Starting phenix.real_space_refine
on Fri Sep 19 05:42:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vyn_43672/09_2025/8vyn_43672.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vyn_43672/09_2025/8vyn_43672.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vyn_43672/09_2025/8vyn_43672.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vyn_43672/09_2025/8vyn_43672.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vyn_43672/09_2025/8vyn_43672.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vyn_43672/09_2025/8vyn_43672.map"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.030
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     123      5.16       5
     C   14973      2.51       5
     N    3975      2.21       5
     O    4692      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 23763
  Number of models: 1
  Model: ""
    Number of chains: 27
    Chain: "A"
      Number of atoms: 4206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4206
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 507}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 4206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4206
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 507}
          Chain breaks: 4
    Chain: "C"
      Number of atoms: 4206
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 523, 4206
          Classifications: {'peptide': 523}
          Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 507}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1017
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
    Chain: "E"
      Number of atoms: 797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 797
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "F"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 944
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
    Chain: "G"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 806
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1017
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
    Chain: "I"
      Number of atoms: 797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 797
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "J"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 944
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
    Chain: "K"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 806
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "L"
      Number of atoms: 1017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 1017
          Classifications: {'peptide': 130}
          Link IDs: {'PTRANS': 3, 'TRANS': 126}
    Chain: "M"
      Number of atoms: 797
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 797
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 8, 'TRANS': 99}
    Chain: "N"
      Number of atoms: 944
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 944
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
    Chain: "O"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 806
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
    Chain: "P"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "Q"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "R"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "S"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "T"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "U"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "V"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "W"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "X"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 5.41, per 1000 atoms: 0.23
  Number of scatterers: 23763
  At special positions: 0
  Unit cell: (174.139, 164.974, 112.482, 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     123     16.00
     O    4692      8.00
     N    3975      7.00
     C   14973      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=33, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  94 " - pdb=" SG  CYS A 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS C 653 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 185 " - pdb=" SG  CYS A 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 222 " - pdb=" SG  CYS C 657 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 574 " - pdb=" SG  CYS A 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 653 " - pdb=" SG  CYS B 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 657 " - pdb=" SG  CYS B 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  94 " - pdb=" SG  CYS B 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 111 " - pdb=" SG  CYS B 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 344 " - pdb=" SG  CYS B 391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 574 " - pdb=" SG  CYS B 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 653 " - pdb=" SG  CYS C 134 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 657 " - pdb=" SG  CYS C 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  94 " - pdb=" SG  CYS C 551 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 111 " - pdb=" SG  CYS C 507 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 185 " - pdb=" SG  CYS C 250 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 344 " - pdb=" SG  CYS C 391 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 574 " - pdb=" SG  CYS C 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  23 " - pdb=" SG  CYS E  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  22 " - pdb=" SG  CYS F  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G  23 " - pdb=" SG  CYS G  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  23 " - pdb=" SG  CYS I  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  22 " - pdb=" SG  CYS J  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS K  23 " - pdb=" SG  CYS K  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M  23 " - pdb=" SG  CYS M  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS O  23 " - pdb=" SG  CYS O  88 " distance=2.03

  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
  Links applied
    BETA1-4
      " NAG P   1 " - " NAG P   2 "
      " NAG P   2 " - " BMA P   3 "
      " NAG Q   1 " - " NAG Q   2 "
      " NAG R   1 " - " NAG R   2 "
      " NAG S   1 " - " NAG S   2 "
      " NAG S   2 " - " BMA S   3 "
      " NAG T   1 " - " NAG T   2 "
      " NAG U   1 " - " NAG U   2 "
      " NAG V   1 " - " NAG V   2 "
      " NAG V   2 " - " BMA V   3 "
      " NAG W   1 " - " NAG W   2 "
      " NAG X   1 " - " NAG X   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A 417 "
      " NAG A 802 " - " ASN A 302 "
      " NAG A 803 " - " ASN A 405 "
      " NAG A 804 " - " ASN A 555 "
      " NAG B 801 " - " ASN B 417 "
      " NAG B 802 " - " ASN B 302 "
      " NAG B 803 " - " ASN B 405 "
      " NAG B 804 " - " ASN B 555 "
      " NAG C 801 " - " ASN C 417 "
      " NAG C 802 " - " ASN C 302 "
      " NAG C 803 " - " ASN C 405 "
      " NAG C 804 " - " ASN C 555 "
      " NAG P   1 " - " ASN A 208 "
      " NAG Q   1 " - " ASN A 383 "
      " NAG R   1 " - " ASN A 281 "
      " NAG S   1 " - " ASN B 208 "
      " NAG T   1 " - " ASN B 383 "
      " NAG U   1 " - " ASN B 281 "
      " NAG V   1 " - " ASN C 208 "
      " NAG W   1 " - " ASN C 383 "
      " NAG X   1 " - " ASN C 281 "
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5514

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 63 sheets defined
      15.2% alpha, 42.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 172 through 183
    Processing helix  chain 'A' and resid 284 through 288
      removed outlier: 3.614A  pdb=" N   SER A 288 " --> pdb=" O   ARG A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 295
      No H-bonds generated for 'chain 'A' and resid 293 through 295'
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 386 through 390
    Processing helix  chain 'A' and resid 392 through 408
    Processing helix  chain 'A' and resid 438 through 447
    Processing helix  chain 'A' and resid 475 through 505
    Processing helix  chain 'A' and resid 506 through 521
    Processing helix  chain 'A' and resid 524 through 534
    Processing helix  chain 'A' and resid 638 through 642
    Processing helix  chain 'B' and resid 172 through 183
    Processing helix  chain 'B' and resid 284 through 288
      removed outlier: 3.609A  pdb=" N   SER B 288 " --> pdb=" O   ARG B 285 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 295
      No H-bonds generated for 'chain 'B' and resid 293 through 295'
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 386 through 390
    Processing helix  chain 'B' and resid 392 through 408
    Processing helix  chain 'B' and resid 438 through 447
    Processing helix  chain 'B' and resid 475 through 505
    Processing helix  chain 'B' and resid 506 through 521
    Processing helix  chain 'B' and resid 524 through 534
    Processing helix  chain 'B' and resid 638 through 642
    Processing helix  chain 'C' and resid 172 through 183
    Processing helix  chain 'C' and resid 284 through 288
      removed outlier: 3.601A  pdb=" N   SER C 288 " --> pdb=" O   ARG C 285 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 293 through 295
      No H-bonds generated for 'chain 'C' and resid 293 through 295'
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 386 through 390
    Processing helix  chain 'C' and resid 392 through 408
    Processing helix  chain 'C' and resid 438 through 447
    Processing helix  chain 'C' and resid 475 through 505
    Processing helix  chain 'C' and resid 506 through 521
    Processing helix  chain 'C' and resid 524 through 534
    Processing helix  chain 'C' and resid 638 through 642
    Processing helix  chain 'D' and resid 28 through 30
      No H-bonds generated for 'chain 'D' and resid 28 through 30'
    Processing helix  chain 'D' and resid 60 through 65
      removed outlier: 4.812A  pdb=" N   GLY D  65 " --> pdb=" O   GLN D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 83 through 87
      removed outlier: 3.993A  pdb=" N   THR D  87 " --> pdb=" O   SER D  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27A through 30
    Processing helix  chain 'F' and resid 83 through 87
    Processing helix  chain 'G' and resid 79 through 83
      removed outlier: 3.556A  pdb=" N   GLU G  83 " --> pdb=" O   SER G  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 30
      No H-bonds generated for 'chain 'H' and resid 28 through 30'
    Processing helix  chain 'H' and resid 60 through 65
      removed outlier: 4.820A  pdb=" N   GLY H  65 " --> pdb=" O   GLN H  61 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 83 through 87
      removed outlier: 3.990A  pdb=" N   THR H  87 " --> pdb=" O   SER H  84 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 27A through 30
    Processing helix  chain 'J' and resid 83 through 87
    Processing helix  chain 'K' and resid 79 through 83
      removed outlier: 3.560A  pdb=" N   GLU K  83 " --> pdb=" O   SER K  80 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 28 through 30
      No H-bonds generated for 'chain 'L' and resid 28 through 30'
    Processing helix  chain 'L' and resid 60 through 65
      removed outlier: 4.815A  pdb=" N   GLY L  65 " --> pdb=" O   GLN L  61 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 83 through 87
      removed outlier: 3.991A  pdb=" N   THR L  87 " --> pdb=" O   SER L  84 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 27A through 30
    Processing helix  chain 'N' and resid 83 through 87
    Processing helix  chain 'O' and resid 79 through 83
      removed outlier: 3.561A  pdb=" N   GLU O  83 " --> pdb=" O   SER O  80 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 82
      removed outlier: 5.071A  pdb=" N   VAL A 579 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ARG A  92 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   ALA A 538 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 82
      removed outlier: 5.071A  pdb=" N   VAL A 579 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.140A  pdb=" N   ARG A  92 " --> pdb=" O   ILE A 601 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   SER C 643 " --> pdb=" O   LEU A 102 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 377
      removed outlier: 6.706A  pdb=" N   VAL A 128 " --> pdb=" O   TRP A 349 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   ALA A 351 " --> pdb=" O   MET A 126 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   MET A 126 " --> pdb=" O   ALA A 351 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   GLU A 353 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   GLY A 124 " --> pdb=" O   GLU A 353 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   THR A 355 " --> pdb=" O   ASP A 122 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   ASP A 122 " --> pdb=" O   THR A 355 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLU A 123 " --> pdb=" O   ILE A 434 " (cutoff:3.500A)
      removed outlier: 4.779A  pdb=" N   GLY A 433 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   ASN A 417 " --> pdb=" O   GLY A 433 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   LYS A 435 " --> pdb=" O   TYR A 415 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   TYR A 415 " --> pdb=" O   LYS A 435 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 167 through 169
    Processing sheet with id=AA5, first strand: chain 'A' and resid 214 through 215
      removed outlier: 7.070A  pdb=" N   LYS A 139 " --> pdb=" O   ASP A 335 " (cutoff:3.500A)
      removed outlier: 4.599A  pdb=" N   ASP A 335 " --> pdb=" O   LYS A 139 " (cutoff:3.500A)
      removed outlier: 4.714A  pdb=" N   LEU A 321 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 6.564A  pdb=" N   LEU A 316 " --> pdb=" O   VAL A 306 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 306 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   THR A 318 " --> pdb=" O   THR A 304 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   THR A 304 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   ARG A 320 " --> pdb=" O   ASN A 302 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 184 through 186
    Processing sheet with id=AA7, first strand: chain 'A' and resid 188 through 189
    Processing sheet with id=AA8, first strand: chain 'A' and resid 573 through 575
    Processing sheet with id=AA9, first strand: chain 'A' and resid 616 through 621
      removed outlier: 6.906A  pdb=" N   ALA A 625 " --> pdb=" O   MET A 636 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   MET A 636 " --> pdb=" O   ALA A 625 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLU A 627 " --> pdb=" O   LYS A 634 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 643 through 644
      removed outlier: 6.269A  pdb=" N   SER A 643 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   ARG B  92 " --> pdb=" O   ILE B 601 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   VAL B 579 " --> pdb=" O   LEU B 562 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 643 through 644
      removed outlier: 6.269A  pdb=" N   SER A 643 " --> pdb=" O   ARG B 104 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ALA B 538 " --> pdb=" O   ALA B 549 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 375 through 377
      removed outlier: 6.712A  pdb=" N   VAL B 128 " --> pdb=" O   TRP B 349 " (cutoff:3.500A)
      removed outlier: 4.620A  pdb=" N   ALA B 351 " --> pdb=" O   MET B 126 " (cutoff:3.500A)
      removed outlier: 6.781A  pdb=" N   MET B 126 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
      removed outlier: 5.628A  pdb=" N   GLU B 353 " --> pdb=" O   GLY B 124 " (cutoff:3.500A)
      removed outlier: 5.481A  pdb=" N   GLY B 124 " --> pdb=" O   GLU B 353 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   THR B 355 " --> pdb=" O   ASP B 122 " (cutoff:3.500A)
      removed outlier: 6.777A  pdb=" N   ASP B 122 " --> pdb=" O   THR B 355 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLU B 123 " --> pdb=" O   ILE B 434 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   GLY B 433 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   ASN B 417 " --> pdb=" O   GLY B 433 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS B 435 " --> pdb=" O   TYR B 415 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   TYR B 415 " --> pdb=" O   LYS B 435 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 167 through 169
    Processing sheet with id=AB5, first strand: chain 'B' and resid 214 through 215
      removed outlier: 7.084A  pdb=" N   LYS B 139 " --> pdb=" O   ASP B 335 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   ASP B 335 " --> pdb=" O   LYS B 139 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   LEU B 321 " --> pdb=" O   ILE B 336 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   LEU B 316 " --> pdb=" O   VAL B 306 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   VAL B 306 " --> pdb=" O   LEU B 316 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   THR B 318 " --> pdb=" O   THR B 304 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   THR B 304 " --> pdb=" O   THR B 318 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   ARG B 320 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 184 through 186
    Processing sheet with id=AB7, first strand: chain 'B' and resid 188 through 189
    Processing sheet with id=AB8, first strand: chain 'B' and resid 573 through 575
    Processing sheet with id=AB9, first strand: chain 'B' and resid 616 through 621
      removed outlier: 6.909A  pdb=" N   ALA B 625 " --> pdb=" O   MET B 636 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   MET B 636 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   GLU B 627 " --> pdb=" O   LYS B 634 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 643 through 644
      removed outlier: 6.253A  pdb=" N   SER B 643 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   ARG C  92 " --> pdb=" O   ILE C 601 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   VAL C 579 " --> pdb=" O   LEU C 562 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 643 through 644
      removed outlier: 6.253A  pdb=" N   SER B 643 " --> pdb=" O   ARG C 104 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   ALA C 538 " --> pdb=" O   ALA C 549 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 375 through 377
      removed outlier: 6.707A  pdb=" N   VAL C 128 " --> pdb=" O   TRP C 349 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ALA C 351 " --> pdb=" O   MET C 126 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   MET C 126 " --> pdb=" O   ALA C 351 " (cutoff:3.500A)
      removed outlier: 5.633A  pdb=" N   GLU C 353 " --> pdb=" O   GLY C 124 " (cutoff:3.500A)
      removed outlier: 5.478A  pdb=" N   GLY C 124 " --> pdb=" O   GLU C 353 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   THR C 355 " --> pdb=" O   ASP C 122 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   ASP C 122 " --> pdb=" O   THR C 355 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   GLU C 123 " --> pdb=" O   ILE C 434 " (cutoff:3.500A)
      removed outlier: 4.778A  pdb=" N   GLY C 433 " --> pdb=" O   ASN C 417 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ASN C 417 " --> pdb=" O   GLY C 433 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   LYS C 435 " --> pdb=" O   TYR C 415 " (cutoff:3.500A)
      removed outlier: 6.399A  pdb=" N   TYR C 415 " --> pdb=" O   LYS C 435 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 167 through 169
    Processing sheet with id=AC5, first strand: chain 'C' and resid 214 through 215
      removed outlier: 7.063A  pdb=" N   LYS C 139 " --> pdb=" O   ASP C 335 " (cutoff:3.500A)
      removed outlier: 4.597A  pdb=" N   ASP C 335 " --> pdb=" O   LYS C 139 " (cutoff:3.500A)
      removed outlier: 4.695A  pdb=" N   LEU C 321 " --> pdb=" O   ILE C 336 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   LEU C 316 " --> pdb=" O   VAL C 306 " (cutoff:3.500A)
      removed outlier: 6.638A  pdb=" N   VAL C 306 " --> pdb=" O   LEU C 316 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   THR C 318 " --> pdb=" O   THR C 304 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   THR C 304 " --> pdb=" O   THR C 318 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ARG C 320 " --> pdb=" O   ASN C 302 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 184 through 186
    Processing sheet with id=AC7, first strand: chain 'C' and resid 188 through 189
    Processing sheet with id=AC8, first strand: chain 'C' and resid 573 through 575
    Processing sheet with id=AC9, first strand: chain 'C' and resid 616 through 621
      removed outlier: 6.913A  pdb=" N   ALA C 625 " --> pdb=" O   MET C 636 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   MET C 636 " --> pdb=" O   ALA C 625 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   GLU C 627 " --> pdb=" O   LYS C 634 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'D' and resid 3 through 6
    Processing sheet with id=AD2, first strand: chain 'D' and resid 10 through 12
      removed outlier: 4.664A  pdb=" N   TYR D  33 " --> pdb=" O   ASP D  95 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   ILE D  34 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 4.446A  pdb=" N   TRP D  50 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   TRP D  36 " --> pdb=" O   MET D  48 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'D' and resid 10 through 12
      removed outlier: 3.792A  pdb=" N   VAL D 102 " --> pdb=" O   LYS D  94 " (cutoff:3.500A)
      removed outlier: 7.238A  pdb=" N   SER D  96 " --> pdb=" O   MET D 100M" (cutoff:3.500A)
      removed outlier: 8.800A  pdb=" N   MET D 100M" --> pdb=" O   SER D  96 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'E' and resid 9 through 11
      removed outlier: 6.415A  pdb=" N   TRP E  35 " --> pdb=" O   LEU E  47 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'E' and resid 9 through 11
    Processing sheet with id=AD6, first strand: chain 'E' and resid 18 through 24
    Processing sheet with id=AD7, first strand: chain 'F' and resid 3 through 6
    Processing sheet with id=AD8, first strand: chain 'F' and resid 57 through 59
      removed outlier: 6.650A  pdb=" N   TRP F  36 " --> pdb=" O   ILE F  48 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ASN F  50 " --> pdb=" O   TRP F  35A" (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   TRP F  35A" --> pdb=" O   ASN F  50 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   TYR F 102 " --> pdb=" O   THR F  94 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'F' and resid 57 through 59
      removed outlier: 6.650A  pdb=" N   TRP F  36 " --> pdb=" O   ILE F  48 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ASN F  50 " --> pdb=" O   TRP F  35A" (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   TRP F  35A" --> pdb=" O   ASN F  50 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'G' and resid 9 through 12
      removed outlier: 6.339A  pdb=" N   TRP G  35 " --> pdb=" O   LEU G  47 " (cutoff:3.500A)
    Processing sheet with id=AE2, first strand: chain 'G' and resid 9 through 12
    Processing sheet with id=AE3, first strand: chain 'G' and resid 19 through 23
    Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.636A  pdb=" N   TYR H  33 " --> pdb=" O   ASP H  95 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   ILE H  34 " --> pdb=" O   TRP H  50 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   TRP H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   TRP H  36 " --> pdb=" O   MET H  48 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.803A  pdb=" N   VAL H 102 " --> pdb=" O   LYS H  94 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   SER H  96 " --> pdb=" O   MET H 100M" (cutoff:3.500A)
      removed outlier: 8.806A  pdb=" N   MET H 100M" --> pdb=" O   SER H  96 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'I' and resid 9 through 11
      removed outlier: 6.417A  pdb=" N   TRP I  35 " --> pdb=" O   LEU I  47 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'I' and resid 9 through 11
    Processing sheet with id=AE9, first strand: chain 'I' and resid 18 through 24
    Processing sheet with id=AF1, first strand: chain 'J' and resid 3 through 6
    Processing sheet with id=AF2, first strand: chain 'J' and resid 57 through 59
      removed outlier: 6.660A  pdb=" N   TRP J  36 " --> pdb=" O   ILE J  48 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ASN J  50 " --> pdb=" O   TRP J  35A" (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   TRP J  35A" --> pdb=" O   ASN J  50 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   TYR J 102 " --> pdb=" O   THR J  94 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'J' and resid 57 through 59
      removed outlier: 6.660A  pdb=" N   TRP J  36 " --> pdb=" O   ILE J  48 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ASN J  50 " --> pdb=" O   TRP J  35A" (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   TRP J  35A" --> pdb=" O   ASN J  50 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'K' and resid 9 through 12
      removed outlier: 6.340A  pdb=" N   TRP K  35 " --> pdb=" O   LEU K  47 " (cutoff:3.500A)
    Processing sheet with id=AF5, first strand: chain 'K' and resid 9 through 12
    Processing sheet with id=AF6, first strand: chain 'K' and resid 19 through 23
    Processing sheet with id=AF7, first strand: chain 'L' and resid 3 through 6
    Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 12
      removed outlier: 4.649A  pdb=" N   TYR L  33 " --> pdb=" O   ASP L  95 " (cutoff:3.500A)
      removed outlier: 6.710A  pdb=" N   ILE L  34 " --> pdb=" O   TRP L  50 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   TRP L  50 " --> pdb=" O   ILE L  34 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   TRP L  36 " --> pdb=" O   MET L  48 " (cutoff:3.500A)
    Processing sheet with id=AF9, first strand: chain 'L' and resid 10 through 12
      removed outlier: 3.788A  pdb=" N   VAL L 102 " --> pdb=" O   LYS L  94 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   SER L  96 " --> pdb=" O   MET L 100M" (cutoff:3.500A)
      removed outlier: 8.794A  pdb=" N   MET L 100M" --> pdb=" O   SER L  96 " (cutoff:3.500A)
    Processing sheet with id=AG1, first strand: chain 'M' and resid 9 through 11
      removed outlier: 6.413A  pdb=" N   TRP M  35 " --> pdb=" O   LEU M  47 " (cutoff:3.500A)
    Processing sheet with id=AG2, first strand: chain 'M' and resid 9 through 11
    Processing sheet with id=AG3, first strand: chain 'M' and resid 18 through 24
    Processing sheet with id=AG4, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AG5, first strand: chain 'N' and resid 57 through 59
      removed outlier: 6.654A  pdb=" N   TRP N  36 " --> pdb=" O   ILE N  48 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ASN N  50 " --> pdb=" O   TRP N  35A" (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   TRP N  35A" --> pdb=" O   ASN N  50 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   TYR N 102 " --> pdb=" O   THR N  94 " (cutoff:3.500A)
    Processing sheet with id=AG6, first strand: chain 'N' and resid 57 through 59
      removed outlier: 6.654A  pdb=" N   TRP N  36 " --> pdb=" O   ILE N  48 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   ASN N  50 " --> pdb=" O   TRP N  35A" (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   TRP N  35A" --> pdb=" O   ASN N  50 " (cutoff:3.500A)
    Processing sheet with id=AG7, first strand: chain 'O' and resid 9 through 12
      removed outlier: 6.348A  pdb=" N   TRP O  35 " --> pdb=" O   LEU O  47 " (cutoff:3.500A)
    Processing sheet with id=AG8, first strand: chain 'O' and resid 9 through 12
    Processing sheet with id=AG9, first strand: chain 'O' and resid 19 through 23

    1056 hydrogen bonds defined for protein.
    2658 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: 5.43

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 7457
        1.34 -     1.46: 4824
        1.46 -     1.58: 11842
        1.58 -     1.70: 0
        1.70 -     1.82: 180
  Bond restraints: 24303
  Sorted by residual:
  bond pdb=" CB  CYS N  92 "
       pdb=" SG  CYS N  92 "
    ideal  model  delta    sigma   weight residual
    1.808  1.778  0.030 3.30e-02 9.18e+02 8.03e-01
  bond pdb=" CB  CYS J  92 "
       pdb=" SG  CYS J  92 "
    ideal  model  delta    sigma   weight residual
    1.808  1.779  0.029 3.30e-02 9.18e+02 7.85e-01
  bond pdb=" CA  ALA A 396 "
       pdb=" C   ALA A 396 "
    ideal  model  delta    sigma   weight residual
    1.523  1.512  0.011 1.30e-02 5.92e+03 7.67e-01
  bond pdb=" CA  ASN C 398 "
       pdb=" C   ASN C 398 "
    ideal  model  delta    sigma   weight residual
    1.523  1.511  0.012 1.35e-02 5.49e+03 7.62e-01
  bond pdb=" CG1 ILE B 618 "
       pdb=" CD1 ILE B 618 "
    ideal  model  delta    sigma   weight residual
    1.513  1.480  0.033 3.90e-02 6.57e+02 7.32e-01
  ... (remaining 24298 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 30733
        1.04 -     2.08: 1870
        2.08 -     3.12: 293
        3.12 -     4.16: 61
        4.16 -     5.20: 28
  Bond angle restraints: 32985
  Sorted by residual:
  angle pdb=" C   TRP C 349 "
        pdb=" N   GLU C 350 "
        pdb=" CA  GLU C 350 "
      ideal   model   delta    sigma   weight residual
     121.63  117.02    4.61 1.92e+00 2.71e-01 5.75e+00
  angle pdb=" C   TRP A 349 "
        pdb=" N   GLU A 350 "
        pdb=" CA  GLU A 350 "
      ideal   model   delta    sigma   weight residual
     121.63  117.05    4.58 1.92e+00 2.71e-01 5.68e+00
  angle pdb=" C   GLY M  77 "
        pdb=" N   LEU M  78 "
        pdb=" CA  LEU M  78 "
      ideal   model   delta    sigma   weight residual
     121.54  126.07   -4.53 1.91e+00 2.74e-01 5.63e+00
  angle pdb=" C   TRP B 349 "
        pdb=" N   GLU B 350 "
        pdb=" CA  GLU B 350 "
      ideal   model   delta    sigma   weight residual
     121.63  117.10    4.53 1.92e+00 2.71e-01 5.57e+00
  angle pdb=" C   GLY I  77 "
        pdb=" N   LEU I  78 "
        pdb=" CA  LEU I  78 "
      ideal   model   delta    sigma   weight residual
     122.82  126.02   -3.20 1.42e+00 4.96e-01 5.09e+00
  ... (remaining 32980 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.46: 14152
       20.46 -    40.92: 542
       40.92 -    61.37: 99
       61.37 -    81.83: 48
       81.83 -   102.29: 12
  Dihedral angle restraints: 14853
    sinusoidal: 6231
      harmonic: 8622
  Sorted by residual:
  dihedral pdb=" CA  VAL C  81 "
           pdb=" C   VAL C  81 "
           pdb=" N   VAL C  82 "
           pdb=" CA  VAL C  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.90  -23.10     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  VAL A  81 "
           pdb=" C   VAL A  81 "
           pdb=" N   VAL A  82 "
           pdb=" CA  VAL A  82 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.91  -23.09     0      5.00e+00 4.00e-02 2.13e+01
  dihedral pdb=" CA  VAL B  81 "
           pdb=" C   VAL B  81 "
           pdb=" N   VAL B  82 "
           pdb=" CA  VAL B  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.94  -23.06     0      5.00e+00 4.00e-02 2.13e+01
  ... (remaining 14850 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 2927
       0.052 -    0.104: 594
       0.104 -    0.156: 161
       0.156 -    0.208: 8
       0.208 -    0.260: 6
  Chirality restraints: 3696
  Sorted by residual:
  chirality pdb=" C1  NAG R   1 "
            pdb=" ND2 ASN A 281 "
            pdb=" C2  NAG R   1 "
            pdb=" O5  NAG R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" C1  NAG X   1 "
            pdb=" ND2 ASN C 281 "
            pdb=" C2  NAG X   1 "
            pdb=" O5  NAG X   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" C1  NAG U   1 "
            pdb=" ND2 ASN B 281 "
            pdb=" C2  NAG U   1 "
            pdb=" O5  NAG U   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.60e+00
  ... (remaining 3693 not shown)

  Planarity restraints: 4209
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 320 "   -0.319 9.50e-02 1.11e+02   1.44e-01 1.67e+01
        pdb=" NE  ARG B 320 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 320 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 320 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 320 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 320 "   -0.318 9.50e-02 1.11e+02   1.44e-01 1.66e+01
        pdb=" NE  ARG C 320 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 320 "   -0.032 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 320 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 320 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 320 "   -0.319 9.50e-02 1.11e+02   1.44e-01 1.65e+01
        pdb=" NE  ARG A 320 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 320 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 320 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 320 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 4206 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 4113
        2.77 -     3.30: 21455
        3.30 -     3.83: 39324
        3.83 -     4.37: 48710
        4.37 -     4.90: 84483
  Nonbonded interactions: 198085
  Sorted by model distance:
  nonbonded pdb=" OG  SER K   2 "
            pdb=" ND2 ASN K  27B"
     model   vdw
     2.237 3.120
  nonbonded pdb=" OG  SER O   2 "
            pdb=" ND2 ASN O  27B"
     model   vdw
     2.241 3.120
  nonbonded pdb=" OG  SER G   2 "
            pdb=" ND2 ASN G  27B"
     model   vdw
     2.248 3.120
  nonbonded pdb=" ND2 ASN A 118 "
            pdb=" OD1 ASP A 120 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" ND2 ASN B 118 "
            pdb=" OD1 ASP B 120 "
     model   vdw
     2.270 3.120
  ... (remaining 198080 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: 0.06
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
  selection = chain 'L'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'I'
  selection = chain 'M'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'J'
  selection = chain 'N'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'K'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'P'
  selection = chain 'S'
  selection = chain 'V'
}
ncs_group {
  reference = chain 'Q'
  selection = chain 'R'
  selection = chain 'T'
  selection = chain 'U'
  selection = chain 'W'
  selection = chain 'X'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             9.700
  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:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     22.140
  Find NCS groups from input model:        0.490
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:7.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
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      :  0.004   0.046  24369  Z= 0.160
  Angle     :  0.584   5.204  33150  Z= 0.315
  Chirality :  0.047   0.260   3696
  Planarity :  0.007   0.144   4188
  Dihedral  : 12.537 102.290   9240
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.26 (0.15), residues: 2904
  helix:  1.97 (0.28), residues: 276
  sheet:  0.09 (0.15), residues: 1005
  loop : -0.70 (0.15), residues: 1623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.035   0.002   ARG C 320 
 TYR   0.020   0.002   TYR C 626 
 PHE   0.015   0.002   PHE G  98 
 TRP   0.016   0.002   TRP N  47 
 HIS   0.005   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (24303)
  covalent geometry    : angle       0.57394 (32985)
  SS BOND              : bond        0.00163 (   33)
  SS BOND              : angle       0.68022 (   66)
  hydrogen bonds       : bond        0.09972 (  924)
  hydrogen bonds       : angle       6.62293 ( 2658)
  link_BETA1-4         : bond        0.00352 (   12)
  link_BETA1-4         : angle       2.25200 (   36)
  link_NAG-ASN         : bond        0.00247 (   21)
  link_NAG-ASN         : angle       1.95455 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  498 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 498
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8160 (mt-10)
REVERT: A  402 GLN cc_start: 0.8245 (tt0) cc_final: 0.7966 (tm-30)
REVERT: A  444 ARG cc_start: 0.8446 (ttp80) cc_final: 0.7990 (ttp-110)
REVERT: B   80 ASP cc_start: 0.8737 (m-30) cc_final: 0.8466 (m-30)
REVERT: B  295 ASP cc_start: 0.7815 (t0) cc_final: 0.7571 (t0)
REVERT: B  402 GLN cc_start: 0.8349 (tt0) cc_final: 0.8138 (mt0)
REVERT: B  444 ARG cc_start: 0.8345 (ttp80) cc_final: 0.7969 (ttp-110)
REVERT: C  444 ARG cc_start: 0.8364 (ttp80) cc_final: 0.8028 (ttp-110)
REVERT: C  612 GLN cc_start: 0.8401 (mt0) cc_final: 0.8115 (mm110)
REVERT: D    3 GLN cc_start: 0.8504 (tt0) cc_final: 0.8078 (pt0)
REVERT: D   69 MET cc_start: 0.8260 (mmt) cc_final: 0.7625 (mmt)
REVERT: E   95 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7263 (ttp-170)
REVERT: H    3 GLN cc_start: 0.8407 (tt0) cc_final: 0.8166 (pt0)
REVERT: I   95 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7281 (ttp-170)
REVERT: L    3 GLN cc_start: 0.8465 (tt0) cc_final: 0.8166 (pt0)
REVERT: M   95 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7333 (ttp-170)
  outliers start: 0
  outliers final: 2
  residues processed: 498
  average time/residue: 0.5263
  time to fit residues: 306.0642
Evaluate side-chains
  330 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 328
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  231 ASP
Chi-restraints excluded: chain C residue  581 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 197 optimal weight:    3.9990
   chunk 215 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 132 optimal weight:    2.9990
   chunk 261 optimal weight:    1.9990
   chunk 248 optimal weight:    5.9990
   chunk 207 optimal weight:    4.9990
   chunk 155 optimal weight:    4.9990
   chunk 244 optimal weight:    1.9990
   chunk 183 optimal weight:    0.5980
   chunk 111 optimal weight:    0.0170
   overall best weight:    1.5224

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

Flipped N/Q/H residues before XYZ refinement:
A 202 HIS
A 341 ASN
A 365 HIS
A 409 ASN
A 447 ASN
A 478 ASN
A 556 GLN
B 341 ASN
B 365 HIS
B 409 ASN
B 447 ASN
B 478 ASN
B 556 GLN
C 286 ASN
C 341 ASN
C 409 ASN
C 447 ASN
C 478 ASN
C 556 GLN
D  53 ASN
E  38 GLN
F  77 GLN
G  17 GLN
G  51 ASN
I  38 GLN
J  50 ASN
K  17 GLN
K  27BASN
M  38 GLN
N  50 ASN
O  17 GLN
O  51 ASN

Total number of N/Q/H flips: 32

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.160445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.129190 restraints weight = 27448.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.55
r_work: 0.3162 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  24369  Z= 0.239
  Angle     :  0.626   7.910  33150  Z= 0.328
  Chirality :  0.047   0.200   3696
  Planarity :  0.004   0.044   4188
  Dihedral  :  7.924  72.181   3946
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  :  8.91 %
    Favored  : 87.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.09 (0.15), residues: 2904
  helix:  2.62 (0.28), residues: 279
  sheet: -0.04 (0.15), residues: 996
  loop : -0.50 (0.15), residues: 1629

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 258 
 TYR   0.019   0.002   TYR O  49 
 PHE   0.018   0.002   PHE B 265 
 TRP   0.015   0.002   TRP D  36 
 HIS   0.007   0.002   HIS L  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00570 (24303)
  covalent geometry    : angle       0.61653 (32985)
  SS BOND              : bond        0.00175 (   33)
  SS BOND              : angle       0.73001 (   66)
  hydrogen bonds       : bond        0.04220 (  924)
  hydrogen bonds       : angle       5.65443 ( 2658)
  link_BETA1-4         : bond        0.00305 (   12)
  link_BETA1-4         : angle       2.32729 (   36)
  link_NAG-ASN         : bond        0.00398 (   21)
  link_NAG-ASN         : angle       1.80435 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 352
  time to evaluate  : 0.644 
Fit side-chains
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.7181 (ttp) cc_final: 0.6935 (ttt)
REVERT: A  248 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7805 (mm)
REVERT: A  298 PHE cc_start: 0.8411 (m-80) cc_final: 0.8204 (m-80)
REVERT: A  326 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7969 (mt-10)
REVERT: A  402 GLN cc_start: 0.8104 (tt0) cc_final: 0.7666 (tm-30)
REVERT: A  444 ARG cc_start: 0.8234 (ttp80) cc_final: 0.7616 (ttp-110)
REVERT: A  607 ARG cc_start: 0.8083 (mpt180) cc_final: 0.7757 (mpt180)
REVERT: A  634 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7206 (tmtm)
REVERT: B  295 ASP cc_start: 0.7704 (t0) cc_final: 0.7412 (t0)
REVERT: B  342 VAL cc_start: 0.8336 (p) cc_final: 0.8112 (m)
REVERT: B  402 GLN cc_start: 0.8145 (tt0) cc_final: 0.7802 (tt0)
REVERT: B  600 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8471 (tt0)
REVERT: C  342 VAL cc_start: 0.8299 (p) cc_final: 0.8058 (m)
REVERT: C  444 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7670 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7102 (m) cc_final: 0.6842 (m)
REVERT: C  612 GLN cc_start: 0.8399 (mt0) cc_final: 0.7769 (mm110)
REVERT: E   95 ARG cc_start: 0.7893 (ttm170) cc_final: 0.6984 (ttp-170)
REVERT: F   77 GLN cc_start: 0.8008 (mt0) cc_final: 0.7803 (mt0)
REVERT: H    3 GLN cc_start: 0.8310 (tt0) cc_final: 0.7680 (pt0)
REVERT: H   72 ASP cc_start: 0.7526 (t0) cc_final: 0.7272 (t0)
REVERT: I   95 ARG cc_start: 0.7938 (ttm170) cc_final: 0.7048 (ttp-170)
REVERT: L    3 GLN cc_start: 0.8415 (tt0) cc_final: 0.7730 (pt0)
REVERT: M   95 ARG cc_start: 0.7900 (ttm170) cc_final: 0.7115 (ttp-170)
  outliers start: 101
  outliers final: 63
  residues processed: 410
  average time/residue: 0.5574
  time to fit residues: 264.2390
Evaluate side-chains
  391 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 325
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  634 LYS
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  231 ASP
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  133 ILE
Chi-restraints excluded: chain C residue  139 LYS
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   30 LYS
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   30 LYS
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   67 VAL
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   80 MET
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   30 LYS
Chi-restraints excluded: chain M residue   63 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   27 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 130 optimal weight:    0.9980
   chunk 170 optimal weight:    0.8980
   chunk 128 optimal weight:    1.9990
   chunk 212 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 184 optimal weight:    0.9980
   chunk 171 optimal weight:    0.0980
   chunk 189 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 264 optimal weight:    1.9990
   chunk 218 optimal weight:    0.4980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
A 286 ASN
A 341 ASN
A 556 GLN
B 341 ASN
B 534 ASN
B 556 GLN
C 202 HIS
C 556 GLN
E  53 GLN
G  51 ASN
I  38 GLN
I  53 GLN
L  62 ASN
M  53 GLN
O  51 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.160869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.127807 restraints weight = 27393.019|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 2.78
r_work: 0.3213 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3082 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  24369  Z= 0.132
  Angle     :  0.529   7.726  33150  Z= 0.278
  Chirality :  0.044   0.176   3696
  Planarity :  0.004   0.038   4188
  Dihedral  :  6.511  51.255   3942
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 11.94 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.02 (0.15), residues: 2904
  helix:  2.97 (0.29), residues: 279
  sheet: -0.04 (0.15), residues: 1014
  loop : -0.44 (0.15), residues: 1611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C 258 
 TYR   0.017   0.001   TYR B 226 
 PHE   0.015   0.001   PHE B 265 
 TRP   0.011   0.001   TRP D  36 
 HIS   0.005   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (24303)
  covalent geometry    : angle       0.52227 (32985)
  SS BOND              : bond        0.00160 (   33)
  SS BOND              : angle       0.65493 (   66)
  hydrogen bonds       : bond        0.03403 (  924)
  hydrogen bonds       : angle       5.32505 ( 2658)
  link_BETA1-4         : bond        0.00304 (   12)
  link_BETA1-4         : angle       2.02132 (   36)
  link_NAG-ASN         : bond        0.00182 (   21)
  link_NAG-ASN         : angle       1.30259 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  431 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 355
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6918 (ttp) cc_final: 0.6593 (ttt)
REVERT: A  211 MET cc_start: 0.7392 (mtp) cc_final: 0.7051 (mtp)
REVERT: A  229 VAL cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (m)
REVERT: A  248 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7479 (mm)
REVERT: A  298 PHE cc_start: 0.8375 (m-80) cc_final: 0.8091 (m-80)
REVERT: A  326 GLU cc_start: 0.8440 (mt-10) cc_final: 0.8028 (mt-10)
REVERT: A  402 GLN cc_start: 0.7641 (tt0) cc_final: 0.6997 (tt0)
REVERT: A  444 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7000 (ttp-110)
REVERT: B   96 MET cc_start: 0.6870 (ttp) cc_final: 0.6586 (ttt)
REVERT: B  295 ASP cc_start: 0.7791 (t0) cc_final: 0.7500 (t0)
REVERT: B  341 ASN cc_start: 0.8190 (t0) cc_final: 0.7990 (t0)
REVERT: B  354 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6973 (mmp80)
REVERT: B  356 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8371 (pt)
REVERT: B  387 SER cc_start: 0.8266 (OUTLIER) cc_final: 0.7781 (p)
REVERT: B  402 GLN cc_start: 0.7648 (tt0) cc_final: 0.7058 (tt0)
REVERT: B  444 ARG cc_start: 0.7481 (ttp80) cc_final: 0.6788 (ttm-80)
REVERT: C  178 HIS cc_start: 0.7218 (m-70) cc_final: 0.6931 (m-70)
REVERT: C  248 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7521 (mm)
REVERT: C  344 CYS cc_start: 0.7127 (t) cc_final: 0.6864 (t)
REVERT: C  354 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7161 (mmp80)
REVERT: C  402 GLN cc_start: 0.7644 (tm-30) cc_final: 0.7053 (tm-30)
REVERT: C  444 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7065 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7331 (m) cc_final: 0.7015 (m)
REVERT: C  612 GLN cc_start: 0.8106 (mt0) cc_final: 0.7258 (mm110)
REVERT: D    3 GLN cc_start: 0.8188 (tt0) cc_final: 0.6995 (pt0)
REVERT: E   30 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6879 (mtpp)
REVERT: E   69 THR cc_start: 0.8487 (p) cc_final: 0.7918 (m)
REVERT: E   95 ARG cc_start: 0.7506 (ttm170) cc_final: 0.6165 (ttp-170)
REVERT: F   77 GLN cc_start: 0.7782 (mt0) cc_final: 0.7511 (mt0)
REVERT: H    3 GLN cc_start: 0.8093 (tt0) cc_final: 0.7112 (pt0)
REVERT: H   72 ASP cc_start: 0.6974 (t0) cc_final: 0.6473 (t0)
REVERT: I   30 LYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6967 (mtpp)
REVERT: I   79 ARG cc_start: 0.5440 (mtt180) cc_final: 0.5219 (mmt90)
REVERT: I   95 ARG cc_start: 0.7566 (ttm170) cc_final: 0.6195 (ttp-170)
REVERT: J   86 ASP cc_start: 0.7322 (m-30) cc_final: 0.6930 (m-30)
REVERT: K   83 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7377 (tt0)
REVERT: L    3 GLN cc_start: 0.8067 (tt0) cc_final: 0.6879 (pt0)
REVERT: M   30 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7044 (mtpp)
REVERT: M   95 ARG cc_start: 0.7474 (ttm170) cc_final: 0.6272 (ttp-170)
  outliers start: 76
  outliers final: 46
  residues processed: 395
  average time/residue: 0.5509
  time to fit residues: 251.9850
Evaluate side-chains
  388 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 332
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  187 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain E residue   30 LYS
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   30 LYS
Chi-restraints excluded: chain I residue   72 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain K residue   27 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   80 MET
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   30 LYS
Chi-restraints excluded: chain M residue   72 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   79 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 153 optimal weight:    0.7980
   chunk 263 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 177 optimal weight:    5.9990
   chunk 104 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 193 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
A 178 HIS
A 556 GLN
B 118 ASN
B 202 HIS
B 556 GLN
C 534 ASN
G  51 ASN
H  53 ASN
I  38 GLN
J  77 GLN
L  53 ASN
O  51 ASN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.158784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.125285 restraints weight = 27301.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 2.68
r_work: 0.3190 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.1892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  24369  Z= 0.184
  Angle     :  0.567   9.250  33150  Z= 0.296
  Chirality :  0.045   0.179   3696
  Planarity :  0.004   0.053   4188
  Dihedral  :  6.006  42.665   3942
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 11.90 %
    Favored  : 84.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.02 (0.15), residues: 2904
  helix:  2.88 (0.29), residues: 279
  sheet: -0.03 (0.15), residues: 1014
  loop : -0.48 (0.16), residues: 1611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 258 
 TYR   0.019   0.002   TYR O  49 
 PHE   0.019   0.002   PHE B 265 
 TRP   0.014   0.002   TRP F  47 
 HIS   0.004   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 (24303)
  covalent geometry    : angle       0.55849 (32985)
  SS BOND              : bond        0.00170 (   33)
  SS BOND              : angle       0.78368 (   66)
  hydrogen bonds       : bond        0.03746 (  924)
  hydrogen bonds       : angle       5.32118 ( 2658)
  link_BETA1-4         : bond        0.00279 (   12)
  link_BETA1-4         : angle       2.22700 (   36)
  link_NAG-ASN         : bond        0.00285 (   21)
  link_NAG-ASN         : angle       1.53498 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 101
    poor density    : 333
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6940 (ttp) cc_final: 0.6604 (ttt)
REVERT: A  229 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8194 (m)
REVERT: A  248 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7478 (mm)
REVERT: A  326 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7903 (mt-10)
REVERT: A  402 GLN cc_start: 0.7578 (tt0) cc_final: 0.6940 (tt0)
REVERT: A  444 ARG cc_start: 0.7705 (ttp80) cc_final: 0.6965 (ttp-110)
REVERT: A  607 ARG cc_start: 0.7547 (mpt180) cc_final: 0.7219 (mpt180)
REVERT: B  248 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7552 (mm)
REVERT: B  295 ASP cc_start: 0.7791 (t0) cc_final: 0.7475 (t0)
REVERT: B  354 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7025 (mmp80)
REVERT: B  402 GLN cc_start: 0.7612 (tt0) cc_final: 0.7026 (tt0)
REVERT: B  444 ARG cc_start: 0.7443 (ttp80) cc_final: 0.6706 (ttm-80)
REVERT: B  600 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8428 (tt0)
REVERT: B  612 GLN cc_start: 0.7841 (mt0) cc_final: 0.7049 (mm110)
REVERT: C  248 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7522 (mm)
REVERT: C  344 CYS cc_start: 0.7060 (t) cc_final: 0.6806 (t)
REVERT: C  354 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6893 (mmp80)
REVERT: C  402 GLN cc_start: 0.7601 (tm-30) cc_final: 0.7137 (tt0)
REVERT: C  444 ARG cc_start: 0.7726 (ttp80) cc_final: 0.6994 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7341 (m) cc_final: 0.6978 (m)
REVERT: C  612 GLN cc_start: 0.8064 (mt0) cc_final: 0.7232 (mm110)
REVERT: E   24 SER cc_start: 0.8015 (OUTLIER) cc_final: 0.7692 (t)
REVERT: E   79 ARG cc_start: 0.5455 (mtt180) cc_final: 0.5221 (mtt90)
REVERT: F   77 GLN cc_start: 0.7820 (mt0) cc_final: 0.7554 (mt0)
REVERT: H    3 GLN cc_start: 0.8061 (tt0) cc_final: 0.7043 (pt0)
REVERT: H   72 ASP cc_start: 0.7002 (t0) cc_final: 0.6428 (t0)
REVERT: I   79 ARG cc_start: 0.5573 (mtt180) cc_final: 0.5317 (mmt90)
REVERT: J   77 GLN cc_start: 0.7734 (mt0) cc_final: 0.7511 (mt0)
REVERT: J   86 ASP cc_start: 0.7310 (m-30) cc_final: 0.6904 (m-30)
REVERT: K   83 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7352 (tt0)
REVERT: M   47 LEU cc_start: 0.7788 (mt) cc_final: 0.7533 (tp)
REVERT: M   79 ARG cc_start: 0.5596 (mtt180) cc_final: 0.5279 (mmt90)
REVERT: M   95 ARG cc_start: 0.7528 (ttm170) cc_final: 0.6254 (ttp-170)
  outliers start: 101
  outliers final: 75
  residues processed: 398
  average time/residue: 0.6077
  time to fit residues: 279.8966
Evaluate side-chains
  402 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 319
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   27 SER
Chi-restraints excluded: chain E residue   30 LYS
Chi-restraints excluded: chain E residue   72 SER
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   62 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   27 SER
Chi-restraints excluded: chain I residue   30 LYS
Chi-restraints excluded: chain I residue   63 SER
Chi-restraints excluded: chain I residue   72 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   67 VAL
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain K residue   42 THR
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   30 LYS
Chi-restraints excluded: chain M residue   63 SER
Chi-restraints excluded: chain M residue   72 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   62 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   79 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 173 optimal weight:    0.9990
   chunk 243 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0070
   chunk 275 optimal weight:    0.5980
   chunk 133 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 216 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 165 optimal weight:    0.9980
   chunk 92 optimal weight:    0.6980
   chunk 249 optimal weight:    2.9990
   overall best weight:    0.5998

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
A 178 HIS
A 286 ASN
A 341 ASN
A 510 GLN
A 534 ASN
A 556 GLN
E  53 GLN
G  51 ASN
I  53 GLN
M  53 GLN
O  51 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.160382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.126299 restraints weight = 27118.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.66
r_work: 0.3212 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3086 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3086
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  24369  Z= 0.123
  Angle     :  0.513   5.979  33150  Z= 0.271
  Chirality :  0.043   0.183   3696
  Planarity :  0.004   0.041   4188
  Dihedral  :  5.464  41.647   3942
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 13.53 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.03 (0.15), residues: 2904
  helix:  3.08 (0.29), residues: 279
  sheet: -0.05 (0.15), residues: 1023
  loop : -0.43 (0.16), residues: 1602

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 258 
 TYR   0.017   0.001   TYR B 226 
 PHE   0.016   0.001   PHE B 265 
 TRP   0.011   0.001   TRP D  36 
 HIS   0.002   0.001   HIS L  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (24303)
  covalent geometry    : angle       0.50661 (32985)
  SS BOND              : bond        0.00165 (   33)
  SS BOND              : angle       0.69111 (   66)
  hydrogen bonds       : bond        0.03253 (  924)
  hydrogen bonds       : angle       5.20271 ( 2658)
  link_BETA1-4         : bond        0.00403 (   12)
  link_BETA1-4         : angle       1.88463 (   36)
  link_NAG-ASN         : bond        0.00188 (   21)
  link_NAG-ASN         : angle       1.24275 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  421 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 334
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6878 (ttp) cc_final: 0.6609 (ttt)
REVERT: A  211 MET cc_start: 0.7440 (mtp) cc_final: 0.7140 (mtp)
REVERT: A  229 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.8217 (m)
REVERT: A  248 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7505 (mm)
REVERT: A  326 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7818 (mt-10)
REVERT: A  354 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.6587 (mmp80)
REVERT: A  402 GLN cc_start: 0.7651 (tt0) cc_final: 0.7056 (tt0)
REVERT: A  444 ARG cc_start: 0.7769 (ttp80) cc_final: 0.7055 (ttp-110)
REVERT: B  248 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7598 (mm)
REVERT: B  295 ASP cc_start: 0.7830 (t0) cc_final: 0.7518 (t0)
REVERT: B  311 ARG cc_start: 0.6959 (ttp80) cc_final: 0.6623 (ttp80)
REVERT: B  354 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7014 (mmp80)
REVERT: B  387 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7786 (p)
REVERT: B  402 GLN cc_start: 0.7633 (tt0) cc_final: 0.7043 (tt0)
REVERT: B  435 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8090 (tttp)
REVERT: B  444 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6760 (ttm-80)
REVERT: B  612 GLN cc_start: 0.7855 (mt0) cc_final: 0.7022 (mm110)
REVERT: C  248 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7527 (mm)
REVERT: C  344 CYS cc_start: 0.7047 (t) cc_final: 0.6786 (t)
REVERT: C  354 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.6970 (mmp80)
REVERT: C  387 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7775 (p)
REVERT: C  402 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7142 (tt0)
REVERT: C  444 ARG cc_start: 0.7744 (ttp80) cc_final: 0.7020 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7309 (m) cc_final: 0.6946 (m)
REVERT: C  612 GLN cc_start: 0.8118 (mt0) cc_final: 0.7316 (mm110)
REVERT: D    3 GLN cc_start: 0.8175 (tt0) cc_final: 0.6995 (pt0)
REVERT: E   30 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6913 (mtpp)
REVERT: E   69 THR cc_start: 0.8505 (p) cc_final: 0.7906 (m)
REVERT: E   79 ARG cc_start: 0.5520 (mtt180) cc_final: 0.5245 (mtt90)
REVERT: F   77 GLN cc_start: 0.7903 (mt0) cc_final: 0.7623 (mt0)
REVERT: H    3 GLN cc_start: 0.8119 (tt0) cc_final: 0.7126 (pt0)
REVERT: H   72 ASP cc_start: 0.6955 (t0) cc_final: 0.6411 (t70)
REVERT: I   30 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6968 (mtpp)
REVERT: I   79 ARG cc_start: 0.5631 (mtt180) cc_final: 0.5402 (mmt90)
REVERT: J   86 ASP cc_start: 0.7440 (m-30) cc_final: 0.7077 (m-30)
REVERT: M   30 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.7098 (mtpp)
REVERT: M   47 LEU cc_start: 0.7808 (mt) cc_final: 0.7582 (tp)
REVERT: M   79 ARG cc_start: 0.5700 (mtt180) cc_final: 0.5388 (mmt90)
REVERT: M   95 ARG cc_start: 0.7512 (ttm170) cc_final: 0.6186 (ttp-170)
  outliers start: 87
  outliers final: 55
  residues processed: 385
  average time/residue: 0.6016
  time to fit residues: 266.9647
Evaluate side-chains
  388 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 320
  time to evaluate  : 0.891 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   27 SER
Chi-restraints excluded: chain E residue   30 LYS
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   30 LYS
Chi-restraints excluded: chain I residue   65 SER
Chi-restraints excluded: chain I residue   72 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   67 VAL
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain L residue   31 ASP
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   30 LYS
Chi-restraints excluded: chain M residue   72 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 209 optimal weight:    3.9990
   chunk 127 optimal weight:    0.4980
   chunk 52 optimal weight:   10.0000
   chunk 272 optimal weight:    4.9990
   chunk 45 optimal weight:    4.9990
   chunk 168 optimal weight:    4.9990
   chunk 158 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0060
   chunk 174 optimal weight:    1.9990
   chunk 258 optimal weight:    5.9990
   overall best weight:    1.0400

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
A 178 HIS
A 556 GLN
B 118 ASN
C 286 ASN
E  53 GLN
G  51 ASN
M  53 GLN
O  51 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.159566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.126068 restraints weight = 27127.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3403 rms_B_bonded: 2.72
r_work: 0.3188 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  24369  Z= 0.175
  Angle     :  0.547   6.670  33150  Z= 0.286
  Chirality :  0.044   0.180   3696
  Planarity :  0.004   0.041   4188
  Dihedral  :  5.450  45.097   3942
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 13.29 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.01 (0.15), residues: 2904
  helix:  2.96 (0.29), residues: 279
  sheet: -0.05 (0.15), residues: 1005
  loop : -0.43 (0.16), residues: 1620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 258 
 TYR   0.021   0.002   TYR A 206 
 PHE   0.019   0.002   PHE B 265 
 TRP   0.014   0.002   TRP F  47 
 HIS   0.003   0.001   HIS B 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (24303)
  covalent geometry    : angle       0.53965 (32985)
  SS BOND              : bond        0.00285 (   33)
  SS BOND              : angle       0.76745 (   66)
  hydrogen bonds       : bond        0.03589 (  924)
  hydrogen bonds       : angle       5.24285 ( 2658)
  link_BETA1-4         : bond        0.00305 (   12)
  link_BETA1-4         : angle       2.00213 (   36)
  link_NAG-ASN         : bond        0.00254 (   21)
  link_NAG-ASN         : angle       1.42053 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 100
    poor density    : 322
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6963 (ttp) cc_final: 0.6681 (ttt)
REVERT: A  211 MET cc_start: 0.7515 (mtp) cc_final: 0.7210 (mtp)
REVERT: A  248 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7535 (mm)
REVERT: A  311 ARG cc_start: 0.7068 (ttm110) cc_final: 0.6859 (ttm110)
REVERT: A  326 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8105 (mt-10)
REVERT: A  354 ARG cc_start: 0.7738 (OUTLIER) cc_final: 0.6859 (mmp80)
REVERT: A  402 GLN cc_start: 0.7716 (tt0) cc_final: 0.7113 (tt0)
REVERT: A  444 ARG cc_start: 0.7779 (ttp80) cc_final: 0.7057 (ttp-110)
REVERT: A  600 GLU cc_start: 0.9010 (OUTLIER) cc_final: 0.8410 (tt0)
REVERT: A  607 ARG cc_start: 0.7694 (mpt180) cc_final: 0.7483 (mpt180)
REVERT: B  248 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7606 (mm)
REVERT: B  295 ASP cc_start: 0.7868 (t0) cc_final: 0.7542 (t0)
REVERT: B  354 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.7037 (mmp80)
REVERT: B  402 GLN cc_start: 0.7672 (tt0) cc_final: 0.7088 (tt0)
REVERT: B  444 ARG cc_start: 0.7542 (ttp80) cc_final: 0.6851 (ttm-80)
REVERT: B  522 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8614 (mttm)
REVERT: B  600 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8603 (tt0)
REVERT: B  612 GLN cc_start: 0.7918 (mt0) cc_final: 0.7098 (mm110)
REVERT: C  248 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7507 (mm)
REVERT: C  344 CYS cc_start: 0.7088 (t) cc_final: 0.6836 (t)
REVERT: C  354 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.6809 (mmp80)
REVERT: C  402 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7203 (tt0)
REVERT: C  444 ARG cc_start: 0.7753 (ttp80) cc_final: 0.7020 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7366 (m) cc_final: 0.7052 (m)
REVERT: C  612 GLN cc_start: 0.8137 (mt0) cc_final: 0.7367 (mm110)
REVERT: E   24 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7780 (t)
REVERT: E   79 ARG cc_start: 0.5601 (mtt180) cc_final: 0.5344 (mtt90)
REVERT: F   77 GLN cc_start: 0.7894 (mt0) cc_final: 0.7601 (mt0)
REVERT: H   72 ASP cc_start: 0.7062 (t0) cc_final: 0.6597 (t0)
REVERT: I   79 ARG cc_start: 0.5697 (mtt180) cc_final: 0.5418 (mmt90)
REVERT: J   86 ASP cc_start: 0.7442 (m-30) cc_final: 0.7092 (m-30)
REVERT: M   79 ARG cc_start: 0.5627 (mtt180) cc_final: 0.5343 (mmt90)
REVERT: M   95 ARG cc_start: 0.7574 (ttm170) cc_final: 0.6231 (ttp-170)
  outliers start: 100
  outliers final: 73
  residues processed: 388
  average time/residue: 0.5571
  time to fit residues: 251.1511
Evaluate side-chains
  396 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 313
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain A residue  600 GLU
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  337 GLN
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  522 LYS
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   27 SER
Chi-restraints excluded: chain E residue   30 LYS
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   62 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   27 SER
Chi-restraints excluded: chain I residue   30 LYS
Chi-restraints excluded: chain I residue   65 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   67 VAL
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   30 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   62 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 243 optimal weight:    0.8980
   chunk 218 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 133 optimal weight:    1.9990
   chunk 181 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 165 optimal weight:    0.9980
   chunk 246 optimal weight:    7.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 556 GLN
B 118 ASN
C 118 ASN
C 286 ASN
E  53 GLN
G  51 ASN
J  77 GLN
M  53 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.159576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.125486 restraints weight = 27222.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.71
r_work: 0.3196 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  24369  Z= 0.155
  Angle     :  0.530   6.481  33150  Z= 0.279
  Chirality :  0.044   0.175   3696
  Planarity :  0.004   0.042   4188
  Dihedral  :  5.354  47.587   3942
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 13.68 %
    Favored  : 82.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.04 (0.15), residues: 2904
  helix:  3.01 (0.29), residues: 279
  sheet: -0.08 (0.15), residues: 1029
  loop : -0.39 (0.16), residues: 1596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 258 
 TYR   0.021   0.001   TYR C 631 
 PHE   0.017   0.002   PHE B 265 
 TRP   0.013   0.001   TRP F  47 
 HIS   0.003   0.001   HIS C 319 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (24303)
  covalent geometry    : angle       0.52203 (32985)
  SS BOND              : bond        0.00196 (   33)
  SS BOND              : angle       1.05264 (   66)
  hydrogen bonds       : bond        0.03435 (  924)
  hydrogen bonds       : angle       5.20680 ( 2658)
  link_BETA1-4         : bond        0.00298 (   12)
  link_BETA1-4         : angle       1.84239 (   36)
  link_NAG-ASN         : bond        0.00203 (   21)
  link_NAG-ASN         : angle       1.33008 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 98
    poor density    : 324
  time to evaluate  : 0.907 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6927 (ttp) cc_final: 0.6676 (ttt)
REVERT: A  211 MET cc_start: 0.7473 (mtp) cc_final: 0.7201 (mtp)
REVERT: A  248 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7490 (mm)
REVERT: A  326 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8049 (mt-10)
REVERT: A  354 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6919 (mmp80)
REVERT: A  402 GLN cc_start: 0.7665 (tt0) cc_final: 0.7073 (tt0)
REVERT: A  444 ARG cc_start: 0.7757 (ttp80) cc_final: 0.7042 (ttp-110)
REVERT: A  607 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7435 (mpt180)
REVERT: B  248 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7577 (mm)
REVERT: B  251 MET cc_start: 0.8072 (ttm) cc_final: 0.7740 (tpp)
REVERT: B  295 ASP cc_start: 0.7847 (t0) cc_final: 0.7524 (t0)
REVERT: B  354 ARG cc_start: 0.7715 (OUTLIER) cc_final: 0.7033 (mmp80)
REVERT: B  402 GLN cc_start: 0.7640 (tt0) cc_final: 0.7058 (tt0)
REVERT: B  444 ARG cc_start: 0.7525 (ttp80) cc_final: 0.6803 (ttm-80)
REVERT: B  600 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.8581 (tt0)
REVERT: B  612 GLN cc_start: 0.7890 (mt0) cc_final: 0.7080 (mm110)
REVERT: C  117 ILE cc_start: 0.6023 (OUTLIER) cc_final: 0.5808 (mt)
REVERT: C  211 MET cc_start: 0.7445 (mtp) cc_final: 0.6786 (mtm)
REVERT: C  248 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7500 (mm)
REVERT: C  251 MET cc_start: 0.7907 (ttp) cc_final: 0.7702 (ttp)
REVERT: C  344 CYS cc_start: 0.7021 (t) cc_final: 0.6802 (t)
REVERT: C  354 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6964 (mmp80)
REVERT: C  402 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7126 (tt0)
REVERT: C  444 ARG cc_start: 0.7722 (ttp80) cc_final: 0.6982 (ttp-110)
REVERT: C  501 GLN cc_start: 0.8343 (mt0) cc_final: 0.8075 (mt0)
REVERT: C  574 CYS cc_start: 0.7242 (m) cc_final: 0.6805 (m)
REVERT: C  612 GLN cc_start: 0.8117 (mt0) cc_final: 0.7312 (mm110)
REVERT: E   24 SER cc_start: 0.8117 (OUTLIER) cc_final: 0.7812 (t)
REVERT: E   79 ARG cc_start: 0.5653 (mtt180) cc_final: 0.5376 (mtt90)
REVERT: F   77 GLN cc_start: 0.7875 (mt0) cc_final: 0.7589 (mt0)
REVERT: H   72 ASP cc_start: 0.6963 (t0) cc_final: 0.6506 (t0)
REVERT: J   86 ASP cc_start: 0.7448 (m-30) cc_final: 0.7103 (m-30)
REVERT: M   79 ARG cc_start: 0.5652 (mtt180) cc_final: 0.5391 (mmt90)
REVERT: M   95 ARG cc_start: 0.7556 (ttm170) cc_final: 0.6198 (ttp-170)
  outliers start: 98
  outliers final: 79
  residues processed: 388
  average time/residue: 0.5501
  time to fit residues: 248.4448
Evaluate side-chains
  396 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 308
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 ILE
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  144 GLN
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  445 LEU
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   27 SER
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   62 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   52 ASN
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   27 SER
Chi-restraints excluded: chain I residue   30 LYS
Chi-restraints excluded: chain I residue   65 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   67 VAL
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain L residue   21 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   27 SER
Chi-restraints excluded: chain M residue   30 LYS
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   62 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   76 ASN
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 114 optimal weight:    3.9990
   chunk 130 optimal weight:    0.9990
   chunk 112 optimal weight:    0.8980
   chunk 176 optimal weight:    5.9990
   chunk 271 optimal weight:    2.9990
   chunk 277 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0040
   chunk 40 optimal weight:    0.9980
   chunk 241 optimal weight:    2.9990
   chunk 203 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.7794

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
A 286 ASN
A 556 GLN
C 286 ASN
E  53 GLN
G  51 ASN
I  53 GLN
L  53 ASN
O  51 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.159777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.125908 restraints weight = 27127.746|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 2.72
r_work: 0.3198 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  24369  Z= 0.141
  Angle     :  0.518   7.560  33150  Z= 0.272
  Chirality :  0.043   0.174   3696
  Planarity :  0.004   0.046   4188
  Dihedral  :  5.263  49.719   3942
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.22 %
    Favored  : 82.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.07 (0.15), residues: 2904
  helix:  2.97 (0.29), residues: 282
  sheet: -0.04 (0.15), residues: 1029
  loop : -0.37 (0.16), residues: 1593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 258 
 TYR   0.019   0.001   TYR A 206 
 PHE   0.017   0.001   PHE B 265 
 TRP   0.012   0.001   TRP F  47 
 HIS   0.003   0.001   HIS A 182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 (24303)
  covalent geometry    : angle       0.51222 (32985)
  SS BOND              : bond        0.00166 (   33)
  SS BOND              : angle       0.80531 (   66)
  hydrogen bonds       : bond        0.03310 (  924)
  hydrogen bonds       : angle       5.15333 ( 2658)
  link_BETA1-4         : bond        0.00319 (   12)
  link_BETA1-4         : angle       1.74550 (   36)
  link_NAG-ASN         : bond        0.00184 (   21)
  link_NAG-ASN         : angle       1.26548 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  413 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 317
  time to evaluate  : 0.913 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6913 (ttp) cc_final: 0.6638 (ttt)
REVERT: A  211 MET cc_start: 0.7417 (mtp) cc_final: 0.7177 (mtp)
REVERT: A  248 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7490 (mm)
REVERT: A  326 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8065 (mt-10)
REVERT: A  354 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7239 (mmp80)
REVERT: A  402 GLN cc_start: 0.7700 (tt0) cc_final: 0.7122 (tt0)
REVERT: A  444 ARG cc_start: 0.7760 (ttp80) cc_final: 0.6895 (ttm-80)
REVERT: A  607 ARG cc_start: 0.7666 (mpt180) cc_final: 0.7417 (mpt180)
REVERT: A  634 LYS cc_start: 0.7849 (tptp) cc_final: 0.7626 (tptp)
REVERT: B  141 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7235 (mtm180)
REVERT: B  248 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7567 (mm)
REVERT: B  295 ASP cc_start: 0.7862 (t0) cc_final: 0.7539 (t0)
REVERT: B  311 ARG cc_start: 0.7047 (ttp80) cc_final: 0.6778 (ttp80)
REVERT: B  354 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7003 (mmp80)
REVERT: B  356 ILE cc_start: 0.8648 (OUTLIER) cc_final: 0.8311 (pt)
REVERT: B  387 SER cc_start: 0.8246 (OUTLIER) cc_final: 0.7779 (p)
REVERT: B  402 GLN cc_start: 0.7622 (tt0) cc_final: 0.7042 (tt0)
REVERT: B  435 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7933 (tttp)
REVERT: B  600 GLU cc_start: 0.9054 (OUTLIER) cc_final: 0.8571 (tt0)
REVERT: B  612 GLN cc_start: 0.7881 (mt0) cc_final: 0.7069 (mm110)
REVERT: C  117 ILE cc_start: 0.5960 (OUTLIER) cc_final: 0.5754 (mt)
REVERT: C  211 MET cc_start: 0.7442 (mtp) cc_final: 0.7152 (mtp)
REVERT: C  248 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7464 (mm)
REVERT: C  327 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7625 (mmm160)
REVERT: C  354 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.6911 (mmp80)
REVERT: C  387 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7783 (p)
REVERT: C  402 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7124 (tt0)
REVERT: C  444 ARG cc_start: 0.7715 (ttp80) cc_final: 0.6919 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7309 (m) cc_final: 0.6888 (m)
REVERT: C  612 GLN cc_start: 0.8110 (mt0) cc_final: 0.7308 (mm110)
REVERT: E   24 SER cc_start: 0.8070 (OUTLIER) cc_final: 0.7793 (t)
REVERT: E   69 THR cc_start: 0.8517 (p) cc_final: 0.7890 (m)
REVERT: E   79 ARG cc_start: 0.5655 (mtt180) cc_final: 0.5382 (mtt90)
REVERT: F   77 GLN cc_start: 0.7881 (mt0) cc_final: 0.7597 (mt0)
REVERT: H   72 ASP cc_start: 0.6881 (t0) cc_final: 0.6439 (t0)
REVERT: J   86 ASP cc_start: 0.7464 (m-30) cc_final: 0.7103 (m-30)
REVERT: L   72 ASP cc_start: 0.7133 (t0) cc_final: 0.6526 (t0)
REVERT: M   79 ARG cc_start: 0.5698 (mtt180) cc_final: 0.5446 (mmt90)
REVERT: M   95 ARG cc_start: 0.7550 (ttm170) cc_final: 0.6195 (ttp-170)
  outliers start: 96
  outliers final: 69
  residues processed: 380
  average time/residue: 0.5608
  time to fit residues: 247.5852
Evaluate side-chains
  389 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 306
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 GLN
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain B residue  435 LYS
Chi-restraints excluded: chain B residue  600 GLU
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  330 SER
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   27 SER
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   20 VAL
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue    5 SER
Chi-restraints excluded: chain I residue   27 SER
Chi-restraints excluded: chain I residue   65 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   67 VAL
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain K residue   42 THR
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain M residue    5 SER
Chi-restraints excluded: chain M residue   27 SER
Chi-restraints excluded: chain M residue   63 SER
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   62 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   76 ASN
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 80 optimal weight:    0.0270
   chunk 151 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 90 optimal weight:    0.7980
   chunk 89 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   chunk 93 optimal weight:    0.3980
   chunk 241 optimal weight:    3.9990
   chunk 218 optimal weight:    0.2980
   chunk 85 optimal weight:    1.9990
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
A 510 GLN
A 556 GLN
B 286 ASN
E  53 GLN
G  51 ASN
I  53 GLN
M  53 GLN
O  51 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.161561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.127928 restraints weight = 27247.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.76
r_work: 0.3222 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3091 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041  24369  Z= 0.104
  Angle     :  0.488   6.529  33150  Z= 0.257
  Chirality :  0.042   0.174   3696
  Planarity :  0.004   0.051   4188
  Dihedral  :  5.003  49.229   3942
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.08 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.16 (0.15), residues: 2904
  helix:  3.15 (0.29), residues: 282
  sheet:  0.17 (0.16), residues: 972
  loop : -0.43 (0.16), residues: 1650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C 311 
 TYR   0.017   0.001   TYR A 226 
 PHE   0.016   0.001   PHE B 265 
 TRP   0.009   0.001   TRP D  36 
 HIS   0.002   0.001   HIS L  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (24303)
  covalent geometry    : angle       0.48358 (32985)
  SS BOND              : bond        0.00132 (   33)
  SS BOND              : angle       0.65933 (   66)
  hydrogen bonds       : bond        0.02999 (  924)
  hydrogen bonds       : angle       5.04154 ( 2658)
  link_BETA1-4         : bond        0.00337 (   12)
  link_BETA1-4         : angle       1.56411 (   36)
  link_NAG-ASN         : bond        0.00179 (   21)
  link_NAG-ASN         : angle       1.08581 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  411 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 82
    poor density    : 329
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   96 MET cc_start: 0.6888 (ttp) cc_final: 0.6627 (ttt)
REVERT: A  211 MET cc_start: 0.7350 (mtp) cc_final: 0.7096 (mtp)
REVERT: A  248 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7441 (mm)
REVERT: A  258 ARG cc_start: 0.7838 (mtm110) cc_final: 0.7632 (mtp-110)
REVERT: A  326 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8020 (mt-10)
REVERT: A  354 ARG cc_start: 0.7613 (OUTLIER) cc_final: 0.6807 (mmp80)
REVERT: A  402 GLN cc_start: 0.7638 (tt0) cc_final: 0.7053 (tt0)
REVERT: A  444 ARG cc_start: 0.7764 (ttp80) cc_final: 0.6903 (ttm-80)
REVERT: A  607 ARG cc_start: 0.7584 (mpt180) cc_final: 0.7330 (mpt180)
REVERT: B  141 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7231 (mtm180)
REVERT: B  248 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7577 (mm)
REVERT: B  251 MET cc_start: 0.7894 (ttm) cc_final: 0.7651 (tpp)
REVERT: B  295 ASP cc_start: 0.7849 (t0) cc_final: 0.7526 (t0)
REVERT: B  311 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6804 (ttp80)
REVERT: B  341 ASN cc_start: 0.8261 (t0) cc_final: 0.7929 (t160)
REVERT: B  354 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.6944 (mmp80)
REVERT: B  356 ILE cc_start: 0.8539 (OUTLIER) cc_final: 0.8179 (mm)
REVERT: B  387 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7772 (p)
REVERT: B  402 GLN cc_start: 0.7616 (tt0) cc_final: 0.7036 (tt0)
REVERT: B  444 ARG cc_start: 0.7507 (ttp80) cc_final: 0.6774 (ttm-80)
REVERT: B  612 GLN cc_start: 0.7883 (mt0) cc_final: 0.7084 (mm110)
REVERT: C  117 ILE cc_start: 0.5935 (OUTLIER) cc_final: 0.5726 (mt)
REVERT: C  211 MET cc_start: 0.7437 (mtp) cc_final: 0.7209 (mtp)
REVERT: C  248 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7581 (mm)
REVERT: C  327 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7621 (mmm160)
REVERT: C  354 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7051 (mmp80)
REVERT: C  356 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8365 (mt)
REVERT: C  387 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7785 (p)
REVERT: C  402 GLN cc_start: 0.7614 (tm-30) cc_final: 0.7118 (tt0)
REVERT: C  444 ARG cc_start: 0.7736 (ttp80) cc_final: 0.6958 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7277 (m) cc_final: 0.6855 (m)
REVERT: C  612 GLN cc_start: 0.8110 (mt0) cc_final: 0.7320 (mm110)
REVERT: C  613 LEU cc_start: 0.8588 (mt) cc_final: 0.8379 (mt)
REVERT: D    3 GLN cc_start: 0.8140 (tt0) cc_final: 0.6932 (pt0)
REVERT: E   24 SER cc_start: 0.8077 (OUTLIER) cc_final: 0.7798 (t)
REVERT: E   69 THR cc_start: 0.8496 (p) cc_final: 0.7930 (m)
REVERT: E   79 ARG cc_start: 0.5603 (mtt180) cc_final: 0.5328 (mtt90)
REVERT: F   77 GLN cc_start: 0.7880 (mt0) cc_final: 0.7586 (mt0)
REVERT: H    3 GLN cc_start: 0.8104 (tt0) cc_final: 0.7082 (pt0)
REVERT: H   72 ASP cc_start: 0.6826 (t0) cc_final: 0.6384 (t0)
REVERT: J   86 ASP cc_start: 0.7414 (m-30) cc_final: 0.7111 (m-30)
REVERT: L   72 ASP cc_start: 0.7114 (t0) cc_final: 0.6540 (t0)
REVERT: M   79 ARG cc_start: 0.5695 (mtt180) cc_final: 0.5472 (mmt90)
REVERT: M   95 ARG cc_start: 0.7497 (ttm170) cc_final: 0.6156 (ttp-170)
REVERT: N   43 LYS cc_start: 0.7561 (mmmt) cc_final: 0.7156 (mmmm)
  outliers start: 82
  outliers final: 54
  residues processed: 383
  average time/residue: 0.5940
  time to fit residues: 263.6306
Evaluate side-chains
  386 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 319
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  144 GLN
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   62 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   52 ASN
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain I residue   27 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   62 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   76 ASN
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 233 optimal weight:    1.9990
   chunk 135 optimal weight:    0.6980
   chunk 108 optimal weight:    0.9990
   chunk 213 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 254 optimal weight:    0.9980
   chunk 221 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0060
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
A 556 GLN
B 286 ASN
D  53 ASN
E  53 GLN
G  51 ASN
I  53 GLN
O  51 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.165599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.134897 restraints weight = 26869.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.39
r_work: 0.3261 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  24369  Z= 0.135
  Angle     :  0.516   8.000  33150  Z= 0.269
  Chirality :  0.043   0.173   3696
  Planarity :  0.004   0.061   4188
  Dihedral  :  5.080  51.138   3942
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.47 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.18 (0.15), residues: 2904
  helix:  3.18 (0.28), residues: 279
  sheet:  0.13 (0.15), residues: 1005
  loop : -0.39 (0.16), residues: 1620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 311 
 TYR   0.019   0.001   TYR O  49 
 PHE   0.020   0.001   PHE B 265 
 TRP   0.012   0.001   TRP J  47 
 HIS   0.003   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (24303)
  covalent geometry    : angle       0.50984 (32985)
  SS BOND              : bond        0.00150 (   33)
  SS BOND              : angle       0.72862 (   66)
  hydrogen bonds       : bond        0.03228 (  924)
  hydrogen bonds       : angle       5.05957 ( 2658)
  link_BETA1-4         : bond        0.00309 (   12)
  link_BETA1-4         : angle       1.73291 (   36)
  link_NAG-ASN         : bond        0.00172 (   21)
  link_NAG-ASN         : angle       1.23767 (   63)

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

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

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  5808 Ramachandran restraints generated.
    2904 Oldfield, 0 Emsley, 2904 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  397 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 319
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  248 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7823 (mm)
REVERT: A  354 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7670 (mmp80)
REVERT: A  402 GLN cc_start: 0.8307 (tt0) cc_final: 0.7988 (tt0)
REVERT: A  444 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7523 (ttm-80)
REVERT: A  607 ARG cc_start: 0.7965 (mpt180) cc_final: 0.7727 (mpt180)
REVERT: B  141 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7700 (mtm180)
REVERT: B  248 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7953 (mm)
REVERT: B  251 MET cc_start: 0.7955 (ttm) cc_final: 0.7753 (tpp)
REVERT: B  295 ASP cc_start: 0.8001 (t0) cc_final: 0.7696 (t0)
REVERT: B  341 ASN cc_start: 0.8401 (t0) cc_final: 0.8110 (t160)
REVERT: B  354 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7403 (mmp80)
REVERT: B  356 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8505 (mm)
REVERT: B  387 SER cc_start: 0.8696 (OUTLIER) cc_final: 0.8374 (p)
REVERT: B  402 GLN cc_start: 0.8362 (tt0) cc_final: 0.7989 (tt0)
REVERT: B  444 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7442 (ttm-80)
REVERT: B  612 GLN cc_start: 0.8150 (mt0) cc_final: 0.7479 (mm110)
REVERT: C  248 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7878 (mm)
REVERT: C  327 ARG cc_start: 0.8245 (mmm160) cc_final: 0.8003 (mmm160)
REVERT: C  354 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7285 (mmp80)
REVERT: C  356 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8654 (mt)
REVERT: C  387 SER cc_start: 0.8632 (OUTLIER) cc_final: 0.8355 (p)
REVERT: C  402 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8022 (tt0)
REVERT: C  444 ARG cc_start: 0.8216 (ttp80) cc_final: 0.7588 (ttp-110)
REVERT: C  574 CYS cc_start: 0.7489 (m) cc_final: 0.7141 (m)
REVERT: C  612 GLN cc_start: 0.8411 (mt0) cc_final: 0.7787 (mm110)
REVERT: E   24 SER cc_start: 0.8262 (OUTLIER) cc_final: 0.8005 (t)
REVERT: E   69 THR cc_start: 0.8801 (p) cc_final: 0.8358 (m)
REVERT: E   79 ARG cc_start: 0.6238 (mtt180) cc_final: 0.6005 (mtt90)
REVERT: F   77 GLN cc_start: 0.8284 (mt0) cc_final: 0.8056 (mt0)
REVERT: H   72 ASP cc_start: 0.7551 (t0) cc_final: 0.7297 (t0)
REVERT: J   86 ASP cc_start: 0.7656 (m-30) cc_final: 0.7436 (m-30)
REVERT: L   72 ASP cc_start: 0.7662 (t0) cc_final: 0.7457 (t0)
REVERT: M   95 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7069 (ttp-170)
REVERT: N   43 LYS cc_start: 0.7925 (mmmt) cc_final: 0.7626 (mmmm)
  outliers start: 78
  outliers final: 60
  residues processed: 371
  average time/residue: 0.6007
  time to fit residues: 258.1089
Evaluate side-chains
  383 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 311
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  139 LYS
Chi-restraints excluded: chain A residue  144 GLN
Chi-restraints excluded: chain A residue  183 SER
Chi-restraints excluded: chain A residue  187 SER
Chi-restraints excluded: chain A residue  210 THR
Chi-restraints excluded: chain A residue  248 LEU
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  330 SER
Chi-restraints excluded: chain A residue  354 ARG
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  363 SER
Chi-restraints excluded: chain A residue  387 SER
Chi-restraints excluded: chain A residue  411 THR
Chi-restraints excluded: chain A residue  565 MET
Chi-restraints excluded: chain A residue  580 VAL
Chi-restraints excluded: chain B residue   81 VAL
Chi-restraints excluded: chain B residue  141 ARG
Chi-restraints excluded: chain B residue  183 SER
Chi-restraints excluded: chain B residue  210 THR
Chi-restraints excluded: chain B residue  229 VAL
Chi-restraints excluded: chain B residue  248 LEU
Chi-restraints excluded: chain B residue  256 THR
Chi-restraints excluded: chain B residue  273 VAL
Chi-restraints excluded: chain B residue  330 SER
Chi-restraints excluded: chain B residue  354 ARG
Chi-restraints excluded: chain B residue  356 ILE
Chi-restraints excluded: chain B residue  363 SER
Chi-restraints excluded: chain B residue  387 SER
Chi-restraints excluded: chain B residue  411 THR
Chi-restraints excluded: chain C residue   81 VAL
Chi-restraints excluded: chain C residue  183 SER
Chi-restraints excluded: chain C residue  229 VAL
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  256 THR
Chi-restraints excluded: chain C residue  273 VAL
Chi-restraints excluded: chain C residue  304 THR
Chi-restraints excluded: chain C residue  354 ARG
Chi-restraints excluded: chain C residue  356 ILE
Chi-restraints excluded: chain C residue  387 SER
Chi-restraints excluded: chain C residue  411 THR
Chi-restraints excluded: chain C residue  580 VAL
Chi-restraints excluded: chain D residue   70 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue   89 MET
Chi-restraints excluded: chain E residue   24 SER
Chi-restraints excluded: chain E residue   95 SER
Chi-restraints excluded: chain F residue    7 SER
Chi-restraints excluded: chain F residue   62 SER
Chi-restraints excluded: chain F residue   63 LEU
Chi-restraints excluded: chain F residue   79 SER
Chi-restraints excluded: chain G residue    2 SER
Chi-restraints excluded: chain G residue   27 SER
Chi-restraints excluded: chain G residue   52 ASN
Chi-restraints excluded: chain G residue   56 SER
Chi-restraints excluded: chain G residue   97 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   87 THR
Chi-restraints excluded: chain H residue   89 MET
Chi-restraints excluded: chain I residue   27 SER
Chi-restraints excluded: chain J residue    7 SER
Chi-restraints excluded: chain J residue   79 SER
Chi-restraints excluded: chain L residue   70 THR
Chi-restraints excluded: chain L residue   87 THR
Chi-restraints excluded: chain N residue    7 SER
Chi-restraints excluded: chain N residue   62 SER
Chi-restraints excluded: chain N residue   67 VAL
Chi-restraints excluded: chain N residue   76 ASN
Chi-restraints excluded: chain N residue   79 SER
Chi-restraints excluded: chain O residue   97 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 288
   random chunks:
   chunk 191 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 287 optimal weight:    0.3980
   chunk 195 optimal weight:    0.1980
   chunk 57 optimal weight:    2.9990
   chunk 181 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0980
   chunk 216 optimal weight:    2.9990
   chunk 230 optimal weight:    4.9990
   chunk 149 optimal weight:    0.0030
   overall best weight:    0.2390

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

Flipped N/Q/H residues before XYZ refinement:
A 286 ASN
B 286 ASN
C 286 ASN
E  53 GLN
G  51 ASN
I  53 GLN
M  53 GLN
O  51 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.168933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.138326 restraints weight = 26638.948|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.37
r_work: 0.3279 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3149 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.3149
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  24369  Z= 0.091
  Angle     :  0.484   8.267  33150  Z= 0.255
  Chirality :  0.042   0.217   3696
  Planarity :  0.004   0.058   4188
  Dihedral  :  4.753  47.903   3942
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 16.47 %
    Favored  : 81.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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:  0.30 (0.16), residues: 2904
  helix:  3.26 (0.28), residues: 282
  sheet:  0.28 (0.16), residues: 978
  loop : -0.36 (0.16), residues: 1644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 258 
 TYR   0.017   0.001   TYR A 226 
 PHE   0.020   0.001   PHE B 265 
 TRP   0.013   0.001   TRP F  35A
 HIS   0.003   0.001   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 (24303)
  covalent geometry    : angle       0.47884 (32985)
  SS BOND              : bond        0.00124 (   33)
  SS BOND              : angle       1.07520 (   66)
  hydrogen bonds       : bond        0.02763 (  924)
  hydrogen bonds       : angle       4.91478 ( 2658)
  link_BETA1-4         : bond        0.00396 (   12)
  link_BETA1-4         : angle       1.42690 (   36)
  link_NAG-ASN         : bond        0.00239 (   21)
  link_NAG-ASN         : angle       0.95966 (   63)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9303.07 seconds
wall clock time: 159 minutes 0.38 seconds (9540.38 seconds total)