Starting phenix.real_space_refine
on Thu Sep 18 10:42:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7bx8_30236/09_2025/7bx8_30236.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7bx8_30236/09_2025/7bx8_30236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7bx8_30236/09_2025/7bx8_30236.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7bx8_30236/09_2025/7bx8_30236.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7bx8_30236/09_2025/7bx8_30236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7bx8_30236/09_2025/7bx8_30236.map"
  }
  resolution = 3.6
  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=   0.008 sd=   0.083
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      68      5.16       5
     C   10508      2.51       5
     N    2818      2.21       5
     O    2910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 98 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16304
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 7655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1038, 7655
          Classifications: {'peptide': 1038}
          Incomplete info: {'truncation_to_alanine': 60}
          Link IDs: {'PTRANS': 75, 'TRANS': 962}
          Chain breaks: 2
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 246
          Unresolved non-hydrogen angles: 309
          Unresolved non-hydrogen dihedrals: 202
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 10, 'ASP:plan': 13, 'PHE:plan': 3, 'GLU:plan': 11, 'GLN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 188
    Chain: "C"
      Number of atoms: 497
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 497
          Classifications: {'peptide': 78}
          Incomplete info: {'truncation_to_alanine': 29}
          Link IDs: {'PTRANS': 3, 'TRANS': 74}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 97
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 72
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 63
  Restraints were copied for chains:
    B, D
  Time building chain proxies: 7.67, per 1000 atoms: 0.47
  Number of scatterers: 16304
  At special positions: 0
  Unit cell: (127.1, 124.64, 139.4, 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      68     16.00
     O    2910      8.00
     N    2818      7.00
     C   10508      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 678.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4084

  Finding SS restraints...
    Secondary structure from input PDB file:
      80 helices and 24 sheets defined
      43.5% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 43
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 219 through 245
    Processing helix  chain 'A' and resid 263 through 280
      removed outlier: 4.094A  pdb=" N   MET A 273 " --> pdb=" O   VAL A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 300
      removed outlier: 3.792A  pdb=" N   MET A 292 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLU A 297 " --> pdb=" O   ALA A 293 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   HIS A 298 " --> pdb=" O   ARG A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 327
    Processing helix  chain 'A' and resid 332 through 337
      removed outlier: 3.884A  pdb=" N   ARG A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 354
      removed outlier: 3.642A  pdb=" N   ALA A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ARG A 353 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 360
    Processing helix  chain 'A' and resid 360 through 366
    Processing helix  chain 'A' and resid 366 through 385
      removed outlier: 3.868A  pdb=" N   MET A 370 " --> pdb=" O   SER A 366 " (cutoff:3.500A)
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 390 through 412
      removed outlier: 3.778A  pdb=" N   ILE A 394 " --> pdb=" O   PRO A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 431
      removed outlier: 3.606A  pdb=" N   THR A 422 " --> pdb=" O   ALA A 418 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN A 431 " --> pdb=" O   THR A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 443
      removed outlier: 4.246A  pdb=" N   VAL A 438 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 456
      removed outlier: 3.886A  pdb=" N   ILE A 448 " --> pdb=" O   GLY A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 474
      Proline residue:  A 467  - end of helix
    Processing helix  chain 'A' and resid 474 through 480
      removed outlier: 3.620A  pdb=" N   VAL A 478 " --> pdb=" O   VAL A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 499
    Processing helix  chain 'A' and resid 527 through 532
      removed outlier: 3.535A  pdb=" N   THR A 532 " --> pdb=" O   ALA A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 546
    Processing helix  chain 'A' and resid 553 through 569
      removed outlier: 3.798A  pdb=" N   ILE A 564 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   MET A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE A 569 " --> pdb=" O   PHE A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 586
    Processing helix  chain 'A' and resid 587 through 600
      removed outlier: 3.500A  pdb=" N   ALA A 591 " --> pdb=" O   ALA A 587 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA A 593 " --> pdb=" O   GLY A 589 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL A 598 " --> pdb=" O   ALA A 594 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 627
      removed outlier: 3.523A  pdb=" N   ARG A 611 " --> pdb=" O   SER A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 676
      removed outlier: 3.530A  pdb=" N   LEU A 672 " --> pdb=" O   TRP A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 687
      removed outlier: 3.793A  pdb=" N   ASP A 684 " --> pdb=" O   SER A 680 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 689 through 713
      removed outlier: 3.921A  pdb=" N   VAL A 693 " --> pdb=" O   ALA A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 726
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing helix  chain 'A' and resid 793 through 797
      removed outlier: 3.568A  pdb=" N   TRP A 796 " --> pdb=" O   ASP A 793 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 855
    Processing helix  chain 'A' and resid 958 through 962
    Processing helix  chain 'A' and resid 1001 through 1008
    Processing helix  chain 'A' and resid 1008 through 1013
      removed outlier: 3.562A  pdb=" N   TRP A1012 " --> pdb=" O   SER A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1018
      removed outlier: 3.610A  pdb=" N   GLY A1018 " --> pdb=" O   GLY A1015 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1020 through 1028
      removed outlier: 3.574A  pdb=" N   ASP A1025 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   LEU A1026 " --> pdb=" O   GLY A1022 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 6 through 20
    Processing helix  chain 'C' and resid 43 through 55
      removed outlier: 3.887A  pdb=" N   ILE C  47 " --> pdb=" O   SER C  43 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 67
      removed outlier: 3.786A  pdb=" N   ALA C  65 " --> pdb=" O   ASP C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 78
      removed outlier: 4.007A  pdb=" N   VAL C  74 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 43
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 219 through 245
    Processing helix  chain 'B' and resid 263 through 280
      removed outlier: 4.093A  pdb=" N   MET B 273 " --> pdb=" O   VAL B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 285 through 300
      removed outlier: 3.793A  pdb=" N   MET B 292 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   GLU B 297 " --> pdb=" O   ALA B 293 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   HIS B 298 " --> pdb=" O   ARG B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 327
    Processing helix  chain 'B' and resid 332 through 337
      removed outlier: 3.883A  pdb=" N   ARG B 337 " --> pdb=" O   SER B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 354
      removed outlier: 3.641A  pdb=" N   ALA B 344 " --> pdb=" O   ASP B 340 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ARG B 353 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 355 through 360
    Processing helix  chain 'B' and resid 360 through 366
    Processing helix  chain 'B' and resid 366 through 385
      removed outlier: 3.867A  pdb=" N   MET B 370 " --> pdb=" O   SER B 366 " (cutoff:3.500A)
      Proline residue:  B 383  - end of helix
    Processing helix  chain 'B' and resid 390 through 412
      removed outlier: 3.777A  pdb=" N   ILE B 394 " --> pdb=" O   PRO B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 431
      removed outlier: 3.606A  pdb=" N   THR B 422 " --> pdb=" O   ALA B 418 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLN B 431 " --> pdb=" O   THR B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 443
      removed outlier: 4.246A  pdb=" N   VAL B 438 " --> pdb=" O   GLY B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 456
      removed outlier: 3.886A  pdb=" N   ILE B 448 " --> pdb=" O   GLY B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 474
      Proline residue:  B 467  - end of helix
    Processing helix  chain 'B' and resid 474 through 480
      removed outlier: 3.620A  pdb=" N   VAL B 478 " --> pdb=" O   VAL B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 499
    Processing helix  chain 'B' and resid 527 through 532
      removed outlier: 3.535A  pdb=" N   THR B 532 " --> pdb=" O   ALA B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 546
    Processing helix  chain 'B' and resid 553 through 569
      removed outlier: 3.798A  pdb=" N   ILE B 564 " --> pdb=" O   LEU B 560 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   MET B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE B 569 " --> pdb=" O   PHE B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 583 through 586
    Processing helix  chain 'B' and resid 587 through 600
      removed outlier: 3.500A  pdb=" N   ALA B 591 " --> pdb=" O   ALA B 587 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA B 593 " --> pdb=" O   GLY B 589 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL B 598 " --> pdb=" O   ALA B 594 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 607 through 627
      removed outlier: 3.524A  pdb=" N   ARG B 611 " --> pdb=" O   SER B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 653 through 676
      removed outlier: 3.530A  pdb=" N   LEU B 672 " --> pdb=" O   TRP B 668 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 687
      removed outlier: 3.792A  pdb=" N   ASP B 684 " --> pdb=" O   SER B 680 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 689 through 713
      removed outlier: 3.922A  pdb=" N   VAL B 693 " --> pdb=" O   ALA B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 718 through 726
    Processing helix  chain 'B' and resid 727 through 729
      No H-bonds generated for 'chain 'B' and resid 727 through 729'
    Processing helix  chain 'B' and resid 793 through 797
      removed outlier: 3.568A  pdb=" N   TRP B 796 " --> pdb=" O   ASP B 793 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 850 through 855
    Processing helix  chain 'B' and resid 958 through 962
    Processing helix  chain 'B' and resid 1001 through 1008
    Processing helix  chain 'B' and resid 1008 through 1013
      removed outlier: 3.561A  pdb=" N   TRP B1012 " --> pdb=" O   SER B1008 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1014 through 1018
      removed outlier: 3.609A  pdb=" N   GLY B1018 " --> pdb=" O   GLY B1015 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1020 through 1028
      removed outlier: 3.574A  pdb=" N   ASP B1025 " --> pdb=" O   LEU B1021 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   LEU B1026 " --> pdb=" O   GLY B1022 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 6 through 20
    Processing helix  chain 'D' and resid 43 through 55
      removed outlier: 3.887A  pdb=" N   ILE D  47 " --> pdb=" O   SER D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 60 through 67
      removed outlier: 3.786A  pdb=" N   ALA D  65 " --> pdb=" O   ASP D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 70 through 78
      removed outlier: 4.007A  pdb=" N   VAL D  74 " --> pdb=" O   VAL D  70 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 218
      removed outlier: 3.615A  pdb=" N   HIS A 217 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL A  49 " --> pdb=" O   SER A1070 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER A1070 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 209
    Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192
    Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 82
    Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 100
      removed outlier: 4.152A  pdb=" N   PHE A  99 " --> pdb=" O   VAL A 116 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL A 116 " --> pdb=" O   PHE A  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 956 through 957
    Processing sheet with id=AA7, first strand: chain 'A' and resid 749 through 750
      removed outlier: 4.268A  pdb=" N   THR A 749 " --> pdb=" O   GLU A 845 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 930 " --> pdb=" O   TYR A 844 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA A 929 " --> pdb=" O   ALA A 888 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR A 889 " --> pdb=" O   VAL A 897 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 826 through 827
    Processing sheet with id=AA9, first strand: chain 'A' and resid 859 through 862
    Processing sheet with id=AB1, first strand: chain 'A' and resid 870 through 871
      removed outlier: 3.507A  pdb=" N   GLY A 870 " --> pdb=" O   THR A 878 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   THR A 878 " --> pdb=" O   GLY A 870 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 986 through 987
    Processing sheet with id=AB3, first strand: chain 'A' and resid 996 through 999
    Processing sheet with id=AB4, first strand: chain 'B' and resid 216 through 218
      removed outlier: 3.615A  pdb=" N   HIS B 217 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   VAL B  49 " --> pdb=" O   SER B1070 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER B1070 " --> pdb=" O   VAL B  49 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 207 through 209
    Processing sheet with id=AB6, first strand: chain 'B' and resid 191 through 192
    Processing sheet with id=AB7, first strand: chain 'B' and resid 81 through 82
    Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 100
      removed outlier: 4.152A  pdb=" N   PHE B  99 " --> pdb=" O   VAL B 116 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL B 116 " --> pdb=" O   PHE B  99 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 956 through 957
    Processing sheet with id=AC1, first strand: chain 'B' and resid 749 through 750
      removed outlier: 4.267A  pdb=" N   THR B 749 " --> pdb=" O   GLU B 845 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL B 930 " --> pdb=" O   TYR B 844 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ALA B 929 " --> pdb=" O   ALA B 888 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   THR B 889 " --> pdb=" O   VAL B 897 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 826 through 827
    Processing sheet with id=AC3, first strand: chain 'B' and resid 859 through 862
    Processing sheet with id=AC4, first strand: chain 'B' and resid 870 through 871
      removed outlier: 3.506A  pdb=" N   GLY B 870 " --> pdb=" O   THR B 878 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR B 878 " --> pdb=" O   GLY B 870 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC4
    Processing sheet with id=AC5, first strand: chain 'B' and resid 986 through 987
    Processing sheet with id=AC6, first strand: chain 'B' and resid 996 through 999

    660 hydrogen bonds defined for protein.
    1884 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.03

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 2623
        1.32 -     1.44: 4387
        1.44 -     1.56: 9558
        1.56 -     1.69: 2
        1.69 -     1.81: 120
  Bond restraints: 16690
  Sorted by residual:
  bond pdb=" N   ASN B 637 "
       pdb=" CA  ASN B 637 "
    ideal  model  delta    sigma   weight residual
    1.457  1.407  0.050 1.29e-02 6.01e+03 1.51e+01
  bond pdb=" N   ASN A 637 "
       pdb=" CA  ASN A 637 "
    ideal  model  delta    sigma   weight residual
    1.457  1.407  0.050 1.29e-02 6.01e+03 1.50e+01
  bond pdb=" C   ASN A 637 "
       pdb=" O   ASN A 637 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.042 1.26e-02 6.30e+03 1.11e+01
  bond pdb=" C   ASN B 637 "
       pdb=" O   ASN B 637 "
    ideal  model  delta    sigma   weight residual
    1.235  1.193  0.042 1.26e-02 6.30e+03 1.10e+01
  bond pdb=" N   LYS A 577 "
       pdb=" CA  LYS A 577 "
    ideal  model  delta    sigma   weight residual
    1.461  1.431  0.030 1.20e-02 6.94e+03 6.25e+00
  ... (remaining 16685 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 21695
        2.59 -     5.17: 963
        5.17 -     7.76: 188
        7.76 -    10.35: 55
       10.35 -    12.93: 9
  Bond angle restraints: 22910
  Sorted by residual:
  angle pdb=" N   PRO B 315 "
        pdb=" CA  PRO B 315 "
        pdb=" C   PRO B 315 "
      ideal   model   delta    sigma   weight residual
     113.40  103.57    9.83 1.34e+00 5.57e-01 5.38e+01
  angle pdb=" N   PRO A 315 "
        pdb=" CA  PRO A 315 "
        pdb=" C   PRO A 315 "
      ideal   model   delta    sigma   weight residual
     113.40  103.58    9.82 1.34e+00 5.57e-01 5.37e+01
  angle pdb=" N   GLY D  21 "
        pdb=" CA  GLY D  21 "
        pdb=" C   GLY D  21 "
      ideal   model   delta    sigma   weight residual
     113.48  124.11  -10.63 1.46e+00 4.69e-01 5.31e+01
  angle pdb=" N   GLY C  21 "
        pdb=" CA  GLY C  21 "
        pdb=" C   GLY C  21 "
      ideal   model   delta    sigma   weight residual
     113.48  124.10  -10.62 1.46e+00 4.69e-01 5.29e+01
  angle pdb=" N   PHE D  33 "
        pdb=" CA  PHE D  33 "
        pdb=" C   PHE D  33 "
      ideal   model   delta    sigma   weight residual
     111.11  119.72   -8.61 1.20e+00 6.94e-01 5.14e+01
  ... (remaining 22905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.94: 8855
       16.94 -    33.89: 737
       33.89 -    50.83: 156
       50.83 -    67.77: 40
       67.77 -    84.72: 10
  Dihedral angle restraints: 9798
    sinusoidal: 3436
      harmonic: 6362
  Sorted by residual:
  dihedral pdb=" CA  VAL B  98 "
           pdb=" C   VAL B  98 "
           pdb=" N   PHE B  99 "
           pdb=" CA  PHE B  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.44   27.56     0      5.00e+00 4.00e-02 3.04e+01
  dihedral pdb=" CA  VAL A  98 "
           pdb=" C   VAL A  98 "
           pdb=" N   PHE A  99 "
           pdb=" CA  PHE A  99 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.47   27.53     0      5.00e+00 4.00e-02 3.03e+01
  dihedral pdb=" CA  LEU B 859 "
           pdb=" C   LEU B 859 "
           pdb=" N   VAL B 860 "
           pdb=" CA  VAL B 860 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.12   23.88     0      5.00e+00 4.00e-02 2.28e+01
  ... (remaining 9795 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 2146
       0.084 -    0.169: 486
       0.169 -    0.253: 94
       0.253 -    0.338: 18
       0.338 -    0.422: 10
  Chirality restraints: 2754
  Sorted by residual:
  chirality pdb=" CA  PHE D  33 "
            pdb=" N   PHE D  33 "
            pdb=" C   PHE D  33 "
            pdb=" CB  PHE D  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" CA  PHE C  33 "
            pdb=" N   PHE C  33 "
            pdb=" C   PHE C  33 "
            pdb=" CB  PHE C  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.45e+00
  chirality pdb=" CB  THR B 910 "
            pdb=" CA  THR B 910 "
            pdb=" OG1 THR B 910 "
            pdb=" CG2 THR B 910 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.18    0.37 2.00e-01 2.50e+01 3.43e+00
  ... (remaining 2751 not shown)

  Planarity restraints: 2922
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 313 "   -0.028 2.00e-02 2.50e+03   5.88e-02 3.45e+01
        pdb=" C   GLU B 313 "    0.101 2.00e-02 2.50e+03
        pdb=" O   GLU B 313 "   -0.041 2.00e-02 2.50e+03
        pdb=" N   ASP B 314 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 313 "   -0.028 2.00e-02 2.50e+03   5.87e-02 3.45e+01
        pdb=" C   GLU A 313 "    0.101 2.00e-02 2.50e+03
        pdb=" O   GLU A 313 "   -0.041 2.00e-02 2.50e+03
        pdb=" N   ASP A 314 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 823 "    0.083 5.00e-02 4.00e+02   1.22e-01 2.40e+01
        pdb=" N   PRO A 824 "   -0.212 5.00e-02 4.00e+02
        pdb=" CA  PRO A 824 "    0.066 5.00e-02 4.00e+02
        pdb=" CD  PRO A 824 "    0.063 5.00e-02 4.00e+02
  ... (remaining 2919 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 4811
        2.82 -     3.34: 15751
        3.34 -     3.86: 26914
        3.86 -     4.38: 29559
        4.38 -     4.90: 51167
  Nonbonded interactions: 128202
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 157 "
            pdb=" O   TYR A 180 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG1 THR B 157 "
            pdb=" O   TYR B 180 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG1 THR A 867 "
            pdb=" OD1 ASP A 943 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG1 THR B 867 "
            pdb=" OD1 ASP B 943 "
     model   vdw
     2.300 3.040
  nonbonded pdb=" O   LEU B 802 "
            pdb=" OG1 THR B 811 "
     model   vdw
     2.312 3.040
  ... (remaining 128197 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'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     18.870
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
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   0.098  16690  Z= 0.366
  Angle     :  1.308  12.933  22910  Z= 0.763
  Chirality :  0.078   0.422   2754
  Planarity :  0.011   0.122   2922
  Dihedral  : 13.917  84.718   5714
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  : 11.55 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.30 %
    Favored  : 87.33 %
  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: -4.54 (0.14), residues: 2216
  helix: -2.64 (0.12), residues: 846
  sheet: -3.12 (0.30), residues: 218
  loop : -3.33 (0.16), residues: 1152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 213 
 TYR   0.037   0.002   TYR D  76 
 PHE   0.034   0.003   PHE B  99 
 TRP   0.018   0.003   TRP B1041 
 HIS   0.014   0.002   HIS B1069 

Details of bonding type rmsd
  covalent geometry    : bond        0.00809 (16690)
  covalent geometry    : angle       1.30847 (22910)
  hydrogen bonds       : bond        0.15434 (  660)
  hydrogen bonds       : angle       8.09332 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 375
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  202 GLN cc_start: 0.7489 (tm-30) cc_final: 0.7187 (tm-30)
REVERT: A  255 ILE cc_start: 0.9101 (mp) cc_final: 0.8776 (mp)
REVERT: A  386 ASN cc_start: 0.8695 (t0) cc_final: 0.8327 (t0)
REVERT: A  554 ARG cc_start: 0.7272 (tmm-80) cc_final: 0.6772 (ttt90)
REVERT: A  565 PHE cc_start: 0.8650 (m-80) cc_final: 0.8425 (m-80)
REVERT: A  592 MET cc_start: 0.9124 (tpp) cc_final: 0.8825 (tpp)
REVERT: A  624 PHE cc_start: 0.8499 (t80) cc_final: 0.8219 (t80)
REVERT: A  698 MET cc_start: 0.8521 (mmm) cc_final: 0.8286 (mmm)
REVERT: A  914 ARG cc_start: 0.8389 (ptp90) cc_final: 0.7978 (ptt-90)
REVERT: A 1006 LEU cc_start: 0.9067 (tp) cc_final: 0.8865 (tt)
REVERT: B   28 TRP cc_start: 0.7951 (t-100) cc_final: 0.7746 (m-10)
REVERT: B  114 MET cc_start: 0.8950 (ttp) cc_final: 0.8676 (ttp)
REVERT: B  255 ILE cc_start: 0.9047 (mp) cc_final: 0.8770 (mp)
REVERT: B  289 ILE cc_start: 0.9226 (mm) cc_final: 0.9021 (mt)
REVERT: B  370 MET cc_start: 0.8052 (ttm) cc_final: 0.7748 (ttm)
REVERT: B  386 ASN cc_start: 0.8676 (t0) cc_final: 0.8254 (t0)
REVERT: B  554 ARG cc_start: 0.7271 (tmm-80) cc_final: 0.6715 (ttt90)
REVERT: B  561 MET cc_start: 0.8263 (mmt) cc_final: 0.7823 (mmt)
REVERT: B  592 MET cc_start: 0.9122 (tpp) cc_final: 0.8548 (tpp)
REVERT: B  624 PHE cc_start: 0.8550 (t80) cc_final: 0.7927 (t80)
REVERT: B  698 MET cc_start: 0.8536 (mmm) cc_final: 0.7823 (mtp)
REVERT: B 1003 TYR cc_start: 0.8580 (m-80) cc_final: 0.8355 (m-80)
REVERT: B 1006 LEU cc_start: 0.9105 (tp) cc_final: 0.8895 (tt)
REVERT: B 1010 ASP cc_start: 0.7380 (m-30) cc_final: 0.7094 (m-30)
  outliers start: 22
  outliers final: 5
  residues processed: 387
  average time/residue: 0.1172
  time to fit residues: 68.8920
Evaluate side-chains
  275 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 270
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  116 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  993 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 216 optimal weight:   20.0000
   chunk 98 optimal weight:    2.9990
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    8.9990
   chunk 200 optimal weight:    5.9990
   chunk 212 optimal weight:   10.0000
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  51 GLN
A  60 GLN
A 112 ASN
A 321 ASN
A 386 ASN
A 431 GLN
A1013 GLN
B  51 GLN
B  60 GLN
B 112 ASN
B 321 ASN
B 386 ASN
B 431 GLN
B1013 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.133587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.098543 restraints weight = 31744.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.101979 restraints weight = 16091.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.104174 restraints weight = 10728.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.105609 restraints weight = 8453.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106348 restraints weight = 7317.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8026
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  16690  Z= 0.172
  Angle     :  0.721  12.493  22910  Z= 0.366
  Chirality :  0.046   0.188   2754
  Planarity :  0.006   0.075   2922
  Dihedral  :  5.727  46.701   2407
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.51 %
    Favored  : 77.89 %
  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: -2.85 (0.16), residues: 2216
  helix: -0.70 (0.15), residues: 874
  sheet: -2.34 (0.35), residues: 198
  loop : -2.86 (0.17), residues: 1144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 525 
 TYR   0.014   0.002   TYR D  55 
 PHE   0.035   0.002   PHE A  99 
 TRP   0.015   0.001   TRP A 944 
 HIS   0.005   0.001   HIS A 252 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 (16690)
  covalent geometry    : angle       0.72139 (22910)
  hydrogen bonds       : bond        0.04343 (  660)
  hydrogen bonds       : angle       5.68783 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  338 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 280
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8381 (pp)
REVERT: A  554 ARG cc_start: 0.7149 (tmm-80) cc_final: 0.6793 (ttt90)
REVERT: A  561 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.7511 (mpp)
REVERT: A  565 PHE cc_start: 0.8698 (m-80) cc_final: 0.8469 (m-80)
REVERT: A  624 PHE cc_start: 0.8602 (t80) cc_final: 0.8290 (t80)
REVERT: A  635 VAL cc_start: 0.8482 (OUTLIER) cc_final: 0.8239 (m)
REVERT: A  698 MET cc_start: 0.8391 (mmm) cc_final: 0.8065 (mmm)
REVERT: A 1006 LEU cc_start: 0.9065 (tp) cc_final: 0.8853 (tt)
REVERT: A 1014 ASP cc_start: 0.8247 (t0) cc_final: 0.7882 (t70)
REVERT: B   46 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8855 (pp)
REVERT: B  114 MET cc_start: 0.8872 (ttp) cc_final: 0.8647 (ttp)
REVERT: B  247 ASP cc_start: 0.6732 (p0) cc_final: 0.6522 (p0)
REVERT: B  301 TYR cc_start: 0.8331 (p90) cc_final: 0.7765 (p90)
REVERT: B  326 MET cc_start: 0.8884 (ttm) cc_final: 0.8667 (ttm)
REVERT: B  370 MET cc_start: 0.8071 (ttm) cc_final: 0.7718 (ttm)
REVERT: B  386 ASN cc_start: 0.8491 (t0) cc_final: 0.7809 (t0)
REVERT: B  413 ARG cc_start: 0.7244 (tpp80) cc_final: 0.6888 (tpp80)
REVERT: B  554 ARG cc_start: 0.7106 (tmm-80) cc_final: 0.6712 (ttt90)
REVERT: B  592 MET cc_start: 0.9189 (tpp) cc_final: 0.8906 (tpt)
REVERT: B  635 VAL cc_start: 0.8491 (OUTLIER) cc_final: 0.8255 (m)
REVERT: B  731 CYS cc_start: 0.7053 (m) cc_final: 0.6822 (m)
REVERT: B  736 ASP cc_start: 0.8237 (p0) cc_final: 0.8035 (p0)
REVERT: B 1006 LEU cc_start: 0.9046 (tp) cc_final: 0.8822 (tt)
REVERT: B 1014 ASP cc_start: 0.8280 (t0) cc_final: 0.8051 (t70)
  outliers start: 58
  outliers final: 35
  residues processed: 320
  average time/residue: 0.1030
  time to fit residues: 51.6518
Evaluate side-chains
  281 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 241
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  527 VAL
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  635 VAL
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  793 ASP
Chi-restraints excluded: chain B residue  823 VAL
Chi-restraints excluded: chain B residue  877 LEU
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 83 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 164 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0040
   chunk 199 optimal weight:    0.0370
   chunk 116 optimal weight:    6.9990
   chunk 214 optimal weight:   20.0000
   chunk 94 optimal weight:    4.9990
   chunk 75 optimal weight:   10.0000
   chunk 128 optimal weight:    8.9990
   overall best weight:    1.5874

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
B 548 HIS
B1013 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.133099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.098810 restraints weight = 31906.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.102234 restraints weight = 15795.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.104579 restraints weight = 10377.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.105991 restraints weight = 8051.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106824 restraints weight = 6946.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  16690  Z= 0.129
  Angle     :  0.645  12.094  22910  Z= 0.320
  Chirality :  0.044   0.195   2754
  Planarity :  0.005   0.050   2922
  Dihedral  :  5.283  45.586   2406
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.40 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 19.19 %
    Favored  : 76.40 %
  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: -2.07 (0.17), residues: 2216
  helix:  0.18 (0.17), residues: 876
  sheet: -2.10 (0.34), residues: 214
  loop : -2.59 (0.17), residues: 1126

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 525 
 TYR   0.021   0.001   TYR A 301 
 PHE   0.023   0.001   PHE A  99 
 TRP   0.015   0.001   TRP B1041 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (16690)
  covalent geometry    : angle       0.64486 (22910)
  hydrogen bonds       : bond        0.03738 (  660)
  hydrogen bonds       : angle       5.12788 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 71
    poor density    : 266
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8349 (pp)
REVERT: A  375 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8833 (mm)
REVERT: A  554 ARG cc_start: 0.7146 (tmm-80) cc_final: 0.6781 (ttt90)
REVERT: A  561 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.6754 (mpp)
REVERT: A  565 PHE cc_start: 0.8610 (m-80) cc_final: 0.8266 (m-80)
REVERT: A  624 PHE cc_start: 0.8545 (t80) cc_final: 0.8270 (t80)
REVERT: A  635 VAL cc_start: 0.8316 (OUTLIER) cc_final: 0.8106 (m)
REVERT: A  659 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8009 (t80)
REVERT: A  736 ASP cc_start: 0.8218 (p0) cc_final: 0.7972 (p0)
REVERT: A 1006 LEU cc_start: 0.9049 (tp) cc_final: 0.8826 (tt)
REVERT: A 1014 ASP cc_start: 0.8153 (t0) cc_final: 0.7836 (t0)
REVERT: B   46 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8328 (pp)
REVERT: B  273 MET cc_start: 0.8749 (tpp) cc_final: 0.8406 (tpt)
REVERT: B  326 MET cc_start: 0.8800 (ttm) cc_final: 0.8573 (ttm)
REVERT: B  370 MET cc_start: 0.8044 (ttm) cc_final: 0.7703 (ttm)
REVERT: B  386 ASN cc_start: 0.8362 (t0) cc_final: 0.7788 (t0)
REVERT: B  413 ARG cc_start: 0.7205 (tpp80) cc_final: 0.6869 (tpp80)
REVERT: B  554 ARG cc_start: 0.7047 (tmm-80) cc_final: 0.6698 (ttt90)
REVERT: B  565 PHE cc_start: 0.8681 (m-80) cc_final: 0.8456 (m-80)
REVERT: B  612 MET cc_start: 0.8950 (mmm) cc_final: 0.8740 (mmm)
REVERT: B  698 MET cc_start: 0.8182 (tpp) cc_final: 0.7587 (mtp)
REVERT: B  736 ASP cc_start: 0.8221 (p0) cc_final: 0.7933 (p0)
REVERT: B 1006 LEU cc_start: 0.9023 (tp) cc_final: 0.8790 (tt)
REVERT: B 1014 ASP cc_start: 0.8214 (t0) cc_final: 0.7978 (t0)
  outliers start: 71
  outliers final: 35
  residues processed: 315
  average time/residue: 0.0983
  time to fit residues: 49.4289
Evaluate side-chains
  287 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 246
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  910 THR
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1033 MET
Chi-restraints excluded: chain C residue   16 ILE
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  686 LEU
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 149 optimal weight:    0.8980
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 95 optimal weight:    7.9990
   chunk 99 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 182 optimal weight:   10.0000
   chunk 17 optimal weight:    0.0870
   chunk 209 optimal weight:   10.0000
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
A 184 ASN
A1013 GLN
B 548 HIS
B1013 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.137955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104760 restraints weight = 31174.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108316 restraints weight = 15432.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.110685 restraints weight = 10101.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112175 restraints weight = 7814.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.112969 restraints weight = 6714.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16690  Z= 0.110
  Angle     :  0.617  11.699  22910  Z= 0.304
  Chirality :  0.043   0.259   2754
  Planarity :  0.005   0.065   2922
  Dihedral  :  4.961  43.229   2406
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.63 %
    Favored  : 93.37 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 20.31 %
    Favored  : 74.78 %
  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: -1.62 (0.18), residues: 2216
  helix:  0.60 (0.17), residues: 882
  sheet: -1.95 (0.34), residues: 214
  loop : -2.37 (0.18), residues: 1120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG B 213 
 TYR   0.020   0.001   TYR A 301 
 PHE   0.028   0.001   PHE B  99 
 TRP   0.027   0.001   TRP B  58 
 HIS   0.003   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (16690)
  covalent geometry    : angle       0.61713 (22910)
  hydrogen bonds       : bond        0.03373 (  660)
  hydrogen bonds       : angle       4.80685 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 79
    poor density    : 280
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   46 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8331 (pp)
REVERT: A  375 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8828 (mm)
REVERT: A  525 ARG cc_start: 0.7583 (OUTLIER) cc_final: 0.7047 (tmm160)
REVERT: A  554 ARG cc_start: 0.6996 (tmm-80) cc_final: 0.6763 (ttp80)
REVERT: A  561 MET cc_start: 0.8220 (OUTLIER) cc_final: 0.6794 (mpp)
REVERT: A  565 PHE cc_start: 0.8315 (m-80) cc_final: 0.8114 (m-80)
REVERT: A  612 MET cc_start: 0.8960 (mmm) cc_final: 0.8694 (mmm)
REVERT: A  624 PHE cc_start: 0.8518 (t80) cc_final: 0.8252 (t80)
REVERT: A  635 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7919 (m)
REVERT: A  659 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7967 (t80)
REVERT: A  736 ASP cc_start: 0.8133 (p0) cc_final: 0.7862 (p0)
REVERT: A  758 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.3889 (pp)
REVERT: A 1014 ASP cc_start: 0.8026 (t0) cc_final: 0.7708 (t0)
REVERT: B   46 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8311 (pp)
REVERT: B  273 MET cc_start: 0.8686 (tpp) cc_final: 0.8199 (tpt)
REVERT: B  326 MET cc_start: 0.8734 (ttm) cc_final: 0.8525 (ttm)
REVERT: B  370 MET cc_start: 0.8031 (ttm) cc_final: 0.7733 (ttm)
REVERT: B  386 ASN cc_start: 0.8381 (t0) cc_final: 0.7810 (t0)
REVERT: B  543 MET cc_start: 0.8207 (mmm) cc_final: 0.7848 (mmm)
REVERT: B  554 ARG cc_start: 0.6961 (tmm-80) cc_final: 0.6685 (ttt90)
REVERT: B  736 ASP cc_start: 0.8056 (p0) cc_final: 0.7573 (p0)
REVERT: B  985 LEU cc_start: 0.9160 (pt) cc_final: 0.8511 (mp)
REVERT: B 1006 LEU cc_start: 0.9011 (tp) cc_final: 0.8757 (tt)
REVERT: B 1014 ASP cc_start: 0.8105 (t0) cc_final: 0.7775 (t0)
  outliers start: 79
  outliers final: 41
  residues processed: 336
  average time/residue: 0.0907
  time to fit residues: 48.8301
Evaluate side-chains
  300 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 251
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  635 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1033 MET
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  532 THR
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1033 MET
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 156 optimal weight:    4.9990
   chunk 118 optimal weight:   10.0000
   chunk 120 optimal weight:   10.0000
   chunk 98 optimal weight:    9.9990
   chunk 165 optimal weight:    1.9990
   chunk 76 optimal weight:    6.9990
   chunk 196 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 174 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
A 548 HIS
B  57 ASN
B 184 ASN
B 483 GLN
B 548 HIS
B1013 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.134213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.099915 restraints weight = 31647.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.103302 restraints weight = 16013.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.105595 restraints weight = 10685.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.107008 restraints weight = 8355.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.107850 restraints weight = 7231.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16690  Z= 0.139
  Angle     :  0.621  11.078  22910  Z= 0.306
  Chirality :  0.043   0.187   2754
  Planarity :  0.005   0.079   2922
  Dihedral  :  4.869  42.259   2406
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 21.30 %
    Favored  : 73.23 %
  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: -1.45 (0.18), residues: 2216
  helix:  0.78 (0.17), residues: 880
  sheet: -1.89 (0.32), residues: 234
  loop : -2.29 (0.18), residues: 1102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 213 
 TYR   0.017   0.001   TYR A 301 
 PHE   0.026   0.001   PHE B  99 
 TRP   0.031   0.001   TRP A  58 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (16690)
  covalent geometry    : angle       0.62113 (22910)
  hydrogen bonds       : bond        0.03453 (  660)
  hydrogen bonds       : angle       4.71925 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 262
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8771 (mm)
REVERT: A  489 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8758 (mm)
REVERT: A  525 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.7203 (tmm160)
REVERT: A  554 ARG cc_start: 0.7003 (tmm-80) cc_final: 0.6736 (ttp80)
REVERT: A  561 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7249 (mpp)
REVERT: A  624 PHE cc_start: 0.8605 (t80) cc_final: 0.8331 (t80)
REVERT: A  659 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7963 (t80)
REVERT: A  736 ASP cc_start: 0.8214 (p0) cc_final: 0.7927 (p0)
REVERT: A  758 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.3674 (pp)
REVERT: A 1014 ASP cc_start: 0.8115 (t0) cc_final: 0.7787 (t0)
REVERT: B  273 MET cc_start: 0.8733 (tpp) cc_final: 0.8198 (tpt)
REVERT: B  326 MET cc_start: 0.8857 (ttm) cc_final: 0.8650 (ttm)
REVERT: B  370 MET cc_start: 0.8082 (ttm) cc_final: 0.7728 (ttm)
REVERT: B  413 ARG cc_start: 0.7988 (mmm-85) cc_final: 0.6926 (mmt90)
REVERT: B  554 ARG cc_start: 0.7131 (tmm-80) cc_final: 0.6785 (ttt90)
REVERT: B  561 MET cc_start: 0.8030 (mmm) cc_final: 0.7825 (mmt)
REVERT: B  698 MET cc_start: 0.8061 (tpp) cc_final: 0.7463 (mtp)
REVERT: B  736 ASP cc_start: 0.8163 (p0) cc_final: 0.7762 (p0)
REVERT: B  758 LEU cc_start: 0.4048 (OUTLIER) cc_final: 0.3550 (pp)
REVERT: B 1014 ASP cc_start: 0.8087 (t0) cc_final: 0.7791 (t0)
  outliers start: 88
  outliers final: 56
  residues processed: 320
  average time/residue: 0.0924
  time to fit residues: 47.5082
Evaluate side-chains
  313 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 250
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  686 LEU
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  985 LEU
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1033 MET
Chi-restraints excluded: chain A residue 1036 TYR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  268 VAL
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  532 THR
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  731 CYS
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  877 LEU
Chi-restraints excluded: chain B residue  883 VAL
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1033 MET
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   chunk 168 optimal weight:    9.9990
   chunk 160 optimal weight:    0.0020
   chunk 86 optimal weight:    2.9990
   chunk 140 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 149 optimal weight:    0.6980
   chunk 166 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 218 optimal weight:   30.0000
   overall best weight:    1.0990

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 483 GLN
A 548 HIS
A1013 GLN
B 548 HIS
B1013 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.136069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.102268 restraints weight = 31477.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.105714 restraints weight = 15752.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.108023 restraints weight = 10424.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.109500 restraints weight = 8115.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.110241 restraints weight = 6971.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16690  Z= 0.110
  Angle     :  0.605  11.034  22910  Z= 0.295
  Chirality :  0.043   0.169   2754
  Planarity :  0.004   0.060   2922
  Dihedral  :  4.736  39.269   2406
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.72 %
    Favored  : 93.28 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 21.93 %
    Favored  : 72.80 %
  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: -1.25 (0.18), residues: 2216
  helix:  0.94 (0.17), residues: 892
  sheet: -1.68 (0.33), residues: 234
  loop : -2.23 (0.18), residues: 1090

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 213 
 TYR   0.017   0.001   TYR A 634 
 PHE   0.024   0.001   PHE B  99 
 TRP   0.020   0.001   TRP B 944 
 HIS   0.002   0.001   HIS B 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (16690)
  covalent geometry    : angle       0.60469 (22910)
  hydrogen bonds       : bond        0.03178 (  660)
  hydrogen bonds       : angle       4.58331 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 85
    poor density    : 270
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8726 (mm)
REVERT: A  489 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8716 (mm)
REVERT: A  525 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.7084 (tmm160)
REVERT: A  554 ARG cc_start: 0.6973 (tmm-80) cc_final: 0.6684 (ttp80)
REVERT: A  561 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.7395 (mpp)
REVERT: A  624 PHE cc_start: 0.8573 (t80) cc_final: 0.8278 (t80)
REVERT: A  659 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.7964 (t80)
REVERT: A  736 ASP cc_start: 0.8157 (p0) cc_final: 0.7753 (p0)
REVERT: A  758 LEU cc_start: 0.4509 (OUTLIER) cc_final: 0.3713 (pp)
REVERT: A  999 SER cc_start: 0.8999 (t) cc_final: 0.8797 (t)
REVERT: A 1014 ASP cc_start: 0.8009 (t0) cc_final: 0.7791 (t0)
REVERT: B  273 MET cc_start: 0.8776 (tpp) cc_final: 0.8100 (tpt)
REVERT: B  326 MET cc_start: 0.8867 (ttm) cc_final: 0.8666 (ttm)
REVERT: B  543 MET cc_start: 0.8415 (mmm) cc_final: 0.8139 (mmm)
REVERT: B  554 ARG cc_start: 0.7024 (tmm-80) cc_final: 0.6711 (ttp80)
REVERT: B  736 ASP cc_start: 0.8133 (p0) cc_final: 0.7726 (p0)
REVERT: B  758 LEU cc_start: 0.3913 (OUTLIER) cc_final: 0.3426 (pp)
REVERT: B 1014 ASP cc_start: 0.8000 (t0) cc_final: 0.7770 (t0)
  outliers start: 85
  outliers final: 55
  residues processed: 328
  average time/residue: 0.0843
  time to fit residues: 44.1481
Evaluate side-chains
  309 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 247
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  243 LEU
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1033 MET
Chi-restraints excluded: chain A residue 1036 TYR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  227 LEU
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  532 THR
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  731 CYS
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  877 LEU
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 100 optimal weight:    8.9990
   chunk 129 optimal weight:   20.0000
   chunk 128 optimal weight:    0.9980
   chunk 15 optimal weight:   10.0000
   chunk 112 optimal weight:    0.9980
   chunk 175 optimal weight:    0.7980
   chunk 150 optimal weight:    7.9990
   chunk 50 optimal weight:    4.9990
   chunk 194 optimal weight:   20.0000
   overall best weight:    3.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
A 548 HIS
B 548 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.130893 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.097018 restraints weight = 31757.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.100326 restraints weight = 15864.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.102524 restraints weight = 10498.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.103893 restraints weight = 8211.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.104592 restraints weight = 7097.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16690  Z= 0.179
  Angle     :  0.662  11.128  22910  Z= 0.325
  Chirality :  0.044   0.177   2754
  Planarity :  0.004   0.046   2922
  Dihedral  :  4.829  38.948   2406
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 22.86 %
    Favored  : 71.99 %
  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: -1.20 (0.18), residues: 2216
  helix:  0.98 (0.18), residues: 892
  sheet: -1.72 (0.32), residues: 238
  loop : -2.19 (0.18), residues: 1086

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 454 
 TYR   0.020   0.002   TYR A 301 
 PHE   0.023   0.001   PHE B  99 
 TRP   0.026   0.001   TRP B 944 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 (16690)
  covalent geometry    : angle       0.66247 (22910)
  hydrogen bonds       : bond        0.03504 (  660)
  hydrogen bonds       : angle       4.65585 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 262
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8857 (mm)
REVERT: A  489 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8762 (mm)
REVERT: A  525 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7312 (tmm160)
REVERT: A  554 ARG cc_start: 0.7307 (tmm-80) cc_final: 0.6897 (ttt90)
REVERT: A  561 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.7487 (mpp)
REVERT: A  624 PHE cc_start: 0.8658 (t80) cc_final: 0.8348 (t80)
REVERT: A  659 PHE cc_start: 0.8356 (OUTLIER) cc_final: 0.8008 (t80)
REVERT: A  736 ASP cc_start: 0.8096 (p0) cc_final: 0.7608 (p0)
REVERT: A  758 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.3766 (pp)
REVERT: A  999 SER cc_start: 0.9022 (t) cc_final: 0.8821 (t)
REVERT: A 1014 ASP cc_start: 0.8052 (t0) cc_final: 0.7796 (t0)
REVERT: A 1016 ILE cc_start: 0.9155 (tp) cc_final: 0.8881 (tp)
REVERT: B  273 MET cc_start: 0.8741 (tpp) cc_final: 0.7978 (tpt)
REVERT: B  326 MET cc_start: 0.8869 (ttm) cc_final: 0.8655 (ttm)
REVERT: B  449 LEU cc_start: 0.8742 (tt) cc_final: 0.8539 (tt)
REVERT: B  554 ARG cc_start: 0.7265 (tmm-80) cc_final: 0.6817 (ttt90)
REVERT: B  736 ASP cc_start: 0.8111 (p0) cc_final: 0.7687 (p0)
REVERT: B  758 LEU cc_start: 0.4247 (OUTLIER) cc_final: 0.3746 (pp)
REVERT: B 1041 TRP cc_start: 0.8171 (m-10) cc_final: 0.7898 (m-90)
  outliers start: 83
  outliers final: 60
  residues processed: 315
  average time/residue: 0.0926
  time to fit residues: 46.4896
Evaluate side-chains
  315 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 248
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  268 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  483 GLN
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  716 THR
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1036 TYR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  215 THR
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  352 SER
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  489 LEU
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  731 CYS
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  785 LEU
Chi-restraints excluded: chain B residue  793 ASP
Chi-restraints excluded: chain B residue  852 THR
Chi-restraints excluded: chain B residue  877 LEU
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1033 MET
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   74 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 202 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 36 optimal weight:    0.2980
   chunk 165 optimal weight:    0.4980
   chunk 91 optimal weight:    3.9990
   chunk 101 optimal weight:    1.9990
   chunk 162 optimal weight:    0.9980
   chunk 144 optimal weight:    0.9990
   chunk 192 optimal weight:    0.3980
   chunk 88 optimal weight:   30.0000
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
B 548 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.136271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.101912 restraints weight = 32026.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.105417 restraints weight = 16150.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.107769 restraints weight = 10741.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.109187 restraints weight = 8386.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.109922 restraints weight = 7258.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16690  Z= 0.108
  Angle     :  0.630  10.667  22910  Z= 0.304
  Chirality :  0.043   0.169   2754
  Planarity :  0.004   0.047   2922
  Dihedral  :  4.692  36.694   2406
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.22 %
    Favored  : 71.49 %
  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: -1.09 (0.18), residues: 2216
  helix:  1.00 (0.18), residues: 892
  sheet: -1.65 (0.32), residues: 240
  loop : -2.06 (0.19), residues: 1084

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.013   0.001   TYR A 301 
 PHE   0.022   0.001   PHE B  99 
 TRP   0.012   0.001   TRP B 944 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (16690)
  covalent geometry    : angle       0.63005 (22910)
  hydrogen bonds       : bond        0.03117 (  660)
  hydrogen bonds       : angle       4.51743 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  337 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 268
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8682 (mm)
REVERT: A  489 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8731 (mm)
REVERT: A  525 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.7255 (tmm-80)
REVERT: A  554 ARG cc_start: 0.7007 (tmm-80) cc_final: 0.6693 (ttp80)
REVERT: A  561 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7629 (mpp)
REVERT: A  624 PHE cc_start: 0.8604 (t80) cc_final: 0.8275 (t80)
REVERT: A  659 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8004 (t80)
REVERT: A  736 ASP cc_start: 0.8049 (p0) cc_final: 0.7675 (p0)
REVERT: A  758 LEU cc_start: 0.4546 (OUTLIER) cc_final: 0.3739 (pp)
REVERT: A  926 ASP cc_start: 0.7718 (t0) cc_final: 0.7367 (m-30)
REVERT: A 1016 ILE cc_start: 0.9137 (tp) cc_final: 0.8908 (tp)
REVERT: B  273 MET cc_start: 0.8745 (tpp) cc_final: 0.8076 (tpt)
REVERT: B  326 MET cc_start: 0.8883 (ttm) cc_final: 0.8677 (ttm)
REVERT: B  525 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.7168 (tmm160)
REVERT: B  554 ARG cc_start: 0.7044 (tmm-80) cc_final: 0.6722 (ttp80)
REVERT: B  561 MET cc_start: 0.8151 (mmm) cc_final: 0.7907 (mmt)
REVERT: B  572 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.6186 (tpp)
REVERT: B  736 ASP cc_start: 0.8104 (p0) cc_final: 0.7744 (p0)
REVERT: B  758 LEU cc_start: 0.3877 (OUTLIER) cc_final: 0.3397 (pp)
REVERT: B 1041 TRP cc_start: 0.8096 (m-10) cc_final: 0.7878 (m-90)
  outliers start: 69
  outliers final: 49
  residues processed: 312
  average time/residue: 0.0897
  time to fit residues: 44.9359
Evaluate side-chains
  313 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 255
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1036 TYR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  125 VAL
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  525 ARG
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  652 VAL
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  731 CYS
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  852 THR
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   57 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 182 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 167 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 156 optimal weight:    3.9990
   chunk 155 optimal weight:    0.9980
   chunk 82 optimal weight:   20.0000
   chunk 170 optimal weight:    4.9990
   chunk 104 optimal weight:    9.9990
   chunk 211 optimal weight:   10.0000
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN
A 548 HIS
B 548 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.134407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.100451 restraints weight = 31859.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103832 restraints weight = 16089.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106080 restraints weight = 10782.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107314 restraints weight = 8501.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108291 restraints weight = 7440.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.3255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16690  Z= 0.176
  Angle     :  0.667   9.846  22910  Z= 0.324
  Chirality :  0.045   0.180   2754
  Planarity :  0.004   0.054   2922
  Dihedral  :  4.765  37.878   2406
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.08 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.78 %
    Favored  : 71.12 %
  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: -1.10 (0.18), residues: 2216
  helix:  1.00 (0.18), residues: 902
  sheet: -1.50 (0.33), residues: 226
  loop : -2.15 (0.18), residues: 1088

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 128 
 TYR   0.018   0.001   TYR A 301 
 PHE   0.022   0.001   PHE B  99 
 TRP   0.018   0.001   TRP B 944 
 HIS   0.005   0.001   HIS B 298 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (16690)
  covalent geometry    : angle       0.66724 (22910)
  hydrogen bonds       : bond        0.03426 (  660)
  hydrogen bonds       : angle       4.59430 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  322 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 256
  time to evaluate  : 0.575 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  375 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8793 (mm)
REVERT: A  489 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8759 (mm)
REVERT: A  525 ARG cc_start: 0.7757 (OUTLIER) cc_final: 0.7402 (tmm-80)
REVERT: A  554 ARG cc_start: 0.7325 (tmm-80) cc_final: 0.7022 (ttt90)
REVERT: A  561 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7774 (mpp)
REVERT: A  624 PHE cc_start: 0.8613 (t80) cc_final: 0.8333 (t80)
REVERT: A  659 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8021 (t80)
REVERT: A  736 ASP cc_start: 0.8002 (p0) cc_final: 0.7656 (p0)
REVERT: A  758 LEU cc_start: 0.4686 (OUTLIER) cc_final: 0.3938 (pp)
REVERT: A  926 ASP cc_start: 0.7755 (t0) cc_final: 0.7431 (m-30)
REVERT: A 1014 ASP cc_start: 0.7528 (t0) cc_final: 0.7272 (t70)
REVERT: A 1016 ILE cc_start: 0.9114 (tp) cc_final: 0.8822 (tp)
REVERT: B  273 MET cc_start: 0.8700 (tpp) cc_final: 0.7962 (tpt)
REVERT: B  326 MET cc_start: 0.8837 (ttm) cc_final: 0.8619 (ttm)
REVERT: B  554 ARG cc_start: 0.7238 (tmm-80) cc_final: 0.6852 (ttt90)
REVERT: B  736 ASP cc_start: 0.7998 (p0) cc_final: 0.7622 (p0)
REVERT: B  758 LEU cc_start: 0.4230 (OUTLIER) cc_final: 0.3749 (pp)
  outliers start: 66
  outliers final: 51
  residues processed: 302
  average time/residue: 0.0958
  time to fit residues: 46.3545
Evaluate side-chains
  308 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 250
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 TRP
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  483 GLN
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  877 LEU
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1036 TYR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   74 VAL
Chi-restraints excluded: chain B residue   28 TRP
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  572 MET
Chi-restraints excluded: chain B residue  731 CYS
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  852 THR
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  947 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1032 VAL
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   57 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 202 optimal weight:    1.9990
   chunk 215 optimal weight:    0.0010
   chunk 107 optimal weight:    0.8980
   chunk 136 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0050
   chunk 21 optimal weight:    9.9990
   chunk 29 optimal weight:    1.9990
   chunk 209 optimal weight:    0.9980
   chunk 101 optimal weight:    0.5980
   chunk 50 optimal weight:    4.9990
   chunk 180 optimal weight:    8.9990
   overall best weight:    0.5000

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

Flipped N/Q/H residues before XYZ refinement:
A 483 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.138343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.104985 restraints weight = 31522.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.108512 restraints weight = 15732.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.110938 restraints weight = 10411.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.112394 restraints weight = 8082.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113129 restraints weight = 6968.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  16690  Z= 0.112
  Angle     :  0.648  11.625  22910  Z= 0.311
  Chirality :  0.043   0.207   2754
  Planarity :  0.004   0.046   2922
  Dihedral  :  4.677  35.707   2406
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 25.40 %
    Favored  : 70.93 %
  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: -0.98 (0.18), residues: 2216
  helix:  1.05 (0.18), residues: 890
  sheet: -1.37 (0.33), residues: 228
  loop : -2.01 (0.19), residues: 1098

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 525 
 TYR   0.014   0.001   TYR A 301 
 PHE   0.022   0.001   PHE B  99 
 TRP   0.017   0.001   TRP B 944 
 HIS   0.004   0.001   HIS A 581 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (16690)
  covalent geometry    : angle       0.64763 (22910)
  hydrogen bonds       : bond        0.03147 (  660)
  hydrogen bonds       : angle       4.49221 ( 1884)

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

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

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4432 Ramachandran restraints generated.
    2216 Oldfield, 0 Emsley, 2216 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 267
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  311 SER cc_start: 0.9035 (p) cc_final: 0.8710 (p)
REVERT: A  375 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8705 (mm)
REVERT: A  489 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8752 (mm)
REVERT: A  525 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.7370 (tmm-80)
REVERT: A  554 ARG cc_start: 0.7059 (tmm-80) cc_final: 0.6737 (ttt90)
REVERT: A  561 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7713 (mpp)
REVERT: A  624 PHE cc_start: 0.8558 (t80) cc_final: 0.8278 (t80)
REVERT: A  659 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7935 (t80)
REVERT: A  736 ASP cc_start: 0.7974 (p0) cc_final: 0.7625 (p0)
REVERT: A  758 LEU cc_start: 0.4691 (OUTLIER) cc_final: 0.3831 (pp)
REVERT: A  926 ASP cc_start: 0.7763 (t0) cc_final: 0.7425 (m-30)
REVERT: A  999 SER cc_start: 0.9072 (t) cc_final: 0.8865 (t)
REVERT: B  129 ASN cc_start: 0.8771 (m110) cc_final: 0.8564 (m-40)
REVERT: B  273 MET cc_start: 0.8711 (tpp) cc_final: 0.8042 (tpt)
REVERT: B  326 MET cc_start: 0.8825 (ttm) cc_final: 0.8608 (ttm)
REVERT: B  386 ASN cc_start: 0.8339 (t0) cc_final: 0.7901 (t0)
REVERT: B  554 ARG cc_start: 0.7038 (tmm-80) cc_final: 0.6796 (ttp80)
REVERT: B  561 MET cc_start: 0.8041 (mmt) cc_final: 0.7831 (mmm)
REVERT: B  736 ASP cc_start: 0.7948 (p0) cc_final: 0.7604 (p0)
REVERT: B  758 LEU cc_start: 0.4035 (OUTLIER) cc_final: 0.3542 (pp)
  outliers start: 59
  outliers final: 47
  residues processed: 307
  average time/residue: 0.0894
  time to fit residues: 44.1117
Evaluate side-chains
  311 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 257
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 LEU
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue   82 THR
Chi-restraints excluded: chain A residue   99 PHE
Chi-restraints excluded: chain A residue  132 VAL
Chi-restraints excluded: chain A residue  178 THR
Chi-restraints excluded: chain A residue  197 THR
Chi-restraints excluded: chain A residue  215 THR
Chi-restraints excluded: chain A residue  329 VAL
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  403 VAL
Chi-restraints excluded: chain A residue  474 VAL
Chi-restraints excluded: chain A residue  489 LEU
Chi-restraints excluded: chain A residue  498 ILE
Chi-restraints excluded: chain A residue  525 ARG
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  600 VAL
Chi-restraints excluded: chain A residue  636 SER
Chi-restraints excluded: chain A residue  652 VAL
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  731 CYS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  779 ILE
Chi-restraints excluded: chain A residue  787 ASN
Chi-restraints excluded: chain A residue  852 THR
Chi-restraints excluded: chain A residue  897 VAL
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  993 VAL
Chi-restraints excluded: chain A residue 1032 VAL
Chi-restraints excluded: chain A residue 1036 TYR
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain B residue   99 PHE
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  150 ILE
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 THR
Chi-restraints excluded: chain B residue  292 MET
Chi-restraints excluded: chain B residue  403 VAL
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  652 VAL
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  731 CYS
Chi-restraints excluded: chain B residue  758 LEU
Chi-restraints excluded: chain B residue  779 ILE
Chi-restraints excluded: chain B residue  852 THR
Chi-restraints excluded: chain B residue  897 VAL
Chi-restraints excluded: chain B residue  932 VAL
Chi-restraints excluded: chain B residue  993 VAL
Chi-restraints excluded: chain B residue 1036 TYR
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   57 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 220
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 187 optimal weight:   10.0000
   chunk 107 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 108 optimal weight:   20.0000
   chunk 84 optimal weight:   20.0000
   chunk 167 optimal weight:    0.9990
   chunk 209 optimal weight:    0.6980
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 548 HIS
B 548 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.134552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.100382 restraints weight = 31823.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.103778 restraints weight = 16144.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.106046 restraints weight = 10840.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.107465 restraints weight = 8539.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.108308 restraints weight = 7401.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.3383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16690  Z= 0.172
  Angle     :  0.673  12.139  22910  Z= 0.326
  Chirality :  0.044   0.175   2754
  Planarity :  0.004   0.042   2922
  Dihedral  :  4.741  36.880   2406
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.99 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 25.16 %
    Favored  : 70.93 %
  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: -1.02 (0.18), residues: 2216
  helix:  1.02 (0.18), residues: 902
  sheet: -1.39 (0.33), residues: 228
  loop : -2.07 (0.19), residues: 1086

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 213 
 TYR   0.018   0.001   TYR A 301 
 PHE   0.022   0.001   PHE B  99 
 TRP   0.018   0.001   TRP B 944 
 HIS   0.006   0.001   HIS A 581 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (16690)
  covalent geometry    : angle       0.67288 (22910)
  hydrogen bonds       : bond        0.03419 (  660)
  hydrogen bonds       : angle       4.57175 ( 1884)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2459.57 seconds
wall clock time: 43 minutes 7.64 seconds (2587.64 seconds total)