-30)
REVERT: C  446 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7576 (mt)
REVERT: C  494 ASP cc_start: 0.7403 (t0) cc_final: 0.6964 (t0)
REVERT: C  524 GLU cc_start: 0.7482 (pm20) cc_final: 0.7251 (mp0)
REVERT: C  539 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7503 (mp0)
REVERT: C  613 ARG cc_start: 0.8359 (tpp80) cc_final: 0.8061 (ttm170)
REVERT: D  859 GLU cc_start: 0.7684 (mm-30) cc_final: 0.6473 (mp0)
  outliers start: 45
  outliers final: 29
  residues processed: 175
  average time/residue: 0.5558
  time to fit residues: 107.9279
Evaluate side-chains
  175 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   53 ASP
Chi-restraints excluded: chain A residue  108 MET
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  331 SER
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  543 LEU
Chi-restraints excluded: chain A residue  583 GLU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  706 TYR
Chi-restraints excluded: chain B residue  782 TYR
Chi-restraints excluded: chain B residue  818 VAL
Chi-restraints excluded: chain B residue  888 THR
Chi-restraints excluded: chain B residue  917 SER
Chi-restraints excluded: chain B residue  919 ASP
Chi-restraints excluded: chain B residue  920 SER
Chi-restraints excluded: chain B residue  927 VAL
Chi-restraints excluded: chain B residue  939 ILE
Chi-restraints excluded: chain C residue   53 ASP
Chi-restraints excluded: chain C residue  168 LYS
Chi-restraints excluded: chain C residue  240 LEU
Chi-restraints excluded: chain C residue  299 GLU
Chi-restraints excluded: chain C residue  427 GLU
Chi-restraints excluded: chain C residue  446 LEU
Chi-restraints excluded: chain C residue  493 VAL
Chi-restraints excluded: chain C residue  539 GLU
Chi-restraints excluded: chain C residue  543 LEU
Chi-restraints excluded: chain C residue  599 LEU
Chi-restraints excluded: chain C residue  706 TYR
Chi-restraints excluded: chain D residue  782 TYR
Chi-restraints excluded: chain D residue  805 ARG
Chi-restraints excluded: chain D residue  818 VAL
Chi-restraints excluded: chain D residue  888 THR
Chi-restraints excluded: chain D residue  917 SER
Chi-restraints excluded: chain D residue  919 ASP
Chi-restraints excluded: chain D residue  920 SER
Chi-restraints excluded: chain D residue  927 VAL
Chi-restraints excluded: chain D residue  939 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 190
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 178 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    1.9990
   chunk 183 optimal weight:    0.8980
   chunk 83 optimal weight:    2.9990
   chunk 125 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 588 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.144464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.118771 restraints weight = 17695.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 1.89
r_work: 0.3291 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16044  Z= 0.145
  Angle     :  0.581   8.375  21814  Z= 0.305
  Chirality :  0.047   0.187   2380
  Planarity :  0.004   0.045   2780
  Dihedral  :  5.900  58.240   2184
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 21.45 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.11 %
    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: -0.47 (0.19), residues: 1922
  helix:  0.70 (0.30), residues: 306
  sheet:  0.30 (0.23), residues: 464
  loop : -0.85 (0.19), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 364 
 TYR   0.017   0.001   TYR A 639 
 PHE   0.029   0.002   PHE A 587 
 TRP   0.020   0.001   TRP C 152 
 HIS   0.004   0.001   HIS C 588 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (16044)
  covalent geometry    : angle       0.58055 (21814)
  hydrogen bonds       : bond        0.03429 (  596)
  hydrogen bonds       : angle       5.11314 ( 1584)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4434.18 seconds
wall clock time: 76 minutes 34.06 seconds (4594.06 seconds total)