Starting phenix.real_space_refine
on Sat Aug 23 15:10:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b7z_44329/08_2025/9b7z_44329_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b7z_44329/08_2025/9b7z_44329.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b7z_44329/08_2025/9b7z_44329_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b7z_44329/08_2025/9b7z_44329_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b7z_44329/08_2025/9b7z_44329.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b7z_44329/08_2025/9b7z_44329.map"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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      70      5.16       5
     C    8192      2.51       5
     N    2278      2.21       5
     O    2402      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 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: 12942
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 6471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 854, 6471
          Classifications: {'peptide': 854}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 63, 'TRANS': 790}
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 18
  Restraints were copied for chains:
    B
  Time building chain proxies: 6.33, per 1000 atoms: 0.49
  Number of scatterers: 12942
  At special positions: 0
  Unit cell: (102.705, 189.545, 93.52, 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      70     16.00
     O    2402      8.00
     N    2278      7.00
     C    8192      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 770.3 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3100

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 9 sheets defined
      44.5% alpha, 11.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 29
    Processing helix  chain 'A' and resid 43 through 47
    Processing helix  chain 'A' and resid 68 through 74
      removed outlier: 3.944A  pdb=" N   THR A  74 " --> pdb=" O   LYS A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 93
    Processing helix  chain 'A' and resid 96 through 101
      removed outlier: 3.714A  pdb=" N   ARG A 101 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 120
      removed outlier: 3.949A  pdb=" N   GLU A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 3.904A  pdb=" N   VAL A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 149
      removed outlier: 4.625A  pdb=" N   LEU A 144 " --> pdb=" O   MET A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 161
      No H-bonds generated for 'chain 'A' and resid 159 through 161'
    Processing helix  chain 'A' and resid 162 through 177
    Processing helix  chain 'A' and resid 193 through 203
      removed outlier: 4.379A  pdb=" N   SER A 197 " --> pdb=" O   LYS A 193 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 239
      No H-bonds generated for 'chain 'A' and resid 237 through 239'
    Processing helix  chain 'A' and resid 265 through 281
      removed outlier: 3.713A  pdb=" N   GLN A 269 " --> pdb=" O   SER A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 299 through 312
      removed outlier: 3.862A  pdb=" N   GLN A 303 " --> pdb=" O   VAL A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 335 through 351
    Processing helix  chain 'A' and resid 366 through 370
    Processing helix  chain 'A' and resid 415 through 420
      removed outlier: 3.680A  pdb=" N   THR A 419 " --> pdb=" O   PRO A 416 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 444
      removed outlier: 3.582A  pdb=" N   VAL A 434 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 447 through 457
    Processing helix  chain 'A' and resid 507 through 512
      removed outlier: 4.000A  pdb=" N   ARG A 512 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 528
    Processing helix  chain 'A' and resid 533 through 540
      removed outlier: 4.054A  pdb=" N   LEU A 537 " --> pdb=" O   LYS A 533 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 570
      removed outlier: 3.641A  pdb=" N   SER A 552 " --> pdb=" O   ASP A 548 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE A 559 " --> pdb=" O   SER A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 592
      removed outlier: 3.819A  pdb=" N   GLY A 588 " --> pdb=" O   GLU A 584 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   TYR A 589 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 613
    Processing helix  chain 'A' and resid 626 through 634
      removed outlier: 3.839A  pdb=" N   LYS A 631 " --> pdb=" O   TRP A 627 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A 632 " --> pdb=" O   GLU A 628 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 667
      removed outlier: 3.552A  pdb=" N   PHE A 661 " --> pdb=" O   PRO A 657 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL A 662 " --> pdb=" O   VAL A 658 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   GLU A 663 " --> pdb=" O   PHE A 659 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN A 664 " --> pdb=" O   GLU A 660 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LYS A 667 " --> pdb=" O   GLU A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 699
      removed outlier: 3.574A  pdb=" N   GLN A 696 " --> pdb=" O   PRO A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 722
    Processing helix  chain 'A' and resid 731 through 740
      removed outlier: 3.524A  pdb=" N   ASN A 735 " --> pdb=" O   SER A 731 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 739 " --> pdb=" O   ASN A 735 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL A 740 " --> pdb=" O   VAL A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 752
    Processing helix  chain 'A' and resid 767 through 775
      removed outlier: 3.616A  pdb=" N   ARG A 773 " --> pdb=" O   ALA A 769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 807
      removed outlier: 3.597A  pdb=" N   PHE A 795 " --> pdb=" O   ASP A 791 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY A 807 " --> pdb=" O   LEU A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 815
      removed outlier: 3.501A  pdb=" N   ALA A 814 " --> pdb=" O   ASN A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 834
      removed outlier: 3.792A  pdb=" N   ILE A 834 " --> pdb=" O   SER A 831 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 846 through 850
      removed outlier: 3.708A  pdb=" N   PHE A 850 " --> pdb=" O   ALA A 847 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 18 through 29
    Processing helix  chain 'B' and resid 43 through 47
    Processing helix  chain 'B' and resid 68 through 74
      removed outlier: 3.943A  pdb=" N   THR B  74 " --> pdb=" O   LYS B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 76 through 93
    Processing helix  chain 'B' and resid 96 through 101
      removed outlier: 3.713A  pdb=" N   ARG B 101 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 120
      removed outlier: 3.950A  pdb=" N   GLU B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 136
      removed outlier: 3.904A  pdb=" N   VAL B 133 " --> pdb=" O   GLY B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 149
      removed outlier: 4.626A  pdb=" N   LEU B 144 " --> pdb=" O   MET B 140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 161
      No H-bonds generated for 'chain 'B' and resid 159 through 161'
    Processing helix  chain 'B' and resid 162 through 177
    Processing helix  chain 'B' and resid 193 through 203
      removed outlier: 4.379A  pdb=" N   SER B 197 " --> pdb=" O   LYS B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 239
      No H-bonds generated for 'chain 'B' and resid 237 through 239'
    Processing helix  chain 'B' and resid 265 through 281
      removed outlier: 3.713A  pdb=" N   GLN B 269 " --> pdb=" O   SER B 265 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 285
      No H-bonds generated for 'chain 'B' and resid 283 through 285'
    Processing helix  chain 'B' and resid 299 through 312
      removed outlier: 3.862A  pdb=" N   GLN B 303 " --> pdb=" O   VAL B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 335 through 351
    Processing helix  chain 'B' and resid 366 through 370
    Processing helix  chain 'B' and resid 415 through 420
      removed outlier: 3.680A  pdb=" N   THR B 419 " --> pdb=" O   PRO B 416 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 444
      removed outlier: 3.582A  pdb=" N   VAL B 434 " --> pdb=" O   THR B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 457
    Processing helix  chain 'B' and resid 507 through 512
      removed outlier: 4.000A  pdb=" N   ARG B 512 " --> pdb=" O   SER B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 528
    Processing helix  chain 'B' and resid 533 through 540
      removed outlier: 4.055A  pdb=" N   LEU B 537 " --> pdb=" O   LYS B 533 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 570
      removed outlier: 3.641A  pdb=" N   SER B 552 " --> pdb=" O   ASP B 548 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   ILE B 559 " --> pdb=" O   SER B 555 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 581 through 592
      removed outlier: 3.819A  pdb=" N   GLY B 588 " --> pdb=" O   GLU B 584 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   TYR B 589 " --> pdb=" O   VAL B 585 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 595 through 613
    Processing helix  chain 'B' and resid 626 through 634
      removed outlier: 3.839A  pdb=" N   LYS B 631 " --> pdb=" O   TRP B 627 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B 632 " --> pdb=" O   GLU B 628 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 654 through 667
      removed outlier: 3.552A  pdb=" N   PHE B 661 " --> pdb=" O   PRO B 657 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B 662 " --> pdb=" O   VAL B 658 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   GLU B 663 " --> pdb=" O   PHE B 659 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   GLN B 664 " --> pdb=" O   GLU B 660 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS B 667 " --> pdb=" O   GLU B 663 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 690 through 699
      removed outlier: 3.575A  pdb=" N   GLN B 696 " --> pdb=" O   PRO B 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 722
    Processing helix  chain 'B' and resid 731 through 740
      removed outlier: 3.523A  pdb=" N   ASN B 735 " --> pdb=" O   SER B 731 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LEU B 739 " --> pdb=" O   ASN B 735 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B 740 " --> pdb=" O   VAL B 736 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 748 through 752
    Processing helix  chain 'B' and resid 767 through 775
      removed outlier: 3.616A  pdb=" N   ARG B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 791 through 807
      removed outlier: 3.597A  pdb=" N   PHE B 795 " --> pdb=" O   ASP B 791 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   GLY B 807 " --> pdb=" O   LEU B 803 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 811 through 815
      removed outlier: 3.502A  pdb=" N   ALA B 814 " --> pdb=" O   ASN B 811 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 834
      removed outlier: 3.792A  pdb=" N   ILE B 834 " --> pdb=" O   SER B 831 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 846 through 850
      removed outlier: 3.708A  pdb=" N   PHE B 850 " --> pdb=" O   ALA B 847 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 374 through 376
      removed outlier: 6.048A  pdb=" N   LEU A 320 " --> pdb=" O   GLN A 375 " (cutoff:3.500A)
      removed outlier: 5.429A  pdb=" N   ASN A 387 " --> pdb=" O   PHE A 287 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR A 289 " --> pdb=" O   ASN A 387 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASN A 399 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR A 251 " --> pdb=" O   ASN A 399 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   HIS A 401 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   ALA A 249 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE A 403 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA A 244 " --> pdb=" O   ILE A   6 " (cutoff:3.500A)
      removed outlier: 4.914A  pdb=" N   VAL A   4 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   LEU A 232 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   MET A   9 " --> pdb=" O   ALA A 230 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   ALA A 230 " --> pdb=" O   MET A   9 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLY A  11 " --> pdb=" O   VAL A 228 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL A 228 " --> pdb=" O   GLY A  11 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 107 " --> pdb=" O   ILE A 155 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   LEU A 157 " --> pdb=" O   VAL A 107 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A 157 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ALA A 156 " --> pdb=" O   ASP B 158 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ALA B 156 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL B 107 " --> pdb=" O   ILE B 155 " (cutoff:3.500A)
      removed outlier: 7.652A  pdb=" N   LEU B 157 " --> pdb=" O   VAL B 107 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 157 " (cutoff:3.500A)
      removed outlier: 6.773A  pdb=" N   VAL B 228 " --> pdb=" O   GLY B  11 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   GLY B  11 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   ALA B 230 " --> pdb=" O   MET B   9 " (cutoff:3.500A)
      removed outlier: 4.605A  pdb=" N   MET B   9 " --> pdb=" O   ALA B 230 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LEU B 232 " --> pdb=" O   ALA B   7 " (cutoff:3.500A)
      removed outlier: 4.913A  pdb=" N   VAL B   4 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   ALA B 244 " --> pdb=" O   ILE B   6 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   ILE B 403 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   ALA B 249 " --> pdb=" O   HIS B 401 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   HIS B 401 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   THR B 251 " --> pdb=" O   ASN B 399 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASN B 399 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 5.428A  pdb=" N   ASN B 387 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR B 289 " --> pdb=" O   ASN B 387 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   LEU B 320 " --> pdb=" O   GLN B 375 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353
      removed outlier: 3.892A  pdb=" N   LEU A 381 " --> pdb=" O   TRP A 353 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 422 through 428
    Processing sheet with id=AA4, first strand: chain 'A' and resid 712 through 713
      removed outlier: 6.674A  pdb=" N   ILE A 577 " --> pdb=" O   LEU A 713 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   CYS A 496 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP A 493 " --> pdb=" O   LEU A 759 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE A 761 " --> pdb=" O   TRP A 493 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE A 495 " --> pdb=" O   ILE A 761 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 622 through 623
      removed outlier: 6.383A  pdb=" N   THR A 650 " --> pdb=" O   ALA A 641 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   VAL A 639 " --> pdb=" O   SER A 652 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 352 through 353
      removed outlier: 3.892A  pdb=" N   LEU B 381 " --> pdb=" O   TRP B 353 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 422 through 428
    Processing sheet with id=AA8, first strand: chain 'B' and resid 712 through 713
      removed outlier: 6.674A  pdb=" N   ILE B 577 " --> pdb=" O   LEU B 713 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   CYS B 496 " --> pdb=" O   VAL B 578 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP B 493 " --> pdb=" O   LEU B 759 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   ILE B 761 " --> pdb=" O   TRP B 493 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   ILE B 495 " --> pdb=" O   ILE B 761 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 622 through 623
      removed outlier: 6.382A  pdb=" N   THR B 650 " --> pdb=" O   ALA B 641 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   VAL B 639 " --> pdb=" O   SER B 652 " (cutoff:3.500A)

    532 hydrogen bonds defined for protein.
    1452 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.70

  Time building geometry restraints manager: 1.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4042
        1.34 -     1.46: 2159
        1.46 -     1.57: 6943
        1.57 -     1.69: 2
        1.69 -     1.81: 110
  Bond restraints: 13256
  Sorted by residual:
  bond pdb=" N   LEU A 615 "
       pdb=" CA  LEU A 615 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 8.30e-03 1.45e+04 1.78e+01
  bond pdb=" N   LEU B 615 "
       pdb=" CA  LEU B 615 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 8.30e-03 1.45e+04 1.67e+01
  bond pdb=" N   GLY B 618 "
       pdb=" CA  GLY B 618 "
    ideal  model  delta    sigma   weight residual
    1.443  1.476 -0.033 8.60e-03 1.35e+04 1.47e+01
  bond pdb=" N   GLY A 618 "
       pdb=" CA  GLY A 618 "
    ideal  model  delta    sigma   weight residual
    1.443  1.476 -0.033 8.60e-03 1.35e+04 1.44e+01
  bond pdb=" N   VAL B 111 "
       pdb=" CA  VAL B 111 "
    ideal  model  delta    sigma   weight residual
    1.455  1.492 -0.037 1.18e-02 7.18e+03 9.90e+00
  ... (remaining 13251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 17535
        2.68 -     5.37: 433
        5.37 -     8.05: 48
        8.05 -    10.74: 10
       10.74 -    13.42: 4
  Bond angle restraints: 18030
  Sorted by residual:
  angle pdb=" N   GLU A 668 "
        pdb=" CA  GLU A 668 "
        pdb=" C   GLU A 668 "
      ideal   model   delta    sigma   weight residual
     108.00  115.53   -7.53 1.48e+00 4.57e-01 2.59e+01
  angle pdb=" N   GLU B 668 "
        pdb=" CA  GLU B 668 "
        pdb=" C   GLU B 668 "
      ideal   model   delta    sigma   weight residual
     108.00  115.52   -7.52 1.48e+00 4.57e-01 2.58e+01
  angle pdb=" CA  GLU A 489 "
        pdb=" CB  GLU A 489 "
        pdb=" CG  GLU A 489 "
      ideal   model   delta    sigma   weight residual
     114.10  123.56   -9.46 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CA  GLU B 489 "
        pdb=" CB  GLU B 489 "
        pdb=" CG  GLU B 489 "
      ideal   model   delta    sigma   weight residual
     114.10  123.52   -9.42 2.00e+00 2.50e-01 2.22e+01
  angle pdb=" CB  MET A 570 "
        pdb=" CG  MET A 570 "
        pdb=" SD  MET A 570 "
      ideal   model   delta    sigma   weight residual
     112.70  126.12  -13.42 3.00e+00 1.11e-01 2.00e+01
  ... (remaining 18025 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.18: 7148
       18.18 -    36.37: 612
       36.37 -    54.55: 160
       54.55 -    72.73: 38
       72.73 -    90.92: 10
  Dihedral angle restraints: 7968
    sinusoidal: 3138
      harmonic: 4830
  Sorted by residual:
  dihedral pdb=" CA  GLU A 820 "
           pdb=" C   GLU A 820 "
           pdb=" N   PHE A 821 "
           pdb=" CA  PHE A 821 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.99  -21.01     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  GLU B 820 "
           pdb=" C   GLU B 820 "
           pdb=" N   PHE B 821 "
           pdb=" CA  PHE B 821 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.04  -20.96     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  ASP A 547 "
           pdb=" C   ASP A 547 "
           pdb=" N   ASP A 548 "
           pdb=" CA  ASP A 548 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.08   16.92     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 7965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1274
       0.049 -    0.097: 497
       0.097 -    0.146: 190
       0.146 -    0.195: 30
       0.195 -    0.243: 11
  Chirality restraints: 2002
  Sorted by residual:
  chirality pdb=" CA  GLU B 668 "
            pdb=" N   GLU B 668 "
            pdb=" C   GLU B 668 "
            pdb=" CB  GLU B 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  GLU A 668 "
            pdb=" N   GLU A 668 "
            pdb=" C   GLU A 668 "
            pdb=" CB  GLU A 668 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.48e+00
  chirality pdb=" CA  PHE A 821 "
            pdb=" N   PHE A 821 "
            pdb=" C   PHE A 821 "
            pdb=" CB  PHE A 821 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1999 not shown)

  Planarity restraints: 2382
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 737 "    0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" CG  ASN B 737 "   -0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 737 "    0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 737 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 737 "   -0.016 2.00e-02 2.50e+03   3.19e-02 1.02e+01
        pdb=" CG  ASN A 737 "    0.055 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 737 "   -0.021 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 737 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 460 "   -0.043 5.00e-02 4.00e+02   6.55e-02 6.85e+00
        pdb=" N   PRO A 461 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO A 461 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 461 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 2379 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 3195
        2.80 -     3.32: 10983
        3.32 -     3.85: 21462
        3.85 -     4.37: 25548
        4.37 -     4.90: 43893
  Nonbonded interactions: 105081
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 253 "
            pdb=" O   GLY B 152 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   GLY A 152 "
            pdb=" OG1 THR B 253 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" O   LEU B  13 "
            pdb=" OG  SER B  16 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   LEU A  13 "
            pdb=" OG  SER A  16 "
     model   vdw
     2.320 3.040
  nonbonded pdb=" O   LEU B  82 "
            pdb=" OG1 THR B  86 "
     model   vdw
     2.324 3.040
  ... (remaining 105076 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.020
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.820
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9073
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      :  0.008   0.061  13256  Z= 0.400
  Angle     :  1.000  13.425  18030  Z= 0.593
  Chirality :  0.060   0.243   2002
  Planarity :  0.009   0.093   2382
  Dihedral  : 15.376  90.917   4868
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 17.22 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.18), residues: 1704
  helix: -1.60 (0.17), residues: 582
  sheet:  0.36 (0.36), residues: 206
  loop : -1.12 (0.18), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 773 
 TYR   0.022   0.003   TYR B 130 
 PHE   0.015   0.002   PHE B 546 
 TRP   0.016   0.002   TRP B 750 
 HIS   0.011   0.002   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00754 (13256)
  covalent geometry    : angle       1.00049 (18030)
  hydrogen bonds       : bond        0.23567 (  532)
  hydrogen bonds       : angle       7.47465 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 157
  time to evaluate  : 0.558 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8361 (mmp-170)
REVERT: A  495 ILE cc_start: 0.9244 (mt) cc_final: 0.8753 (mp)
REVERT: A  556 LEU cc_start: 0.9301 (mm) cc_final: 0.9031 (mp)
REVERT: A  611 LYS cc_start: 0.9109 (tttt) cc_final: 0.8830 (ptmt)
REVERT: A  627 TRP cc_start: 0.8415 (t-100) cc_final: 0.8114 (t-100)
REVERT: A  680 MET cc_start: 0.8924 (tpp) cc_final: 0.8451 (tpt)
REVERT: A  682 PHE cc_start: 0.8966 (m-80) cc_final: 0.8556 (m-80)
REVERT: B  240 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8372 (mmp-170)
REVERT: B  495 ILE cc_start: 0.9230 (mt) cc_final: 0.8727 (mp)
REVERT: B  556 LEU cc_start: 0.9307 (mm) cc_final: 0.9043 (mp)
REVERT: B  611 LYS cc_start: 0.9116 (tttt) cc_final: 0.8834 (ptmt)
REVERT: B  627 TRP cc_start: 0.8380 (t-100) cc_final: 0.8126 (t-100)
REVERT: B  680 MET cc_start: 0.8912 (tpp) cc_final: 0.8422 (tpt)
REVERT: B  682 PHE cc_start: 0.8990 (m-80) cc_final: 0.8573 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 161
  average time/residue: 0.8058
  time to fit residues: 138.9661
Evaluate side-chains
  106 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 104
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain B residue  704 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:   20.0000
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 551 HIS
A 655 GLN
A 737 ASN
B 551 HIS
B 655 GLN
B 737 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.087045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.050086 restraints weight = 29032.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 2.66
r_work: 0.2589 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2471 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9045
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13256  Z= 0.146
  Angle     :  0.618   7.768  18030  Z= 0.312
  Chirality :  0.044   0.142   2002
  Planarity :  0.006   0.052   2382
  Dihedral  :  6.288 130.622   1826
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.51 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.41 (0.19), residues: 1704
  helix: -0.06 (0.20), residues: 608
  sheet:  0.51 (0.34), residues: 216
  loop : -0.53 (0.20), residues: 880

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 790 
 TYR   0.023   0.002   TYR B 277 
 PHE   0.013   0.001   PHE A 530 
 TRP   0.011   0.001   TRP B  40 
 HIS   0.004   0.001   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (13256)
  covalent geometry    : angle       0.61825 (18030)
  hydrogen bonds       : bond        0.05290 (  532)
  hydrogen bonds       : angle       5.20453 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 0.542 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9080 (mmt-90) cc_final: 0.8222 (mmm160)
REVERT: A  530 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.7880 (t80)
REVERT: A  556 LEU cc_start: 0.9185 (mm) cc_final: 0.8956 (mp)
REVERT: A  611 LYS cc_start: 0.9099 (tttt) cc_final: 0.8893 (ptmt)
REVERT: A  680 MET cc_start: 0.8997 (tpp) cc_final: 0.8671 (mpp)
REVERT: A  682 PHE cc_start: 0.8633 (m-80) cc_final: 0.8337 (m-80)
REVERT: A  686 PHE cc_start: 0.8581 (m-10) cc_final: 0.8347 (m-10)
REVERT: B  240 ARG cc_start: 0.9077 (mmt-90) cc_final: 0.8228 (mmm160)
REVERT: B  499 MET cc_start: 0.8822 (pmm) cc_final: 0.8546 (pmm)
REVERT: B  530 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7836 (t80)
REVERT: B  556 LEU cc_start: 0.9191 (mm) cc_final: 0.8962 (mp)
REVERT: B  611 LYS cc_start: 0.9094 (tttt) cc_final: 0.8877 (ptmt)
REVERT: B  680 MET cc_start: 0.8995 (tpp) cc_final: 0.8655 (mpp)
REVERT: B  682 PHE cc_start: 0.8662 (m-80) cc_final: 0.8446 (m-80)
REVERT: B  686 PHE cc_start: 0.8578 (m-10) cc_final: 0.8348 (m-10)
REVERT: B  687 MET cc_start: 0.8284 (mtm) cc_final: 0.8072 (mtt)
  outliers start: 34
  outliers final: 14
  residues processed: 128
  average time/residue: 0.6919
  time to fit residues: 96.2563
Evaluate side-chains
  109 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  329 MET
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  527 VAL
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 163 optimal weight:    0.0070
   chunk 132 optimal weight:    0.1980
   chunk 148 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 50 optimal weight:   10.0000
   chunk 89 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   chunk 21 optimal weight:    4.9990
   chunk 105 optimal weight:    0.0870
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
A 737 ASN
B 328 ASN
B 737 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.088621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.051962 restraints weight = 29150.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.2761 rms_B_bonded: 2.67
r_work: 0.2644 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2526 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9002
moved from start:          0.2136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13256  Z= 0.099
  Angle     :  0.553   7.746  18030  Z= 0.272
  Chirality :  0.042   0.166   2002
  Planarity :  0.005   0.047   2382
  Dihedral  :  5.376 104.520   1826
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 17.15 %
    Favored  : 80.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.20), residues: 1704
  helix:  0.64 (0.21), residues: 618
  sheet:  0.43 (0.34), residues: 218
  loop : -0.18 (0.21), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 728 
 TYR   0.024   0.002   TYR B 277 
 PHE   0.011   0.001   PHE A 530 
 TRP   0.024   0.001   TRP B 627 
 HIS   0.003   0.000   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (13256)
  covalent geometry    : angle       0.55257 (18030)
  hydrogen bonds       : bond        0.04003 (  532)
  hydrogen bonds       : angle       4.87683 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.641 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9061 (mmt-90) cc_final: 0.8096 (mmm160)
REVERT: A  530 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: A  556 LEU cc_start: 0.9182 (mm) cc_final: 0.8948 (mp)
REVERT: A  573 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8366 (mmm160)
REVERT: A  680 MET cc_start: 0.9021 (tpp) cc_final: 0.8549 (mpp)
REVERT: A  721 GLN cc_start: 0.9114 (OUTLIER) cc_final: 0.8851 (mp10)
REVERT: B  240 ARG cc_start: 0.9068 (mmt-90) cc_final: 0.8121 (mmm160)
REVERT: B  499 MET cc_start: 0.8747 (pmm) cc_final: 0.8480 (pmm)
REVERT: B  530 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7845 (t80)
REVERT: B  556 LEU cc_start: 0.9185 (mm) cc_final: 0.8952 (mp)
REVERT: B  573 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8308 (mmm160)
REVERT: B  682 PHE cc_start: 0.8653 (m-80) cc_final: 0.8297 (m-80)
REVERT: B  721 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8864 (mp10)
  outliers start: 28
  outliers final: 8
  residues processed: 125
  average time/residue: 0.8776
  time to fit residues: 117.6315
Evaluate side-chains
  102 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 147 optimal weight:   10.0000
   chunk 119 optimal weight:    0.9980
   chunk 10 optimal weight:    4.9990
   chunk 62 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 107 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 121 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    1.7184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.084894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.047653 restraints weight = 29146.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.2645 rms_B_bonded: 2.64
r_work: 0.2523 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2404 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9092
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13256  Z= 0.183
  Angle     :  0.619   8.150  18030  Z= 0.307
  Chirality :  0.046   0.184   2002
  Planarity :  0.005   0.046   2382
  Dihedral  :  4.495  44.337   1826
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 16.71 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.20), residues: 1704
  helix:  0.75 (0.21), residues: 622
  sheet:  0.40 (0.33), residues: 236
  loop : -0.07 (0.22), residues: 846

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 728 
 TYR   0.020   0.002   TYR B 277 
 PHE   0.012   0.001   PHE B  65 
 TRP   0.008   0.001   TRP A 627 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (13256)
  covalent geometry    : angle       0.61902 (18030)
  hydrogen bonds       : bond        0.05267 (  532)
  hydrogen bonds       : angle       4.85473 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 95
  time to evaluate  : 0.448 
Fit side-chains
REVERT: A  240 ARG cc_start: 0.9081 (mmt-90) cc_final: 0.8065 (mmm160)
REVERT: A  499 MET cc_start: 0.8787 (pmm) cc_final: 0.7913 (ptt)
REVERT: A  530 PHE cc_start: 0.8359 (OUTLIER) cc_final: 0.7827 (t80)
REVERT: A  556 LEU cc_start: 0.9183 (mm) cc_final: 0.8972 (mp)
REVERT: A  573 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8322 (mmm160)
REVERT: A  680 MET cc_start: 0.9140 (tpp) cc_final: 0.8486 (mpp)
REVERT: A  721 GLN cc_start: 0.9150 (OUTLIER) cc_final: 0.8862 (mp10)
REVERT: B  240 ARG cc_start: 0.9082 (mmt-90) cc_final: 0.8349 (mmm160)
REVERT: B  530 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.7829 (t80)
REVERT: B  556 LEU cc_start: 0.9171 (mm) cc_final: 0.8956 (mp)
REVERT: B  573 ARG cc_start: 0.8716 (mmm-85) cc_final: 0.8283 (mmm160)
REVERT: B  680 MET cc_start: 0.8912 (mmm) cc_final: 0.8684 (mmm)
REVERT: B  682 PHE cc_start: 0.8779 (m-80) cc_final: 0.8431 (m-80)
REVERT: B  721 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8859 (mp10)
  outliers start: 39
  outliers final: 14
  residues processed: 127
  average time/residue: 0.7411
  time to fit residues: 101.9214
Evaluate side-chains
  108 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   chunk 10 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 116 optimal weight:    0.9990
   chunk 152 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 746 GLN
B 746 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.086179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.049235 restraints weight = 29199.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.2686 rms_B_bonded: 2.66
r_work: 0.2566 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2447 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9061
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13256  Z= 0.116
  Angle     :  0.576   8.606  18030  Z= 0.281
  Chirality :  0.044   0.185   2002
  Planarity :  0.004   0.045   2382
  Dihedral  :  3.866  16.295   1820
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.93 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.64 (0.21), residues: 1704
  helix:  1.17 (0.22), residues: 610
  sheet:  0.40 (0.33), residues: 238
  loop : -0.01 (0.22), residues: 856

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 728 
 TYR   0.021   0.002   TYR B 277 
 PHE   0.016   0.001   PHE A 682 
 TRP   0.009   0.001   TRP A  40 
 HIS   0.003   0.000   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (13256)
  covalent geometry    : angle       0.57628 (18030)
  hydrogen bonds       : bond        0.04180 (  532)
  hydrogen bonds       : angle       4.71402 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 0.539 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9439 (mp)
REVERT: A  240 ARG cc_start: 0.9054 (mmt-90) cc_final: 0.8239 (mmp-170)
REVERT: A  530 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7804 (t80)
REVERT: A  573 ARG cc_start: 0.8782 (mmm-85) cc_final: 0.8343 (mmm160)
REVERT: A  680 MET cc_start: 0.9112 (tpp) cc_final: 0.8480 (mpp)
REVERT: A  682 PHE cc_start: 0.8577 (m-80) cc_final: 0.8334 (m-80)
REVERT: A  721 GLN cc_start: 0.9131 (OUTLIER) cc_final: 0.8850 (mp10)
REVERT: B   57 LEU cc_start: 0.9675 (OUTLIER) cc_final: 0.9393 (mp)
REVERT: B  240 ARG cc_start: 0.9064 (mmt-90) cc_final: 0.8248 (mmp-170)
REVERT: B  499 MET cc_start: 0.8730 (pmm) cc_final: 0.7891 (ptp)
REVERT: B  530 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.7830 (t80)
REVERT: B  573 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8307 (mmm160)
REVERT: B  680 MET cc_start: 0.8823 (mmm) cc_final: 0.8494 (mmm)
REVERT: B  682 PHE cc_start: 0.8692 (m-80) cc_final: 0.8288 (m-80)
REVERT: B  721 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8861 (mp10)
  outliers start: 32
  outliers final: 14
  residues processed: 120
  average time/residue: 0.6945
  time to fit residues: 90.4073
Evaluate side-chains
  107 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  704 GLU
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  704 GLU
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 167 optimal weight:    3.9990
   chunk 146 optimal weight:    6.9990
   chunk 130 optimal weight:    1.9990
   chunk 55 optimal weight:    6.9990
   chunk 106 optimal weight:    5.9990
   chunk 58 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 115 optimal weight:    0.4980
   chunk 38 optimal weight:    2.9990
   overall best weight:    2.2988

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

Flipped N/Q/H residues before XYZ refinement:
A 746 GLN
B 746 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.083875 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.046713 restraints weight = 28984.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.2619 rms_B_bonded: 2.63
r_work: 0.2497 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2378 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9108
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  13256  Z= 0.226
  Angle     :  0.644   8.443  18030  Z= 0.319
  Chirality :  0.047   0.207   2002
  Planarity :  0.005   0.044   2382
  Dihedral  :  4.104  17.962   1820
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 16.79 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.21), residues: 1704
  helix:  1.00 (0.21), residues: 624
  sheet:  0.36 (0.32), residues: 266
  loop :  0.09 (0.23), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 202 
 TYR   0.020   0.002   TYR B 277 
 PHE   0.013   0.002   PHE A 682 
 TRP   0.012   0.001   TRP B  40 
 HIS   0.003   0.001   HIS A 789 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 (13256)
  covalent geometry    : angle       0.64375 (18030)
  hydrogen bonds       : bond        0.05404 (  532)
  hydrogen bonds       : angle       4.85225 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 90
  time to evaluate  : 0.463 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9445 (mp)
REVERT: A  240 ARG cc_start: 0.9076 (mmt-90) cc_final: 0.7983 (mmm160)
REVERT: A  465 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.8803 (mtm)
REVERT: A  499 MET cc_start: 0.8735 (pmm) cc_final: 0.7982 (ptt)
REVERT: A  530 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7838 (t80)
REVERT: A  573 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8339 (mmm160)
REVERT: A  680 MET cc_start: 0.9108 (tpp) cc_final: 0.8457 (mpp)
REVERT: A  682 PHE cc_start: 0.8599 (m-80) cc_final: 0.8342 (m-80)
REVERT: A  721 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8885 (mp10)
REVERT: B   57 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9417 (mp)
REVERT: B  240 ARG cc_start: 0.9090 (mmt-90) cc_final: 0.7976 (mmm160)
REVERT: B  499 MET cc_start: 0.8722 (pmm) cc_final: 0.7991 (ptt)
REVERT: B  530 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7809 (t80)
REVERT: B  573 ARG cc_start: 0.8748 (mmm-85) cc_final: 0.8290 (mmm160)
REVERT: B  680 MET cc_start: 0.8838 (mmm) cc_final: 0.8524 (mmm)
REVERT: B  682 PHE cc_start: 0.8660 (m-80) cc_final: 0.8196 (m-80)
REVERT: B  721 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8892 (mp10)
  outliers start: 46
  outliers final: 20
  residues processed: 119
  average time/residue: 0.6003
  time to fit residues: 78.4159
Evaluate side-chains
  112 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 85
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  407 ASN
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 145 optimal weight:    6.9990
   chunk 152 optimal weight:   20.0000
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    0.3980
   chunk 72 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 789 HIS
B 746 GLN
B 789 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.084946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.047965 restraints weight = 28897.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2657 rms_B_bonded: 2.64
r_work: 0.2539 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2422 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9083
moved from start:          0.2625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13256  Z= 0.142
  Angle     :  0.594   8.744  18030  Z= 0.290
  Chirality :  0.044   0.184   2002
  Planarity :  0.004   0.043   2382
  Dihedral  :  3.967  16.934   1820
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.00 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.80 (0.21), residues: 1704
  helix:  1.27 (0.22), residues: 612
  sheet:  0.49 (0.32), residues: 256
  loop :  0.10 (0.23), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 728 
 TYR   0.020   0.002   TYR B 277 
 PHE   0.013   0.001   PHE A 682 
 TRP   0.012   0.001   TRP B  40 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (13256)
  covalent geometry    : angle       0.59396 (18030)
  hydrogen bonds       : bond        0.04533 (  532)
  hydrogen bonds       : angle       4.74963 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 91
  time to evaluate  : 0.431 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9695 (OUTLIER) cc_final: 0.9445 (mp)
REVERT: A  240 ARG cc_start: 0.9056 (mmt-90) cc_final: 0.7907 (mmm160)
REVERT: A  465 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.8786 (mtm)
REVERT: A  499 MET cc_start: 0.8698 (pmm) cc_final: 0.7945 (ptt)
REVERT: A  530 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7832 (t80)
REVERT: A  573 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8385 (mmm160)
REVERT: A  680 MET cc_start: 0.9085 (tpp) cc_final: 0.8453 (mpp)
REVERT: A  682 PHE cc_start: 0.8540 (m-80) cc_final: 0.8168 (m-80)
REVERT: A  687 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8138 (ptp)
REVERT: A  721 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8810 (mp10)
REVERT: A  825 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8673 (ptt90)
REVERT: B   57 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9458 (mp)
REVERT: B  240 ARG cc_start: 0.9055 (mmt-90) cc_final: 0.7905 (mmm160)
REVERT: B  499 MET cc_start: 0.8715 (pmm) cc_final: 0.7983 (ptt)
REVERT: B  530 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7784 (t80)
REVERT: B  573 ARG cc_start: 0.8756 (mmm-85) cc_final: 0.8301 (mmm160)
REVERT: B  680 MET cc_start: 0.8820 (mmm) cc_final: 0.8464 (mpp)
REVERT: B  682 PHE cc_start: 0.8639 (m-80) cc_final: 0.8028 (m-80)
REVERT: B  721 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8811 (mp10)
REVERT: B  746 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8261 (tp40)
REVERT: B  825 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8681 (ptt90)
  outliers start: 37
  outliers final: 15
  residues processed: 118
  average time/residue: 0.6076
  time to fit residues: 78.6385
Evaluate side-chains
  113 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  825 ARG
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  506 MET
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  746 GLN
Chi-restraints excluded: chain B residue  825 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 132 optimal weight:    5.9990
   chunk 55 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 148 optimal weight:    0.0970
   chunk 165 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 143 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 746 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.084881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.047988 restraints weight = 28935.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.2647 rms_B_bonded: 2.65
r_work: 0.2526 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.2407 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9080
moved from start:          0.2665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13256  Z= 0.141
  Angle     :  0.597   8.759  18030  Z= 0.293
  Chirality :  0.044   0.182   2002
  Planarity :  0.004   0.043   2382
  Dihedral  :  3.912  16.998   1820
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 16.93 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.21), residues: 1704
  helix:  1.32 (0.22), residues: 612
  sheet:  0.50 (0.32), residues: 256
  loop :  0.09 (0.23), residues: 836

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 728 
 TYR   0.021   0.002   TYR A 277 
 PHE   0.012   0.001   PHE A 682 
 TRP   0.011   0.001   TRP B  40 
 HIS   0.002   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (13256)
  covalent geometry    : angle       0.59663 (18030)
  hydrogen bonds       : bond        0.04494 (  532)
  hydrogen bonds       : angle       4.71091 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 89
  time to evaluate  : 0.531 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9691 (OUTLIER) cc_final: 0.9439 (mp)
REVERT: A  240 ARG cc_start: 0.9070 (mmt-90) cc_final: 0.7996 (mmm160)
REVERT: A  465 MET cc_start: 0.9519 (OUTLIER) cc_final: 0.8739 (mtm)
REVERT: A  499 MET cc_start: 0.8684 (pmm) cc_final: 0.7947 (ptt)
REVERT: A  530 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7855 (t80)
REVERT: A  573 ARG cc_start: 0.8816 (mmm-85) cc_final: 0.8412 (mmm160)
REVERT: A  680 MET cc_start: 0.9084 (tpp) cc_final: 0.8477 (mpp)
REVERT: A  682 PHE cc_start: 0.8487 (m-80) cc_final: 0.8077 (m-80)
REVERT: A  687 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8183 (ptp)
REVERT: A  721 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8802 (mp10)
REVERT: A  825 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8682 (ptt90)
REVERT: B   57 LEU cc_start: 0.9678 (OUTLIER) cc_final: 0.9447 (mp)
REVERT: B  240 ARG cc_start: 0.9066 (mmt-90) cc_final: 0.7991 (mmm160)
REVERT: B  465 MET cc_start: 0.9516 (OUTLIER) cc_final: 0.8733 (mtm)
REVERT: B  499 MET cc_start: 0.8716 (pmm) cc_final: 0.8009 (ptt)
REVERT: B  530 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7814 (t80)
REVERT: B  573 ARG cc_start: 0.8793 (mmm-85) cc_final: 0.8378 (mmm160)
REVERT: B  680 MET cc_start: 0.8766 (mmm) cc_final: 0.8432 (mpp)
REVERT: B  682 PHE cc_start: 0.8588 (m-80) cc_final: 0.8201 (m-80)
REVERT: B  687 MET cc_start: 0.8179 (mpt) cc_final: 0.7796 (mpt)
REVERT: B  721 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8814 (mp10)
REVERT: B  746 GLN cc_start: 0.8639 (OUTLIER) cc_final: 0.8158 (tp40)
REVERT: B  825 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8679 (ptt90)
  outliers start: 36
  outliers final: 18
  residues processed: 117
  average time/residue: 0.6163
  time to fit residues: 79.3272
Evaluate side-chains
  116 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 86
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  538 LEU
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  825 ARG
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  506 MET
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  746 GLN
Chi-restraints excluded: chain B residue  825 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 155 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 26 optimal weight:    5.9990
   chunk 29 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 108 optimal weight:    0.0570
   chunk 56 optimal weight:    3.9990
   chunk 145 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    2.4106

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

Flipped N/Q/H residues before XYZ refinement:
** A 737 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 746 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.083527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.046450 restraints weight = 29298.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.2616 rms_B_bonded: 2.65
r_work: 0.2494 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2377 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9117
moved from start:          0.2699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  13256  Z= 0.236
  Angle     :  0.661   9.055  18030  Z= 0.327
  Chirality :  0.047   0.172   2002
  Planarity :  0.005   0.043   2382
  Dihedral  :  4.136  18.124   1820
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.37 %
    Favored  : 79.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.21), residues: 1704
  helix:  1.06 (0.21), residues: 624
  sheet:  0.38 (0.31), residues: 266
  loop :  0.11 (0.23), residues: 814

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 728 
 TYR   0.021   0.002   TYR B 277 
 PHE   0.013   0.002   PHE A  65 
 TRP   0.009   0.001   TRP A  40 
 HIS   0.003   0.001   HIS A 331 

Details of bonding type rmsd
  covalent geometry    : bond        0.00572 (13256)
  covalent geometry    : angle       0.66124 (18030)
  hydrogen bonds       : bond        0.05417 (  532)
  hydrogen bonds       : angle       4.83636 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 88
  time to evaluate  : 0.550 
Fit side-chains
REVERT: A   57 LEU cc_start: 0.9701 (OUTLIER) cc_final: 0.9453 (mp)
REVERT: A  240 ARG cc_start: 0.9095 (mmt-90) cc_final: 0.7979 (mmm160)
REVERT: A  465 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.8778 (mtm)
REVERT: A  499 MET cc_start: 0.8747 (pmm) cc_final: 0.8071 (ptt)
REVERT: A  530 PHE cc_start: 0.8358 (OUTLIER) cc_final: 0.7831 (t80)
REVERT: A  573 ARG cc_start: 0.8814 (mmm-85) cc_final: 0.8399 (mmm160)
REVERT: A  680 MET cc_start: 0.9072 (tpp) cc_final: 0.8470 (mpp)
REVERT: A  682 PHE cc_start: 0.8438 (m-80) cc_final: 0.8076 (m-80)
REVERT: A  687 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8218 (ptp)
REVERT: A  721 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8893 (mp10)
REVERT: A  825 ARG cc_start: 0.9121 (OUTLIER) cc_final: 0.8656 (ptt90)
REVERT: B   57 LEU cc_start: 0.9702 (OUTLIER) cc_final: 0.9434 (mp)
REVERT: B  240 ARG cc_start: 0.9091 (mmt-90) cc_final: 0.7979 (mmm160)
REVERT: B  465 MET cc_start: 0.9546 (OUTLIER) cc_final: 0.8791 (mtm)
REVERT: B  499 MET cc_start: 0.8778 (pmm) cc_final: 0.8141 (ptt)
REVERT: B  530 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7793 (t80)
REVERT: B  573 ARG cc_start: 0.8796 (mmm-85) cc_final: 0.8377 (mmm160)
REVERT: B  680 MET cc_start: 0.8646 (mmm) cc_final: 0.8415 (mpp)
REVERT: B  682 PHE cc_start: 0.8469 (m-80) cc_final: 0.8106 (m-80)
REVERT: B  687 MET cc_start: 0.8149 (mpt) cc_final: 0.7687 (mpt)
REVERT: B  721 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8885 (mp10)
REVERT: B  825 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8666 (ptt90)
  outliers start: 38
  outliers final: 19
  residues processed: 116
  average time/residue: 0.5867
  time to fit residues: 74.9036
Evaluate side-chains
  118 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue   91 VAL
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  407 ASN
Chi-restraints excluded: chain A residue  465 MET
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  825 ARG
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue   91 VAL
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  407 ASN
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  825 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 81 optimal weight:    0.0670
   chunk 152 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.7720

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

Flipped N/Q/H residues before XYZ refinement:
A 746 GLN
** B 746 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 = 0.3500 r_free = 0.3500 target = 0.085363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.048493 restraints weight = 29145.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.2672 rms_B_bonded: 2.67
r_work: 0.2553 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2435 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9072
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13256  Z= 0.116
  Angle     :  0.597   9.321  18030  Z= 0.289
  Chirality :  0.044   0.195   2002
  Planarity :  0.004   0.043   2382
  Dihedral  :  3.884  17.211   1820
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.38 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.21), residues: 1704
  helix:  1.40 (0.22), residues: 612
  sheet:  0.40 (0.32), residues: 260
  loop :  0.11 (0.23), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG B 728 
 TYR   0.021   0.002   TYR B 277 
 PHE   0.012   0.001   PHE A 682 
 TRP   0.011   0.001   TRP A  40 
 HIS   0.002   0.000   HIS B 580 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13256)
  covalent geometry    : angle       0.59729 (18030)
  hydrogen bonds       : bond        0.04129 (  532)
  hydrogen bonds       : angle       4.68982 ( 1452)

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

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

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3408 Ramachandran restraints generated.
    1704 Oldfield, 0 Emsley, 1704 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 LEU cc_start: 0.9682 (OUTLIER) cc_final: 0.9430 (mp)
REVERT: A  240 ARG cc_start: 0.9058 (mmt-90) cc_final: 0.7981 (mmm160)
REVERT: A  499 MET cc_start: 0.8694 (pmm) cc_final: 0.8027 (ptt)
REVERT: A  530 PHE cc_start: 0.8331 (OUTLIER) cc_final: 0.7821 (t80)
REVERT: A  573 ARG cc_start: 0.8825 (mmm-85) cc_final: 0.8405 (mmm160)
REVERT: A  680 MET cc_start: 0.9054 (tpp) cc_final: 0.8470 (mpp)
REVERT: A  682 PHE cc_start: 0.8425 (m-80) cc_final: 0.8043 (m-80)
REVERT: A  687 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8340 (ptp)
REVERT: A  721 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8832 (mp10)
REVERT: A  746 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8277 (tp40)
REVERT: A  825 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8692 (ptt90)
REVERT: B   57 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9460 (mp)
REVERT: B  240 ARG cc_start: 0.9053 (mmt-90) cc_final: 0.7966 (mmm160)
REVERT: B  499 MET cc_start: 0.8724 (pmm) cc_final: 0.8111 (ptt)
REVERT: B  506 MET cc_start: 0.8896 (mtp) cc_final: 0.8688 (mtm)
REVERT: B  530 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.7839 (t80)
REVERT: B  573 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8403 (mmm160)
REVERT: B  682 PHE cc_start: 0.8444 (m-80) cc_final: 0.8070 (m-80)
REVERT: B  687 MET cc_start: 0.8257 (OUTLIER) cc_final: 0.7820 (mpt)
REVERT: B  721 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8815 (mp10)
REVERT: B  825 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8720 (ptt90)
  outliers start: 26
  outliers final: 14
  residues processed: 106
  average time/residue: 0.6738
  time to fit residues: 77.9020
Evaluate side-chains
  109 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 VAL
Chi-restraints excluded: chain A residue   57 LEU
Chi-restraints excluded: chain A residue  111 VAL
Chi-restraints excluded: chain A residue  112 SER
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  530 PHE
Chi-restraints excluded: chain A residue  687 MET
Chi-restraints excluded: chain A residue  702 ILE
Chi-restraints excluded: chain A residue  721 GLN
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  746 GLN
Chi-restraints excluded: chain A residue  825 ARG
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   57 LEU
Chi-restraints excluded: chain B residue  105 THR
Chi-restraints excluded: chain B residue  111 VAL
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  530 PHE
Chi-restraints excluded: chain B residue  538 LEU
Chi-restraints excluded: chain B residue  687 MET
Chi-restraints excluded: chain B residue  702 ILE
Chi-restraints excluded: chain B residue  721 GLN
Chi-restraints excluded: chain B residue  743 VAL
Chi-restraints excluded: chain B residue  825 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 170
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 34 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 138 optimal weight:    8.9990
   chunk 94 optimal weight:    3.9990
   chunk 146 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 144 optimal weight:    0.0030
   chunk 10 optimal weight:    4.9990
   overall best weight:    0.9196

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

Flipped N/Q/H residues before XYZ refinement:
A 746 GLN
B 746 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.085307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.048511 restraints weight = 29076.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.2681 rms_B_bonded: 2.67
r_work: 0.2564 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2448 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9076
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13256  Z= 0.121
  Angle     :  0.601   9.836  18030  Z= 0.290
  Chirality :  0.044   0.192   2002
  Planarity :  0.004   0.044   2382
  Dihedral  :  3.879  17.068   1820
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 17.87 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.21), residues: 1704
  helix:  1.28 (0.22), residues: 626
  sheet:  0.45 (0.32), residues: 256
  loop :  0.15 (0.23), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 728 
 TYR   0.021   0.002   TYR A 277 
 PHE   0.012   0.001   PHE A 682 
 TRP   0.011   0.001   TRP A  40 
 HIS   0.002   0.000   HIS B  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (13256)
  covalent geometry    : angle       0.60096 (18030)
  hydrogen bonds       : bond        0.04159 (  532)
  hydrogen bonds       : angle       4.67606 ( 1452)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6644.36 seconds
wall clock time: 113 minutes 35.17 seconds (6815.17 seconds total)