Starting phenix.real_space_refine
on Sun Jun 22 13:28:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8x56_38064/06_2025/8x56_38064.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8x56_38064/06_2025/8x56_38064.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8x56_38064/06_2025/8x56_38064.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8x56_38064/06_2025/8x56_38064.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8x56_38064/06_2025/8x56_38064.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8x56_38064/06_2025/8x56_38064.cif"
  }
  resolution = 3.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.053
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     114      5.16       5
     C   16422      2.51       5
     N    4197      2.21       5
     O    5016      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 102 residue(s): 0.07s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 25749
  Number of models: 1
  Model: ""
    Number of chains: 21
    Chain: "A"
      Number of atoms: 8318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1063, 8318
          Classifications: {'peptide': 1063}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 55, 'TRANS': 1007}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 8318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1063, 8318
          Classifications: {'peptide': 1063}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 55, 'TRANS': 1007}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 8318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1063, 8318
          Classifications: {'peptide': 1063}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 55, 'TRANS': 1007}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "E"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "F"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "G"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "H"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "I"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "J"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "K"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "L"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "M"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "N"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "O"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "P"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: "Q"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 25
          Unusual residues: {'BMA': 1, 'NAG': 1}
          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: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "B"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
    Chain: "C"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 140
          Unusual residues: {'NAG': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 30
          Unresolved non-hydrogen chiralities: 10
  Time building chain proxies: 15.40, per 1000 atoms: 0.60
  Number of scatterers: 25749
  At special positions: 0
  Unit cell: (143.52, 142.48, 189.28, 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     114     16.00
     O    5016      8.00
     N    4197      7.00
     C   16422      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=38, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 131 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 291 " - pdb=" SG  CYS A 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 617 " - pdb=" SG  CYS A 649 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 662 " - pdb=" SG  CYS A 671 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 738 " - pdb=" SG  CYS A 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 840 " - pdb=" SG  CYS A 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 840 " - pdb=" SG  CYS B 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 131 " - pdb=" SG  CYS C 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 291 " - pdb=" SG  CYS C 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 617 " - pdb=" SG  CYS C 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 662 " - pdb=" SG  CYS C 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 738 " - pdb=" SG  CYS C 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 743 " - pdb=" SG  CYS C 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 840 " - pdb=" SG  CYS C 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1032 " - pdb=" SG  CYS C1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1126 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " BMA D   2 "
      " NAG E   1 " - " BMA E   2 "
      " NAG F   1 " - " BMA F   2 "
      " NAG G   1 " - " BMA G   2 "
      " NAG H   1 " - " BMA H   2 "
      " NAG I   1 " - " BMA I   2 "
      " NAG J   1 " - " BMA J   2 "
      " NAG K   1 " - " BMA K   2 "
      " NAG L   1 " - " BMA L   2 "
      " NAG M   1 " - " BMA M   2 "
      " NAG N   1 " - " BMA N   2 "
      " NAG O   1 " - " BMA O   2 "
      " NAG P   1 " - " BMA P   2 "
      " NAG Q   1 " - " BMA Q   2 "
      " NAG R   1 " - " BMA R   2 "
    NAG-ASN
      " NAG A1301 " - " ASN A 122 "
      " NAG A1302 " - " ASN A 343 "
      " NAG A1303 " - " ASN A 331 "
      " NAG A1304 " - " ASN A 616 "
      " NAG A1305 " - " ASN A 657 "
      " NAG A1306 " - " ASN A 709 "
      " NAG A1307 " - " ASN A1074 "
      " NAG A1308 " - " ASN A  61 "
      " NAG A1309 " - " ASN A 165 "
      " NAG A1310 " - " ASN A 234 "
      " NAG B1301 " - " ASN B 122 "
      " NAG B1302 " - " ASN B  61 "
      " NAG B1303 " - " ASN B 165 "
      " NAG B1304 " - " ASN B 234 "
      " NAG B1305 " - " ASN B 331 "
      " NAG B1306 " - " ASN B 616 "
      " NAG B1307 " - " ASN B 657 "
      " NAG B1308 " - " ASN B 709 "
      " NAG B1309 " - " ASN B1074 "
      " NAG B1310 " - " ASN B 343 "
      " NAG C1301 " - " ASN C 122 "
      " NAG C1302 " - " ASN C  61 "
      " NAG C1303 " - " ASN C 165 "
      " NAG C1304 " - " ASN C 234 "
      " NAG C1305 " - " ASN C 616 "
      " NAG C1306 " - " ASN C 657 "
      " NAG C1307 " - " ASN C 709 "
      " NAG C1308 " - " ASN C1074 "
      " NAG C1309 " - " ASN C 343 "
      " NAG C1310 " - " ASN C 331 "
      " NAG E   1 " - " ASN A1134 "
      " NAG F   1 " - " ASN A 801 "
      " NAG G   1 " - " ASN A 717 "
      " NAG H   1 " - " ASN A1098 "
      " NAG I   1 " - " ASN B 282 "
      " NAG J   1 " - " ASN B1134 "
      " NAG K   1 " - " ASN B 801 "
      " NAG L   1 " - " ASN B 717 "
      " NAG M   1 " - " ASN B1098 "
      " NAG N   1 " - " ASN C 282 "
      " NAG O   1 " - " ASN C1134 "
      " NAG P   1 " - " ASN C 801 "
      " NAG Q   1 " - " ASN C 717 "
      " NAG R   1 " - " ASN C1098 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 6.60
  Conformation dependent library (CDL) restraints added in 3.4 seconds
  

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  5958

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 53 sheets defined
      25.3% alpha, 20.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 294 through 303
    Processing helix  chain 'A' and resid 337 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.647A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 371
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.968A  pdb=" N   SER A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
      removed outlier: 3.858A  pdb=" N   TYR A 421 " --> pdb=" O   ASN A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 506
      removed outlier: 3.703A  pdb=" N   GLN A 506 " --> pdb=" O   VAL A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 627
    Processing helix  chain 'A' and resid 737 through 743
    Processing helix  chain 'A' and resid 746 through 755
      removed outlier: 3.790A  pdb=" N   GLN A 755 " --> pdb=" O   ASN A 751 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 783
    Processing helix  chain 'A' and resid 816 through 825
    Processing helix  chain 'A' and resid 848 through 856
      removed outlier: 3.594A  pdb=" N   ASN A 856 " --> pdb=" O   ALA A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 884
    Processing helix  chain 'A' and resid 897 through 908
    Processing helix  chain 'A' and resid 912 through 919
      removed outlier: 4.175A  pdb=" N   LEU A 916 " --> pdb=" O   THR A 912 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 941
      removed outlier: 3.855A  pdb=" N   GLN A 935 " --> pdb=" O   ILE A 931 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ASP A 936 " --> pdb=" O   GLY A 932 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 945 through 965
    Processing helix  chain 'A' and resid 966 through 968
      No H-bonds generated for 'chain 'A' and resid 966 through 968'
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 985 through 1033
      removed outlier: 4.991A  pdb=" N   VAL A 991 " --> pdb=" O   PRO A 987 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLN A 992 " --> pdb=" O   GLU A 988 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 303
    Processing helix  chain 'B' and resid 337 through 343
    Processing helix  chain 'B' and resid 365 through 372
      removed outlier: 3.550A  pdb=" N   PHE B 371 " --> pdb=" O   VAL B 367 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ALA B 372 " --> pdb=" O   LEU B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 410
      removed outlier: 3.876A  pdb=" N   SER B 408 " --> pdb=" O   GLY B 404 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
      removed outlier: 3.598A  pdb=" N   TYR B 421 " --> pdb=" O   ASN B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
    Processing helix  chain 'B' and resid 543 through 546
    Processing helix  chain 'B' and resid 616 through 627
      removed outlier: 3.829A  pdb=" N   VAL B 620 " --> pdb=" O   ASN B 616 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 737 through 743
    Processing helix  chain 'B' and resid 746 through 755
    Processing helix  chain 'B' and resid 760 through 783
    Processing helix  chain 'B' and resid 816 through 826
    Processing helix  chain 'B' and resid 840 through 844
      removed outlier: 4.361A  pdb=" N   ILE B 844 " --> pdb=" O   LEU B 841 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 848 through 856
    Processing helix  chain 'B' and resid 866 through 884
      removed outlier: 3.623A  pdb=" N   ALA B 871 " --> pdb=" O   ASP B 867 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 886 through 890
    Processing helix  chain 'B' and resid 897 through 908
    Processing helix  chain 'B' and resid 913 through 919
    Processing helix  chain 'B' and resid 919 through 941
      removed outlier: 3.661A  pdb=" N   GLN B 935 " --> pdb=" O   ILE B 931 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP B 936 " --> pdb=" O   GLY B 932 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 945 through 965
    Processing helix  chain 'B' and resid 966 through 968
      No H-bonds generated for 'chain 'B' and resid 966 through 968'
    Processing helix  chain 'B' and resid 976 through 984
      removed outlier: 4.510A  pdb=" N   SER B 982 " --> pdb=" O   ASN B 978 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 985 through 1033
      removed outlier: 6.050A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   GLN B 992 " --> pdb=" O   GLU B 988 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 303
    Processing helix  chain 'C' and resid 337 through 343
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.620A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 371
    Processing helix  chain 'C' and resid 403 through 410
      removed outlier: 3.649A  pdb=" N   VAL C 407 " --> pdb=" O   LYS C 403 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   SER C 408 " --> pdb=" O   GLY C 404 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing helix  chain 'C' and resid 502 through 506
    Processing helix  chain 'C' and resid 618 through 627
    Processing helix  chain 'C' and resid 737 through 743
    Processing helix  chain 'C' and resid 746 through 755
    Processing helix  chain 'C' and resid 760 through 783
    Processing helix  chain 'C' and resid 816 through 825
    Processing helix  chain 'C' and resid 840 through 844
      removed outlier: 4.408A  pdb=" N   ILE C 844 " --> pdb=" O   LEU C 841 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 848 through 855
    Processing helix  chain 'C' and resid 866 through 884
      removed outlier: 3.581A  pdb=" N   ALA C 871 " --> pdb=" O   ASP C 867 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 886 through 890
    Processing helix  chain 'C' and resid 897 through 909
    Processing helix  chain 'C' and resid 912 through 919
      removed outlier: 4.436A  pdb=" N   LEU C 916 " --> pdb=" O   THR C 912 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 919 through 941
      removed outlier: 3.742A  pdb=" N   GLN C 935 " --> pdb=" O   ILE C 931 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP C 936 " --> pdb=" O   GLY C 932 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 945 through 965
      removed outlier: 3.502A  pdb=" N   GLN C 965 " --> pdb=" O   THR C 961 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 966 through 968
      No H-bonds generated for 'chain 'C' and resid 966 through 968'
    Processing helix  chain 'C' and resid 976 through 982
    Processing helix  chain 'C' and resid 985 through 1033
      removed outlier: 5.470A  pdb=" N   VAL C 991 " --> pdb=" O   PRO C 987 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   GLN C 992 " --> pdb=" O   GLU C 988 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30
      removed outlier: 7.277A  pdb=" N   ASN A  61 " --> pdb=" O   TYR A 269 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   TYR A 269 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 267 " --> pdb=" O   THR A  63 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   PHE A  65 " --> pdb=" O   TYR A 265 " (cutoff:3.500A)
      removed outlier: 5.178A  pdb=" N   TYR A 265 " --> pdb=" O   PHE A  65 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LYS A 206 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LYS A 195 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      removed outlier: 6.204A  pdb=" N   PHE A 201 " --> pdb=" O   ASP A 228 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ASP A 228 " --> pdb=" O   PHE A 201 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 226 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLU A 224 " --> pdb=" O   SER A 205 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   HIS A 207 " --> pdb=" O   ALA A 222 " (cutoff:3.500A)
      removed outlier: 9.229A  pdb=" N   ALA A 222 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43
    Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55
      removed outlier: 3.514A  pdb=" N   ARG A 273 " --> pdb=" O   ASP A  53 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP A 287 " --> pdb=" O   LYS A 278 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85
      removed outlier: 3.601A  pdb=" N   GLY A 107 " --> pdb=" O   ARG A 237 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   GLY A 103 " --> pdb=" O   LEU A 241 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 118
      removed outlier: 3.621A  pdb=" N   LYS A 129 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 316
      removed outlier: 7.172A  pdb=" N   VAL A 595 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLY A 594 " --> pdb=" O   GLN A 613 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   SER A 596 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   CYS A 649 " --> pdb=" O   TYR A 612 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY A 648 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 326
      removed outlier: 6.764A  pdb=" N   GLU A 324 " --> pdb=" O   ASN A 540 " (cutoff:3.500A)
      removed outlier: 8.753A  pdb=" N   ASN A 542 " --> pdb=" O   GLU A 324 " (cutoff:3.500A)
      removed outlier: 8.245A  pdb=" N   ILE A 326 " --> pdb=" O   ASN A 542 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   PHE A 543 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 4.038A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   ALA A 435 " --> pdb=" O   PHE A 375 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.932A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474
      removed outlier: 3.914A  pdb=" N   TYR A 489 " --> pdb=" O   TYR A 473 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 565 through 566
      removed outlier: 6.863A  pdb=" N   PHE A 565 " --> pdb=" O   PHE C  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'A' and resid 575 through 577
    Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 660
      removed outlier: 3.629A  pdb=" N   GLU A 654 " --> pdb=" O   ILE A 692 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   THR A 696 " --> pdb=" O   VAL A 656 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ASN A 658 " --> pdb=" O   THR A 696 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   SER A 691 " --> pdb=" O   GLN A 675 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   TYR A 695 " --> pdb=" O   CYS A 671 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 701 through 702
      removed outlier: 6.811A  pdb=" N   ALA A 701 " --> pdb=" O   ILE C 788 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'A' and resid 713 through 715
      removed outlier: 3.844A  pdb=" N   ILE A 714 " --> pdb=" O   LYS A1073 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LYS A1073 " --> pdb=" O   ILE A 714 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 728
      removed outlier: 7.207A  pdb=" N   GLY A1059 " --> pdb=" O   SER A1055 " (cutoff:3.500A)
      removed outlier: 5.570A  pdb=" N   SER A1055 " --> pdb=" O   GLY A1059 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL A1061 " --> pdb=" O   PRO A1053 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   LEU A1063 " --> pdb=" O   SER A1051 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   SER A1051 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   VAL A1065 " --> pdb=" O   LEU A1049 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 734
      removed outlier: 4.198A  pdb=" N   LYS A 733 " --> pdb=" O   LEU A 861 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 788 through 790
      removed outlier: 5.586A  pdb=" N   ILE A 788 " --> pdb=" O   ASN B 703 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC1
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122
      removed outlier: 3.577A  pdb=" N   CYS A1082 " --> pdb=" O   VAL A1133 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097
    Processing sheet with id=AC4, first strand: chain 'B' and resid 26 through 30
      removed outlier: 6.999A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   PHE B  65 " --> pdb=" O   TYR B 265 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   TYR B 265 " --> pdb=" O   PHE B  65 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   ASP B 264 " --> pdb=" O   THR B  95 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   THR B  95 " --> pdb=" O   ASP B 264 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   VAL B  90 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE B 194 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   THR B 208 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLU B 191 " --> pdb=" O   LYS B 206 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LYS B 206 " --> pdb=" O   GLU B 191 " (cutoff:3.500A)
      removed outlier: 6.037A  pdb=" N   PHE B 201 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ASP B 228 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 6.950A  pdb=" N   ILE B 203 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   HIS B 207 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
      removed outlier: 9.906A  pdb=" N   ALA B 222 " --> pdb=" O   HIS B 207 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   VAL B  36 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 50 through 55
      removed outlier: 3.698A  pdb=" N   ARG B 273 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'B' and resid 84 through 85
      removed outlier: 3.703A  pdb=" N   LEU B 117 " --> pdb=" O   PHE B 106 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL B 130 " --> pdb=" O   PHE B 168 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   PHE B 168 " --> pdb=" O   VAL B 130 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 316
      removed outlier: 7.311A  pdb=" N   VAL B 595 " --> pdb=" O   THR B 315 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY B 594 " --> pdb=" O   GLN B 613 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 326
      removed outlier: 4.239A  pdb=" N   GLU B 324 " --> pdb=" O   CYS B 538 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.847A  pdb=" N   ASN B 354 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.821A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AD3, first strand: chain 'B' and resid 473 through 474
      removed outlier: 3.951A  pdb=" N   TYR B 489 " --> pdb=" O   TYR B 473 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 575 through 577
    Processing sheet with id=AD5, first strand: chain 'B' and resid 654 through 660
      removed outlier: 5.964A  pdb=" N   GLU B 654 " --> pdb=" O   ALA B 694 " (cutoff:3.500A)
      removed outlier: 8.444A  pdb=" N   THR B 696 " --> pdb=" O   GLU B 654 " (cutoff:3.500A)
      removed outlier: 8.805A  pdb=" N   VAL B 656 " --> pdb=" O   THR B 696 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   ILE B 670 " --> pdb=" O   ILE B 666 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 713 through 715
      removed outlier: 3.590A  pdb=" N   ILE B 714 " --> pdb=" O   LYS B1073 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   LYS B1073 " --> pdb=" O   ILE B 714 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'B' and resid 718 through 722
      removed outlier: 3.548A  pdb=" N   GLU B 725 " --> pdb=" O   PHE B1062 " (cutoff:3.500A)
    Processing sheet with id=AD8, first strand: chain 'B' and resid 718 through 722
      removed outlier: 5.601A  pdb=" N   TYR B1067 " --> pdb=" O   HIS B1048 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   HIS B1048 " --> pdb=" O   TYR B1067 " (cutoff:3.500A)
    Processing sheet with id=AD9, first strand: chain 'B' and resid 733 through 734
      removed outlier: 4.378A  pdb=" N   LYS B 733 " --> pdb=" O   LEU B 861 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'B' and resid 787 through 788
    Processing sheet with id=AE2, first strand: chain 'B' and resid 1077 through 1078
      removed outlier: 3.527A  pdb=" N   ALA B1078 " --> pdb=" O   PHE B1095 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE B1095 " --> pdb=" O   ALA B1078 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL B1094 " --> pdb=" O   THR B1105 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   THR B1105 " --> pdb=" O   VAL B1094 " (cutoff:3.500A)
    Processing sheet with id=AE3, first strand: chain 'B' and resid 1120 through 1122
    Processing sheet with id=AE4, first strand: chain 'C' and resid 27 through 30
      removed outlier: 3.520A  pdb=" N   VAL C  62 " --> pdb=" O   THR C  29 " (cutoff:3.500A)
      removed outlier: 6.893A  pdb=" N   ASN C  61 " --> pdb=" O   TYR C 269 " (cutoff:3.500A)
      removed outlier: 5.266A  pdb=" N   TYR C 269 " --> pdb=" O   ASN C  61 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   PHE C  65 " --> pdb=" O   TYR C 265 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TYR C 265 " --> pdb=" O   PHE C  65 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   PHE C 201 " --> pdb=" O   ASP C 228 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASP C 228 " --> pdb=" O   PHE C 201 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   ILE C 203 " --> pdb=" O   LEU C 226 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   HIS C 207 " --> pdb=" O   ALA C 222 " (cutoff:3.500A)
      removed outlier: 8.857A  pdb=" N   ALA C 222 " --> pdb=" O   HIS C 207 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   VAL C  36 " --> pdb=" O   LEU C 223 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'C' and resid 50 through 55
      removed outlier: 3.775A  pdb=" N   ASP C 287 " --> pdb=" O   LYS C 278 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'C' and resid 84 through 85
      removed outlier: 4.081A  pdb=" N   GLY C 107 " --> pdb=" O   ARG C 237 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   TRP C 104 " --> pdb=" O   ILE C 119 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   VAL C 120 " --> pdb=" O   PHE C 127 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   PHE C 168 " --> pdb=" O   VAL C 130 " (cutoff:3.500A)
    Processing sheet with id=AE7, first strand: chain 'C' and resid 311 through 316
      removed outlier: 3.507A  pdb=" N   THR C 315 " --> pdb=" O   VAL C 595 " (cutoff:3.500A)
      removed outlier: 7.502A  pdb=" N   VAL C 595 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLY C 594 " --> pdb=" O   GLN C 613 " (cutoff:3.500A)
    Processing sheet with id=AE8, first strand: chain 'C' and resid 325 through 326
      removed outlier: 3.542A  pdb=" N   THR C 553 " --> pdb=" O   ASP C 586 " (cutoff:3.500A)
    Processing sheet with id=AE9, first strand: chain 'C' and resid 354 through 358
      removed outlier: 3.589A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
    Processing sheet with id=AF1, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AF2, first strand: chain 'C' and resid 473 through 474
      removed outlier: 4.104A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)
    Processing sheet with id=AF3, first strand: chain 'C' and resid 654 through 660
      removed outlier: 6.542A  pdb=" N   GLU C 654 " --> pdb=" O   ALA C 694 " (cutoff:3.500A)
      removed outlier: 8.786A  pdb=" N   THR C 696 " --> pdb=" O   GLU C 654 " (cutoff:3.500A)
      removed outlier: 9.072A  pdb=" N   VAL C 656 " --> pdb=" O   THR C 696 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   ILE C 670 " --> pdb=" O   ILE C 666 " (cutoff:3.500A)
    Processing sheet with id=AF4, first strand: chain 'C' and resid 713 through 715
      removed outlier: 3.638A  pdb=" N   LYS C1073 " --> pdb=" O   ILE C 714 " (cutoff:3.500A)
    Processing sheet with id=AF5, first strand: chain 'C' and resid 718 through 728
      removed outlier: 3.608A  pdb=" N   GLU C 725 " --> pdb=" O   PHE C1062 " (cutoff:3.500A)
      removed outlier: 7.334A  pdb=" N   GLY C1059 " --> pdb=" O   SER C1055 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   SER C1055 " --> pdb=" O   GLY C1059 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   VAL C1061 " --> pdb=" O   PRO C1053 " (cutoff:3.500A)
      removed outlier: 6.233A  pdb=" N   LEU C1063 " --> pdb=" O   SER C1051 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   SER C1051 " --> pdb=" O   LEU C1063 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   VAL C1065 " --> pdb=" O   LEU C1049 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'C' and resid 733 through 734
      removed outlier: 4.335A  pdb=" N   LYS C 733 " --> pdb=" O   LEU C 861 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'C' and resid 1120 through 1122
      removed outlier: 3.814A  pdb=" N   CYS C1082 " --> pdb=" O   VAL C1133 " (cutoff:3.500A)
    Processing sheet with id=AF8, first strand: chain 'C' and resid 1094 through 1097

    891 hydrogen bonds defined for protein.
    2466 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: 11.38

  Time building geometry restraints manager: 7.80 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: 8118
        1.34 -     1.47: 6745
        1.47 -     1.60: 11345
        1.60 -     1.72: 0
        1.72 -     1.85: 141
  Bond restraints: 26349
  Sorted by residual:
  bond pdb=" N   PHE C 329 "
       pdb=" CA  PHE C 329 "
    ideal  model  delta    sigma   weight residual
    1.453  1.483 -0.030 8.30e-03 1.45e+04 1.30e+01
  bond pdb=" N   ILE C 212 "
       pdb=" CA  ILE C 212 "
    ideal  model  delta    sigma   weight residual
    1.459  1.502 -0.043 1.25e-02 6.40e+03 1.19e+01
  bond pdb=" N   ILE C 210 "
       pdb=" CA  ILE C 210 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.15e+00
  bond pdb=" N   LYS C 529 "
       pdb=" CA  LYS C 529 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.18e-02 7.18e+03 8.91e+00
  bond pdb=" N   THR C 208 "
       pdb=" CA  THR C 208 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.028 9.30e-03 1.16e+04 8.79e+00
  ... (remaining 26344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 34587
        1.97 -     3.95: 1027
        3.95 -     5.92: 186
        5.92 -     7.90: 48
        7.90 -     9.87: 8
  Bond angle restraints: 35856
  Sorted by residual:
  angle pdb=" C   ASN C1074 "
        pdb=" N   PHE C1075 "
        pdb=" CA  PHE C1075 "
      ideal   model   delta    sigma   weight residual
     121.90  115.46    6.44 1.26e+00 6.30e-01 2.61e+01
  angle pdb=" N   LEU B 387 "
        pdb=" CA  LEU B 387 "
        pdb=" C   LEU B 387 "
      ideal   model   delta    sigma   weight residual
     114.62  108.81    5.81 1.14e+00 7.69e-01 2.60e+01
  angle pdb=" C   ASN A1074 "
        pdb=" N   PHE A1075 "
        pdb=" CA  PHE A1075 "
      ideal   model   delta    sigma   weight residual
     121.90  115.59    6.31 1.26e+00 6.30e-01 2.50e+01
  angle pdb=" N   ILE C 834 "
        pdb=" CA  ILE C 834 "
        pdb=" C   ILE C 834 "
      ideal   model   delta    sigma   weight residual
     112.96  108.46    4.50 1.00e+00 1.00e+00 2.03e+01
  angle pdb=" C   PHE B  32 "
        pdb=" CA  PHE B  32 "
        pdb=" CB  PHE B  32 "
      ideal   model   delta    sigma   weight residual
     115.89  110.37    5.52 1.32e+00 5.74e-01 1.75e+01
  ... (remaining 35851 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.08: 14604
       23.08 -    46.16: 1421
       46.16 -    69.24: 162
       69.24 -    92.32: 143
       92.32 -   115.40: 113
  Dihedral angle restraints: 16443
    sinusoidal: 7167
      harmonic: 9276
  Sorted by residual:
  dihedral pdb=" CB  CYS B 738 "
           pdb=" SG  CYS B 738 "
           pdb=" SG  CYS B 760 "
           pdb=" CB  CYS B 760 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00    9.82   83.18     1      1.00e+01 1.00e-02 8.46e+01
  dihedral pdb=" CB  CYS B 617 "
           pdb=" SG  CYS B 617 "
           pdb=" SG  CYS B 649 "
           pdb=" CB  CYS B 649 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   26.01   66.99     1      1.00e+01 1.00e-02 5.85e+01
  dihedral pdb=" CB  CYS C 131 "
           pdb=" SG  CYS C 131 "
           pdb=" SG  CYS C 166 "
           pdb=" CB  CYS C 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   33.06   59.94     1      1.00e+01 1.00e-02 4.79e+01
  ... (remaining 16440 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.180: 4185
       0.180 -    0.360: 32
       0.360 -    0.540: 0
       0.540 -    0.721: 0
       0.721 -    0.901: 3
  Chirality restraints: 4220
  Sorted by residual:
  chirality pdb=" C1  NAG H   1 "
            pdb=" ND2 ASN A1098 "
            pdb=" C2  NAG H   1 "
            pdb=" O5  NAG H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.50   -0.90 2.00e-01 2.50e+01 2.03e+01
  chirality pdb=" C1  NAG R   1 "
            pdb=" ND2 ASN C1098 "
            pdb=" C2  NAG R   1 "
            pdb=" O5  NAG R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.51   -0.89 2.00e-01 2.50e+01 1.96e+01
  chirality pdb=" C1  NAG M   1 "
            pdb=" ND2 ASN B1098 "
            pdb=" C2  NAG M   1 "
            pdb=" O5  NAG M   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.52   -0.88 2.00e-01 2.50e+01 1.92e+01
  ... (remaining 4217 not shown)

  Planarity restraints: 4598
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  81 "    0.057 5.00e-02 4.00e+02   8.57e-02 1.18e+01
        pdb=" N   PRO A  82 "   -0.148 5.00e-02 4.00e+02
        pdb=" CA  PRO A  82 "    0.045 5.00e-02 4.00e+02
        pdb=" CD  PRO A  82 "    0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 216 "   -0.053 5.00e-02 4.00e+02   8.03e-02 1.03e+01
        pdb=" N   PRO B 217 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO B 217 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 217 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 237 "    0.288 9.50e-02 1.11e+02   1.29e-01 1.02e+01
        pdb=" NE  ARG C 237 "   -0.018 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 237 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 237 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 237 "    0.009 2.00e-02 2.50e+03
  ... (remaining 4595 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 449
        2.63 -     3.20: 23986
        3.20 -     3.77: 40142
        3.77 -     4.33: 53976
        4.33 -     4.90: 87247
  Nonbonded interactions: 205800
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 532 "
            pdb=" N   LEU B 533 "
     model   vdw
     2.064 3.120
  nonbonded pdb=" O   CYS A 590 "
            pdb=" OH  TYR C 837 "
     model   vdw
     2.115 3.040
  nonbonded pdb=" OG1 THR C 124 "
            pdb=" O7  NAG C1301 "
     model   vdw
     2.138 3.040
  nonbonded pdb=" NE2 GLN C 173 "
            pdb=" O   PRO C 174 "
     model   vdw
     2.138 3.120
  nonbonded pdb=" O   ASN B 978 "
            pdb=" OG1 THR C 547 "
     model   vdw
     2.148 3.040
  ... (remaining 205795 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
  selection = chain 'Q'
  selection = chain 'R'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.870
  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:             0.020
  Extract box with map and model:          0.960
  Check model and map are aligned:         0.180
  Set scattering table:                    0.240
  Process input model:                     61.420
  Find NCS groups from input model:        1.730
  Set up NCS constraints:                  0.210
  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:3.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   69.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
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   0.049  26447  Z= 0.228
  Angle     :  0.867  18.118  36109  Z= 0.438
  Chirality :  0.056   0.901   4220
  Planarity :  0.006   0.129   4554
  Dihedral  : 21.396 115.405  10371
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  6.96 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  : 27.32 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.65 (0.15), residues: 3159
  helix:  0.91 (0.20), residues: 699
  sheet: -0.93 (0.21), residues: 584
  loop : -2.04 (0.14), residues: 1876

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP B 633 
 HIS   0.010   0.001   HIS C 339 
 PHE   0.034   0.001   PHE C 342 
 TYR   0.023   0.001   TYR A 365 
 ARG   0.006   0.001   ARG C1107 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00853 (   44)
  link_NAG-ASN         : angle       4.91707 (  132)
  link_BETA1-4         : bond        0.00478 (   15)
  link_BETA1-4         : angle       2.37167 (   45)
  hydrogen bonds       : bond        0.20853 (  887)
  hydrogen bonds       : angle       8.35984 ( 2466)
  SS BOND              : bond        0.00464 (   38)
  SS BOND              : angle       1.71028 (   76)
  covalent geometry    : bond        0.00422 (26349)
  covalent geometry    : angle       0.80896 (35856)
  Misc. bond           : bond        0.00045 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 172
  time to evaluate  : 2.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  697 MET cc_start: 0.8885 (mmm) cc_final: 0.8585 (mmp)
REVERT: A  896 ILE cc_start: 0.8637 (tp) cc_final: 0.8075 (tt)
REVERT: A 1050 MET cc_start: 0.7898 (ptp) cc_final: 0.7559 (ptp)
REVERT: A 1107 ARG cc_start: 0.7615 (mmt-90) cc_final: 0.7343 (mmt-90)
REVERT: B  377 PHE cc_start: 0.7024 (t80) cc_final: 0.6746 (t80)
REVERT: B  985 ASP cc_start: 0.7608 (p0) cc_final: 0.7390 (p0)
REVERT: C  699 LEU cc_start: 0.8592 (mt) cc_final: 0.8363 (mp)
  outliers start: 16
  outliers final: 8
  residues processed: 184
  average time/residue: 0.3448
  time to fit residues: 106.4825
Evaluate side-chains
  160 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 2.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain B residue   61 ASN
Chi-restraints excluded: chain B residue   88 ASP
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain C residue   61 ASN
Chi-restraints excluded: chain C residue  341 VAL
Chi-restraints excluded: chain C residue  620 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 268 optimal weight:    4.9990
   chunk 241 optimal weight:    7.9990
   chunk 133 optimal weight:    9.9990
   chunk 82 optimal weight:    0.6980
   chunk 162 optimal weight:    6.9990
   chunk 128 optimal weight:    2.9990
   chunk 249 optimal weight:    0.0770
   chunk 96 optimal weight:    8.9990
   chunk 151 optimal weight:    8.9990
   chunk 185 optimal weight:    2.9990
   chunk 288 optimal weight:   30.0000
   overall best weight:    2.3544

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 207 HIS
** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 218 GLN
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.093374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.066837 restraints weight = 93552.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.068767 restraints weight = 58561.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.069751 restraints weight = 38206.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3298
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.1026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  26447  Z= 0.183
  Angle     :  0.792  17.093  36109  Z= 0.376
  Chirality :  0.051   0.655   4220
  Planarity :  0.005   0.071   4554
  Dihedral  : 14.947 107.852   4663
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.47 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 24.25 %
    Favored  : 72.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.52 (0.15), residues: 3159
  helix:  1.00 (0.20), residues: 716
  sheet: -0.99 (0.20), residues: 624
  loop : -1.94 (0.14), residues: 1819

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 633 
 HIS   0.005   0.001   HIS A 625 
 PHE   0.014   0.001   PHE C1042 
 TYR   0.026   0.002   TYR B 204 
 ARG   0.005   0.001   ARG C  34 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00805 (   44)
  link_NAG-ASN         : angle       4.82600 (  132)
  link_BETA1-4         : bond        0.00268 (   15)
  link_BETA1-4         : angle       3.47800 (   45)
  hydrogen bonds       : bond        0.04883 (  887)
  hydrogen bonds       : angle       6.28816 ( 2466)
  SS BOND              : bond        0.00387 (   38)
  SS BOND              : angle       1.55555 (   76)
  covalent geometry    : bond        0.00411 (26349)
  covalent geometry    : angle       0.72478 (35856)
  Misc. bond           : bond        0.00025 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 87
    poor density    : 156
  time to evaluate  : 2.767 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8272 (tm-30) cc_final: 0.8001 (tm-30)
REVERT: A  127 PHE cc_start: 0.8207 (t80) cc_final: 0.7834 (t80)
REVERT: A  177 MET cc_start: 0.5711 (mmt) cc_final: 0.3417 (tmm)
REVERT: A  220 PHE cc_start: 0.6499 (OUTLIER) cc_final: 0.6266 (t80)
REVERT: A  896 ILE cc_start: 0.8800 (tp) cc_final: 0.8284 (tt)
REVERT: B  102 ARG cc_start: 0.3803 (ptt180) cc_final: 0.3464 (ptt-90)
REVERT: B  164 ASN cc_start: 0.6031 (OUTLIER) cc_final: 0.5491 (p0)
REVERT: B  200 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6687 (t80)
REVERT: B  204 TYR cc_start: 0.7454 (m-10) cc_final: 0.6937 (m-10)
REVERT: B  697 MET cc_start: 0.8371 (mmt) cc_final: 0.8150 (tpt)
REVERT: B  869 MET cc_start: 0.8822 (pmm) cc_final: 0.8582 (pmm)
REVERT: B  904 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.7253 (m-10)
REVERT: C  173 GLN cc_start: 0.6976 (tp-100) cc_final: 0.6775 (tp-100)
REVERT: C  378 LYS cc_start: 0.9507 (mmmt) cc_final: 0.9277 (mmmt)
REVERT: C  726 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8521 (mm)
REVERT: C  756 TYR cc_start: 0.8003 (OUTLIER) cc_final: 0.7373 (t80)
REVERT: C  816 SER cc_start: 0.7495 (OUTLIER) cc_final: 0.7234 (m)
REVERT: C 1029 MET cc_start: 0.8787 (tpp) cc_final: 0.8554 (tpp)
  outliers start: 87
  outliers final: 42
  residues processed: 227
  average time/residue: 0.3264
  time to fit residues: 124.5577
Evaluate side-chains
  185 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 136
  time to evaluate  : 2.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  739 THR
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  978 ASN
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1051 SER
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  731 MET
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  904 TYR
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue 1077 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  726 ILE
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1136 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 310 optimal weight:    4.9990
   chunk 173 optimal weight:    0.9990
   chunk 147 optimal weight:    6.9990
   chunk 223 optimal weight:   10.0000
   chunk 275 optimal weight:    0.8980
   chunk 130 optimal weight:    2.9990
   chunk 144 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 293 optimal weight:    0.9990
   chunk 298 optimal weight:    0.5980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 926 GLN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.094500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.068206 restraints weight = 93514.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.070238 restraints weight = 57826.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.071225 restraints weight = 36901.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.1334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  26447  Z= 0.129
  Angle     :  0.733  16.605  36109  Z= 0.344
  Chirality :  0.050   0.615   4220
  Planarity :  0.005   0.067   4554
  Dihedral  : 10.885 106.945   4656
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.77 %
    Favored  : 93.13 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 24.07 %
    Favored  : 72.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.15), residues: 3159
  helix:  1.12 (0.20), residues: 716
  sheet: -1.06 (0.20), residues: 621
  loop : -1.90 (0.14), residues: 1822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.001   HIS C 339 
 PHE   0.026   0.001   PHE A 562 
 TYR   0.020   0.001   TYR A 837 
 ARG   0.003   0.000   ARG C1107 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00752 (   44)
  link_NAG-ASN         : angle       4.67417 (  132)
  link_BETA1-4         : bond        0.00395 (   15)
  link_BETA1-4         : angle       3.25958 (   45)
  hydrogen bonds       : bond        0.04212 (  887)
  hydrogen bonds       : angle       5.82835 ( 2466)
  SS BOND              : bond        0.00368 (   38)
  SS BOND              : angle       1.38279 (   76)
  covalent geometry    : bond        0.00289 (26349)
  covalent geometry    : angle       0.66535 (35856)
  Misc. bond           : bond        0.00050 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 161
  time to evaluate  : 3.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8204 (t80) cc_final: 0.7802 (t80)
REVERT: A  177 MET cc_start: 0.5739 (mmt) cc_final: 0.3893 (tmm)
REVERT: A  190 ARG cc_start: 0.7741 (mtt90) cc_final: 0.7524 (mtt90)
REVERT: A  392 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8159 (m-80)
REVERT: A  697 MET cc_start: 0.8818 (mmm) cc_final: 0.8606 (mmp)
REVERT: B  102 ARG cc_start: 0.4210 (ptt180) cc_final: 0.3982 (mtt90)
REVERT: B  164 ASN cc_start: 0.5964 (OUTLIER) cc_final: 0.5441 (p0)
REVERT: B  204 TYR cc_start: 0.7285 (m-10) cc_final: 0.6725 (m-10)
REVERT: B  697 MET cc_start: 0.8392 (mmt) cc_final: 0.8149 (tpt)
REVERT: B  904 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7233 (m-10)
REVERT: C  173 GLN cc_start: 0.6918 (tp-100) cc_final: 0.6706 (tp-100)
REVERT: C  378 LYS cc_start: 0.9505 (mmmt) cc_final: 0.9259 (mmmt)
REVERT: C  756 TYR cc_start: 0.7862 (OUTLIER) cc_final: 0.7276 (t80)
  outliers start: 94
  outliers final: 52
  residues processed: 241
  average time/residue: 0.3996
  time to fit residues: 162.5468
Evaluate side-chains
  193 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 137
  time to evaluate  : 3.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  911 VAL
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  731 MET
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  904 TYR
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1136 THR
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 24 optimal weight:    5.9990
   chunk 138 optimal weight:    6.9990
   chunk 163 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0270
   chunk 174 optimal weight:    3.9990
   chunk 181 optimal weight:    8.9990
   chunk 110 optimal weight:   20.0000
   chunk 227 optimal weight:    9.9990
   overall best weight:    3.3844

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

Flipped N/Q/H residues before XYZ refinement:
** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 188 ASN
A 321 GLN
A 777 ASN
** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 487 ASN
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 188 ASN
C 360 ASN
C 437 ASN
C 955 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.091092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065571 restraints weight = 95165.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.066393 restraints weight = 63356.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.066935 restraints weight = 45838.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  26447  Z= 0.237
  Angle     :  0.767  16.069  36109  Z= 0.370
  Chirality :  0.050   0.626   4220
  Planarity :  0.005   0.062   4554
  Dihedral  :  8.501 103.696   4654
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.82 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 23.24 %
    Favored  : 71.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.54 (0.15), residues: 3159
  helix:  0.99 (0.20), residues: 716
  sheet: -0.94 (0.21), residues: 613
  loop : -1.98 (0.14), residues: 1830

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 633 
 HIS   0.007   0.001   HIS B  49 
 PHE   0.022   0.002   PHE B 592 
 TYR   0.023   0.002   TYR B 495 
 ARG   0.005   0.001   ARG B 319 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00763 (   44)
  link_NAG-ASN         : angle       4.65479 (  132)
  link_BETA1-4         : bond        0.00248 (   15)
  link_BETA1-4         : angle       3.22077 (   45)
  hydrogen bonds       : bond        0.04478 (  887)
  hydrogen bonds       : angle       5.70941 ( 2466)
  SS BOND              : bond        0.00474 (   38)
  SS BOND              : angle       1.53802 (   76)
  covalent geometry    : bond        0.00533 (26349)
  covalent geometry    : angle       0.70334 (35856)
  Misc. bond           : bond        0.00086 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 144
    poor density    : 138
  time to evaluate  : 3.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 GLN cc_start: 0.8299 (tm-30) cc_final: 0.7992 (tm-30)
REVERT: A  105 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8744 (mm)
REVERT: A  177 MET cc_start: 0.5344 (mmt) cc_final: 0.3271 (tmm)
REVERT: A  630 THR cc_start: 0.8285 (m) cc_final: 0.8012 (m)
REVERT: A  737 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7682 (p0)
REVERT: A  740 MET cc_start: 0.8185 (ttm) cc_final: 0.7162 (ttm)
REVERT: A 1031 GLU cc_start: 0.7260 (mt-10) cc_final: 0.7017 (tt0)
REVERT: B  102 ARG cc_start: 0.4346 (ptt180) cc_final: 0.4061 (mtt90)
REVERT: B  164 ASN cc_start: 0.5917 (OUTLIER) cc_final: 0.5420 (p0)
REVERT: B  204 TYR cc_start: 0.7570 (m-10) cc_final: 0.7119 (m-10)
REVERT: B  904 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7286 (m-10)
REVERT: B  996 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9275 (mm)
REVERT: C  328 ARG cc_start: 0.6357 (OUTLIER) cc_final: 0.5012 (ttm-80)
REVERT: C  378 LYS cc_start: 0.9498 (mmmt) cc_final: 0.9248 (mmmt)
REVERT: C  532 ASN cc_start: 0.8957 (t0) cc_final: 0.8700 (t0)
REVERT: C  756 TYR cc_start: 0.7881 (OUTLIER) cc_final: 0.7398 (t80)
REVERT: C  816 SER cc_start: 0.7695 (OUTLIER) cc_final: 0.7452 (m)
  outliers start: 144
  outliers final: 87
  residues processed: 268
  average time/residue: 0.4059
  time to fit residues: 183.6727
Evaluate side-chains
  216 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 95
    poor density    : 121
  time to evaluate  : 2.688 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   41 LYS
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  188 ASN
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  333 THR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  632 THR
Chi-restraints excluded: chain A residue  723 THR
Chi-restraints excluded: chain A residue  737 ASP
Chi-restraints excluded: chain A residue  739 THR
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  902 MET
Chi-restraints excluded: chain A residue  978 ASN
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  374 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  547 THR
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  602 THR
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  676 THR
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  731 MET
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue  904 TYR
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue  996 LEU
Chi-restraints excluded: chain B residue 1077 THR
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  312 ILE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  629 LEU
Chi-restraints excluded: chain C residue  731 MET
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  973 ILE
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 195 optimal weight:    2.9990
   chunk 167 optimal weight:    6.9990
   chunk 252 optimal weight:    0.9980
   chunk 166 optimal weight:    3.9990
   chunk 153 optimal weight:    3.9990
   chunk 6 optimal weight:   20.0000
   chunk 242 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 188 ASN
B 762 GLN
B 774 GLN
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 919 ASN
C1083 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.090639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.063258 restraints weight = 95809.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.065595 restraints weight = 54729.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.066106 restraints weight = 33173.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.2223

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  26447  Z= 0.154
  Angle     :  0.706  15.323  36109  Z= 0.338
  Chirality :  0.049   0.607   4220
  Planarity :  0.005   0.054   4554
  Dihedral  :  7.891 101.811   4654
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.15 %
    Favored  : 92.75 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 24.32 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.15), residues: 3159
  helix:  1.13 (0.20), residues: 717
  sheet: -1.02 (0.20), residues: 626
  loop : -1.97 (0.14), residues: 1816

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 633 
 HIS   0.005   0.001   HIS C 339 
 PHE   0.030   0.001   PHE B 592 
 TYR   0.019   0.001   TYR B 495 
 ARG   0.013   0.000   ARG B 319 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00735 (   44)
  link_NAG-ASN         : angle       4.50253 (  132)
  link_BETA1-4         : bond        0.00245 (   15)
  link_BETA1-4         : angle       2.79034 (   45)
  hydrogen bonds       : bond        0.04060 (  887)
  hydrogen bonds       : angle       5.44887 ( 2466)
  SS BOND              : bond        0.00439 (   38)
  SS BOND              : angle       1.45394 (   76)
  covalent geometry    : bond        0.00351 (26349)
  covalent geometry    : angle       0.64263 (35856)
  Misc. bond           : bond        0.00079 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 123
    poor density    : 134
  time to evaluate  : 2.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8790 (t80) cc_final: 0.8185 (t80)
REVERT: A  177 MET cc_start: 0.5821 (mmt) cc_final: 0.3967 (tmm)
REVERT: A  220 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.6263 (t80)
REVERT: A  630 THR cc_start: 0.8268 (m) cc_final: 0.8059 (p)
REVERT: A  900 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8521 (pmm)
REVERT: A  909 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8472 (tp)
REVERT: B  164 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.5737 (p0)
REVERT: B  546 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7848 (pp)
REVERT: B  740 MET cc_start: 0.7826 (tpt) cc_final: 0.7599 (tpt)
REVERT: C  173 GLN cc_start: 0.7065 (tp40) cc_final: 0.6780 (tp-100)
REVERT: C  378 LYS cc_start: 0.9512 (mmmt) cc_final: 0.9262 (mmmt)
REVERT: C  532 ASN cc_start: 0.9070 (t0) cc_final: 0.8690 (t0)
REVERT: C  756 TYR cc_start: 0.7970 (OUTLIER) cc_final: 0.7454 (t80)
REVERT: C  759 PHE cc_start: 0.7448 (OUTLIER) cc_final: 0.7170 (m-80)
REVERT: C  816 SER cc_start: 0.7900 (OUTLIER) cc_final: 0.7653 (m)
REVERT: C  973 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8218 (tp)
REVERT: C 1029 MET cc_start: 0.8568 (tpp) cc_final: 0.8202 (tpp)
  outliers start: 123
  outliers final: 82
  residues processed: 238
  average time/residue: 0.3354
  time to fit residues: 135.8194
Evaluate side-chains
  215 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 91
    poor density    : 124
  time to evaluate  : 2.750 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  902 MET
Chi-restraints excluded: chain A residue  909 ILE
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1077 THR
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  374 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  574 ASP
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  712 ILE
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue 1050 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  228 ASP
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  304 LYS
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  395 VAL
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  759 PHE
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  973 ILE
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1060 VAL
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 83 optimal weight:    0.1980
   chunk 207 optimal weight:    0.9980
   chunk 238 optimal weight:    0.9980
   chunk 117 optimal weight:    9.9990
   chunk 116 optimal weight:   10.0000
   chunk 69 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 95 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 295 optimal weight:    4.9990
   overall best weight:    1.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
A 628 GLN
A 853 GLN
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1083 HIS
** B1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 919 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.090363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.063498 restraints weight = 95500.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.064948 restraints weight = 56643.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.065820 restraints weight = 37806.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  26447  Z= 0.149
  Angle     :  0.693  15.236  36109  Z= 0.332
  Chirality :  0.049   0.604   4220
  Planarity :  0.005   0.052   4554
  Dihedral  :  7.560 101.408   4653
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.31 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 24.43 %
    Favored  : 70.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.15), residues: 3159
  helix:  1.29 (0.20), residues: 706
  sheet: -0.92 (0.20), residues: 647
  loop : -1.99 (0.14), residues: 1806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 633 
 HIS   0.006   0.001   HIS C 339 
 PHE   0.027   0.001   PHE B 168 
 TYR   0.024   0.001   TYR C 636 
 ARG   0.005   0.000   ARG B 102 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00718 (   44)
  link_NAG-ASN         : angle       4.40028 (  132)
  link_BETA1-4         : bond        0.00276 (   15)
  link_BETA1-4         : angle       2.52205 (   45)
  hydrogen bonds       : bond        0.03931 (  887)
  hydrogen bonds       : angle       5.29596 ( 2466)
  SS BOND              : bond        0.00373 (   38)
  SS BOND              : angle       1.32964 (   76)
  covalent geometry    : bond        0.00339 (26349)
  covalent geometry    : angle       0.63335 (35856)
  Misc. bond           : bond        0.00052 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 129
    poor density    : 136
  time to evaluate  : 2.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8794 (t80) cc_final: 0.8144 (t80)
REVERT: A  177 MET cc_start: 0.5826 (mmt) cc_final: 0.3841 (tmm)
REVERT: A  220 PHE cc_start: 0.6509 (OUTLIER) cc_final: 0.6292 (t80)
REVERT: A  495 TYR cc_start: 0.3869 (OUTLIER) cc_final: 0.3605 (m-10)
REVERT: A  630 THR cc_start: 0.8229 (m) cc_final: 0.7957 (m)
REVERT: A  856 ASN cc_start: 0.8358 (p0) cc_final: 0.8035 (m110)
REVERT: A  900 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8550 (pmm)
REVERT: B  164 ASN cc_start: 0.6242 (OUTLIER) cc_final: 0.5791 (p0)
REVERT: B  204 TYR cc_start: 0.7595 (m-10) cc_final: 0.7076 (m-10)
REVERT: B  495 TYR cc_start: -0.0070 (OUTLIER) cc_final: -0.1210 (t80)
REVERT: B 1029 MET cc_start: 0.9226 (tpp) cc_final: 0.8951 (tpp)
REVERT: C  173 GLN cc_start: 0.6786 (tp40) cc_final: 0.6459 (tp-100)
REVERT: C  378 LYS cc_start: 0.9508 (mmmt) cc_final: 0.9276 (mmmt)
REVERT: C  532 ASN cc_start: 0.9078 (t0) cc_final: 0.8724 (t0)
REVERT: C  756 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7510 (t80)
REVERT: C  816 SER cc_start: 0.8004 (OUTLIER) cc_final: 0.7747 (m)
REVERT: C  973 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8271 (tp)
REVERT: C 1029 MET cc_start: 0.8542 (tpp) cc_final: 0.7823 (tpp)
  outliers start: 129
  outliers final: 82
  residues processed: 249
  average time/residue: 0.3165
  time to fit residues: 133.8713
Evaluate side-chains
  222 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 90
    poor density    : 132
  time to evaluate  : 2.634 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  220 PHE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  240 THR
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue  902 MET
Chi-restraints excluded: chain A residue  978 ASN
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1077 THR
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  574 ASP
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue  996 LEU
Chi-restraints excluded: chain B residue 1050 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  629 LEU
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  973 ILE
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1060 VAL
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 314 optimal weight:    9.9990
   chunk 299 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 154 optimal weight:   10.0000
   chunk 280 optimal weight:    0.7980
   chunk 46 optimal weight:    0.2980
   chunk 201 optimal weight:    3.9990
   chunk 79 optimal weight:    0.7980
   chunk 266 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1119 ASN
** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.091069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.063381 restraints weight = 96271.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.066032 restraints weight = 57946.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.066791 restraints weight = 34438.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  26447  Z= 0.121
  Angle     :  0.674  14.812  36109  Z= 0.321
  Chirality :  0.048   0.608   4220
  Planarity :  0.004   0.052   4554
  Dihedral  :  7.342  97.923   4653
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.09 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 24.79 %
    Favored  : 71.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.32 (0.15), residues: 3159
  helix:  1.31 (0.20), residues: 714
  sheet: -0.82 (0.20), residues: 663
  loop : -1.90 (0.14), residues: 1782

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.006   0.001   HIS C 339 
 PHE   0.022   0.001   PHE A 562 
 TYR   0.015   0.001   TYR A1067 
 ARG   0.004   0.000   ARG C1107 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00701 (   44)
  link_NAG-ASN         : angle       4.28809 (  132)
  link_BETA1-4         : bond        0.00349 (   15)
  link_BETA1-4         : angle       2.33781 (   45)
  hydrogen bonds       : bond        0.03714 (  887)
  hydrogen bonds       : angle       5.12575 ( 2466)
  SS BOND              : bond        0.00384 (   38)
  SS BOND              : angle       1.29662 (   76)
  covalent geometry    : bond        0.00272 (26349)
  covalent geometry    : angle       0.61580 (35856)
  Misc. bond           : bond        0.00046 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 113
    poor density    : 144
  time to evaluate  : 2.698 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8735 (t80) cc_final: 0.8077 (t80)
REVERT: A  177 MET cc_start: 0.5614 (mmt) cc_final: 0.3831 (tmm)
REVERT: A  495 TYR cc_start: 0.3900 (OUTLIER) cc_final: 0.3632 (m-80)
REVERT: A  630 THR cc_start: 0.8183 (m) cc_final: 0.7905 (m)
REVERT: A  697 MET cc_start: 0.8704 (mmm) cc_final: 0.8231 (mmm)
REVERT: A  740 MET cc_start: 0.8586 (ttp) cc_final: 0.7763 (ttm)
REVERT: A  900 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8522 (pmm)
REVERT: B   54 LEU cc_start: 0.8893 (mm) cc_final: 0.8598 (mt)
REVERT: B  164 ASN cc_start: 0.6159 (OUTLIER) cc_final: 0.5665 (p0)
REVERT: B  204 TYR cc_start: 0.7392 (m-10) cc_final: 0.6920 (m-10)
REVERT: B  546 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7919 (pp)
REVERT: B  740 MET cc_start: 0.7843 (tpt) cc_final: 0.7633 (tpt)
REVERT: C  173 GLN cc_start: 0.6908 (tp40) cc_final: 0.6569 (tp-100)
REVERT: C  328 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.4786 (ttm-80)
REVERT: C  378 LYS cc_start: 0.9517 (mmmt) cc_final: 0.9283 (mmmt)
REVERT: C  532 ASN cc_start: 0.9083 (t0) cc_final: 0.8835 (t0)
REVERT: C  697 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7627 (mtm)
REVERT: C  756 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.7456 (t80)
REVERT: C  816 SER cc_start: 0.7906 (OUTLIER) cc_final: 0.7661 (m)
REVERT: C  973 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8153 (tp)
REVERT: C 1029 MET cc_start: 0.8498 (tpp) cc_final: 0.7826 (tpp)
  outliers start: 113
  outliers final: 80
  residues processed: 243
  average time/residue: 0.3273
  time to fit residues: 134.8405
Evaluate side-chains
  221 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 89
    poor density    : 132
  time to evaluate  : 2.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  760 CYS
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  332 VAL
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  574 ASP
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  611 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  676 THR
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  849 LEU
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue  996 LEU
Chi-restraints excluded: chain B residue 1050 MET
Chi-restraints excluded: chain B residue 1118 ASP
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  304 LYS
Chi-restraints excluded: chain C residue  312 ILE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  574 ASP
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  697 MET
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  973 ILE
Chi-restraints excluded: chain C residue 1060 VAL
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 180 optimal weight:    3.9990
   chunk 199 optimal weight:    0.8980
   chunk 267 optimal weight:    7.9990
   chunk 34 optimal weight:   20.0000
   chunk 226 optimal weight:    0.9980
   chunk 311 optimal weight:    5.9990
   chunk 166 optimal weight:    1.9990
   chunk 122 optimal weight:    4.9990
   chunk 308 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 278 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.091352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.063660 restraints weight = 95673.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.066358 restraints weight = 57954.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.067025 restraints weight = 33934.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  26447  Z= 0.116
  Angle     :  0.674  14.801  36109  Z= 0.318
  Chirality :  0.048   0.606   4220
  Planarity :  0.004   0.050   4554
  Dihedral  :  7.172  97.252   4651
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 9.51
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.31 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.19 %
    Favored  : 71.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.15), residues: 3159
  helix:  1.36 (0.20), residues: 713
  sheet: -0.80 (0.20), residues: 671
  loop : -1.86 (0.15), residues: 1775

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 436 
 HIS   0.007   0.001   HIS B 339 
 PHE   0.025   0.001   PHE B  92 
 TYR   0.025   0.001   TYR C 170 
 ARG   0.008   0.000   ARG C1107 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00692 (   44)
  link_NAG-ASN         : angle       4.22092 (  132)
  link_BETA1-4         : bond        0.00356 (   15)
  link_BETA1-4         : angle       2.26348 (   45)
  hydrogen bonds       : bond        0.03631 (  887)
  hydrogen bonds       : angle       5.02783 ( 2466)
  SS BOND              : bond        0.00340 (   38)
  SS BOND              : angle       1.32677 (   76)
  covalent geometry    : bond        0.00261 (26349)
  covalent geometry    : angle       0.61834 (35856)
  Misc. bond           : bond        0.00039 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 102
    poor density    : 144
  time to evaluate  : 2.798 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8777 (t80) cc_final: 0.8104 (t80)
REVERT: A  177 MET cc_start: 0.5641 (mmt) cc_final: 0.3846 (tmm)
REVERT: A  495 TYR cc_start: 0.3975 (OUTLIER) cc_final: 0.3686 (m-80)
REVERT: A  630 THR cc_start: 0.8164 (m) cc_final: 0.7888 (m)
REVERT: A  856 ASN cc_start: 0.8327 (p0) cc_final: 0.8010 (m110)
REVERT: A  900 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8587 (pmm)
REVERT: B   54 LEU cc_start: 0.8906 (mm) cc_final: 0.8610 (mt)
REVERT: B  164 ASN cc_start: 0.6249 (OUTLIER) cc_final: 0.5747 (p0)
REVERT: B  189 LEU cc_start: 0.8678 (tt) cc_final: 0.8445 (mp)
REVERT: B  204 TYR cc_start: 0.7439 (m-10) cc_final: 0.6941 (m-10)
REVERT: B  546 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7921 (pp)
REVERT: B  740 MET cc_start: 0.7834 (tpt) cc_final: 0.7526 (tpt)
REVERT: B  869 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.7998 (pmm)
REVERT: B  909 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8892 (tp)
REVERT: B 1029 MET cc_start: 0.9227 (tpp) cc_final: 0.8936 (tpp)
REVERT: B 1031 GLU cc_start: 0.8471 (tp30) cc_final: 0.8252 (tp30)
REVERT: C  328 ARG cc_start: 0.6187 (OUTLIER) cc_final: 0.4785 (ttm-80)
REVERT: C  378 LYS cc_start: 0.9513 (mmmt) cc_final: 0.9276 (mmmt)
REVERT: C  532 ASN cc_start: 0.9117 (t0) cc_final: 0.8876 (t0)
REVERT: C  586 ASP cc_start: 0.7368 (t0) cc_final: 0.7152 (t0)
REVERT: C  756 TYR cc_start: 0.7995 (OUTLIER) cc_final: 0.7432 (t80)
REVERT: C  816 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7701 (m)
REVERT: C 1029 MET cc_start: 0.8458 (tpp) cc_final: 0.7759 (tpp)
  outliers start: 102
  outliers final: 83
  residues processed: 233
  average time/residue: 0.3316
  time to fit residues: 129.1549
Evaluate side-chains
  227 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 135
  time to evaluate  : 2.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1077 THR
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  546 LEU
Chi-restraints excluded: chain B residue  574 ASP
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  676 THR
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  849 LEU
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue  909 ILE
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue  996 LEU
Chi-restraints excluded: chain B residue 1050 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  312 ILE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  574 ASP
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1060 VAL
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9980
   chunk 249 optimal weight:    8.9990
   chunk 31 optimal weight:    5.9990
   chunk 136 optimal weight:   20.0000
   chunk 183 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 195 optimal weight:    0.6980
   chunk 146 optimal weight:    8.9990
   chunk 118 optimal weight:    2.9990
   chunk 174 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.090169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.062961 restraints weight = 96001.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.065267 restraints weight = 54673.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.065872 restraints weight = 33091.578|
|-----------------------------------------------------------------------------|
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8088
moved from start:          0.3010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.086  26447  Z= 0.153
  Angle     :  0.695  15.165  36109  Z= 0.331
  Chirality :  0.048   0.606   4220
  Planarity :  0.004   0.050   4554
  Dihedral  :  7.153  98.639   4651
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.50 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 25.37 %
    Favored  : 70.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.15), residues: 3159
  helix:  1.31 (0.20), residues: 715
  sheet: -0.76 (0.20), residues: 660
  loop : -1.84 (0.15), residues: 1784

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.007   0.001   HIS C 339 
 PHE   0.024   0.001   PHE B  92 
 TYR   0.023   0.001   TYR C 636 
 ARG   0.005   0.000   ARG C1107 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00662 (   44)
  link_NAG-ASN         : angle       4.18104 (  132)
  link_BETA1-4         : bond        0.00296 (   15)
  link_BETA1-4         : angle       2.25113 (   45)
  hydrogen bonds       : bond        0.03805 (  887)
  hydrogen bonds       : angle       5.08422 ( 2466)
  SS BOND              : bond        0.00363 (   38)
  SS BOND              : angle       2.14853 (   76)
  covalent geometry    : bond        0.00351 (26349)
  covalent geometry    : angle       0.63661 (35856)
  Misc. bond           : bond        0.00031 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 105
    poor density    : 136
  time to evaluate  : 4.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8747 (t80) cc_final: 0.8064 (t80)
REVERT: A  392 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8113 (m-80)
REVERT: A  495 TYR cc_start: 0.3985 (OUTLIER) cc_final: 0.3666 (m-80)
REVERT: A  630 THR cc_start: 0.8163 (m) cc_final: 0.7858 (m)
REVERT: A  731 MET cc_start: 0.8910 (ptp) cc_final: 0.8500 (ptt)
REVERT: A  900 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8647 (pmm)
REVERT: B   54 LEU cc_start: 0.8957 (mm) cc_final: 0.8668 (mt)
REVERT: B  164 ASN cc_start: 0.6390 (OUTLIER) cc_final: 0.5932 (p0)
REVERT: B  204 TYR cc_start: 0.7507 (m-10) cc_final: 0.6979 (m-10)
REVERT: B  495 TYR cc_start: 0.0390 (OUTLIER) cc_final: -0.0943 (t80)
REVERT: B  740 MET cc_start: 0.7738 (tpt) cc_final: 0.7518 (tpt)
REVERT: B  869 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.7920 (pmm)
REVERT: B  909 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8905 (tp)
REVERT: B 1029 MET cc_start: 0.9196 (tpp) cc_final: 0.8914 (tpp)
REVERT: C  328 ARG cc_start: 0.6300 (OUTLIER) cc_final: 0.4901 (ttm-80)
REVERT: C  378 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9270 (mmmt)
REVERT: C  532 ASN cc_start: 0.9109 (t0) cc_final: 0.8601 (p0)
REVERT: C  756 TYR cc_start: 0.7933 (OUTLIER) cc_final: 0.7509 (t80)
REVERT: C  816 SER cc_start: 0.7960 (OUTLIER) cc_final: 0.7714 (m)
REVERT: C  973 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8167 (tp)
REVERT: C 1029 MET cc_start: 0.8497 (tpp) cc_final: 0.7767 (tpp)
  outliers start: 105
  outliers final: 83
  residues processed: 228
  average time/residue: 0.3517
  time to fit residues: 136.2454
Evaluate side-chains
  224 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 130
  time to evaluate  : 2.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain A residue  590 CYS
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  739 THR
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1077 THR
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  574 ASP
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  676 THR
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  849 LEU
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue  909 ILE
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue  996 LEU
Chi-restraints excluded: chain B residue 1050 MET
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  312 ILE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  629 LEU
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  805 ILE
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  973 ILE
Chi-restraints excluded: chain C residue 1060 VAL
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 81 optimal weight:    0.0270
   chunk 276 optimal weight:    0.8980
   chunk 153 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 316 optimal weight:    5.9990
   chunk 233 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 32 optimal weight:    8.9990
   chunk 255 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    1.5842

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

Flipped N/Q/H residues before XYZ refinement:
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 774 GLN
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.090303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.063179 restraints weight = 95907.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.065075 restraints weight = 56920.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.066074 restraints weight = 34924.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.3132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.078  26447  Z= 0.140
  Angle     :  0.699  15.050  36109  Z= 0.331
  Chirality :  0.048   0.610   4220
  Planarity :  0.004   0.051   4554
  Dihedral  :  7.093  98.869   4651
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.31 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 25.69 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.15), residues: 3159
  helix:  1.38 (0.20), residues: 713
  sheet: -0.76 (0.20), residues: 656
  loop : -1.82 (0.15), residues: 1790

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.001   TRP C 104 
 HIS   0.007   0.001   HIS C 339 
 PHE   0.024   0.001   PHE B  92 
 TYR   0.026   0.001   TYR C 170 
 ARG   0.004   0.000   ARG C 102 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00662 (   44)
  link_NAG-ASN         : angle       4.12750 (  132)
  link_BETA1-4         : bond        0.00316 (   15)
  link_BETA1-4         : angle       2.18045 (   45)
  hydrogen bonds       : bond        0.03704 (  887)
  hydrogen bonds       : angle       5.03140 ( 2466)
  SS BOND              : bond        0.00401 (   38)
  SS BOND              : angle       2.11823 (   76)
  covalent geometry    : bond        0.00326 (26349)
  covalent geometry    : angle       0.64299 (35856)
  Misc. bond           : bond        0.00035 (    1)

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

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

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  6318 Ramachandran restraints generated.
    3159 Oldfield, 0 Emsley, 3159 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 99
    poor density    : 138
  time to evaluate  : 2.844 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 PHE cc_start: 0.8770 (t80) cc_final: 0.8109 (t80)
REVERT: A  392 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8122 (m-80)
REVERT: A  495 TYR cc_start: 0.3994 (OUTLIER) cc_final: 0.3738 (m-80)
REVERT: A  630 THR cc_start: 0.8143 (m) cc_final: 0.7863 (m)
REVERT: A  731 MET cc_start: 0.8897 (ptp) cc_final: 0.8483 (ptt)
REVERT: B   54 LEU cc_start: 0.8980 (mm) cc_final: 0.8689 (mt)
REVERT: B   90 VAL cc_start: 0.8915 (m) cc_final: 0.8664 (p)
REVERT: B  164 ASN cc_start: 0.6361 (OUTLIER) cc_final: 0.5923 (p0)
REVERT: B  200 TYR cc_start: 0.7872 (OUTLIER) cc_final: 0.7294 (t80)
REVERT: B  204 TYR cc_start: 0.7430 (m-10) cc_final: 0.6859 (m-10)
REVERT: B  495 TYR cc_start: 0.0846 (OUTLIER) cc_final: -0.0469 (t80)
REVERT: B  740 MET cc_start: 0.7753 (tpt) cc_final: 0.7431 (tpt)
REVERT: B  855 PHE cc_start: 0.6934 (t80) cc_final: 0.6734 (t80)
REVERT: B  869 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.7920 (pmm)
REVERT: B  909 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8897 (tp)
REVERT: B  974 SER cc_start: 0.9033 (t) cc_final: 0.8512 (m)
REVERT: B 1029 MET cc_start: 0.9198 (tpp) cc_final: 0.8946 (tpp)
REVERT: C  102 ARG cc_start: 0.5118 (mtt180) cc_final: 0.4873 (mtt180)
REVERT: C  328 ARG cc_start: 0.6288 (OUTLIER) cc_final: 0.4858 (ttm-80)
REVERT: C  378 LYS cc_start: 0.9513 (mmmt) cc_final: 0.9279 (mmmt)
REVERT: C  532 ASN cc_start: 0.9111 (t0) cc_final: 0.8621 (p0)
REVERT: C  756 TYR cc_start: 0.7932 (OUTLIER) cc_final: 0.7502 (t80)
REVERT: C  816 SER cc_start: 0.7968 (OUTLIER) cc_final: 0.7724 (m)
REVERT: C  973 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8158 (tp)
REVERT: C 1029 MET cc_start: 0.8465 (tpp) cc_final: 0.7764 (tpp)
REVERT: C 1107 ARG cc_start: 0.7598 (mtt90) cc_final: 0.7368 (mtt90)
  outliers start: 99
  outliers final: 83
  residues processed: 224
  average time/residue: 0.3313
  time to fit residues: 125.4996
Evaluate side-chains
  225 residues out of total 2784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 94
    poor density    : 131
  time to evaluate  : 2.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  164 ASN
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  227 VAL
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  392 PHE
Chi-restraints excluded: chain A residue  449 TYR
Chi-restraints excluded: chain A residue  495 TYR
Chi-restraints excluded: chain A residue  523 THR
Chi-restraints excluded: chain A residue  576 VAL
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  705 VAL
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  759 PHE
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  860 VAL
Chi-restraints excluded: chain A residue  900 MET
Chi-restraints excluded: chain A residue 1050 MET
Chi-restraints excluded: chain A residue 1077 THR
Chi-restraints excluded: chain A residue 1097 SER
Chi-restraints excluded: chain A residue 1101 HIS
Chi-restraints excluded: chain A residue 1104 VAL
Chi-restraints excluded: chain A residue 1128 VAL
Chi-restraints excluded: chain A residue 1141 LEU
Chi-restraints excluded: chain B residue   66 HIS
Chi-restraints excluded: chain B residue  133 PHE
Chi-restraints excluded: chain B residue  164 ASN
Chi-restraints excluded: chain B residue  186 PHE
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  205 SER
Chi-restraints excluded: chain B residue  238 PHE
Chi-restraints excluded: chain B residue  277 LEU
Chi-restraints excluded: chain B residue  371 PHE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  495 TYR
Chi-restraints excluded: chain B residue  574 ASP
Chi-restraints excluded: chain B residue  595 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain B residue  676 THR
Chi-restraints excluded: chain B residue  699 LEU
Chi-restraints excluded: chain B residue  705 VAL
Chi-restraints excluded: chain B residue  781 VAL
Chi-restraints excluded: chain B residue  820 ASP
Chi-restraints excluded: chain B residue  849 LEU
Chi-restraints excluded: chain B residue  860 VAL
Chi-restraints excluded: chain B residue  866 THR
Chi-restraints excluded: chain B residue  869 MET
Chi-restraints excluded: chain B residue  873 TYR
Chi-restraints excluded: chain B residue  882 ILE
Chi-restraints excluded: chain B residue  896 ILE
Chi-restraints excluded: chain B residue  906 PHE
Chi-restraints excluded: chain B residue  909 ILE
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  976 VAL
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  979 ASP
Chi-restraints excluded: chain B residue  996 LEU
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue   95 THR
Chi-restraints excluded: chain C residue  105 ILE
Chi-restraints excluded: chain C residue  159 VAL
Chi-restraints excluded: chain C residue  238 PHE
Chi-restraints excluded: chain C residue  267 VAL
Chi-restraints excluded: chain C residue  312 ILE
Chi-restraints excluded: chain C residue  324 GLU
Chi-restraints excluded: chain C residue  328 ARG
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  396 TYR
Chi-restraints excluded: chain C residue  492 LEU
Chi-restraints excluded: chain C residue  547 THR
Chi-restraints excluded: chain C residue  574 ASP
Chi-restraints excluded: chain C residue  595 VAL
Chi-restraints excluded: chain C residue  599 THR
Chi-restraints excluded: chain C residue  620 VAL
Chi-restraints excluded: chain C residue  747 THR
Chi-restraints excluded: chain C residue  756 TYR
Chi-restraints excluded: chain C residue  770 ILE
Chi-restraints excluded: chain C residue  778 THR
Chi-restraints excluded: chain C residue  781 VAL
Chi-restraints excluded: chain C residue  816 SER
Chi-restraints excluded: chain C residue  866 THR
Chi-restraints excluded: chain C residue  869 MET
Chi-restraints excluded: chain C residue  918 GLU
Chi-restraints excluded: chain C residue  973 ILE
Chi-restraints excluded: chain C residue  977 LEU
Chi-restraints excluded: chain C residue 1037 SER
Chi-restraints excluded: chain C residue 1060 VAL
Chi-restraints excluded: chain C residue 1137 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 318
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 126 optimal weight:    1.9990
   chunk 217 optimal weight:    0.2980
   chunk 21 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 165 optimal weight:    8.9990
   chunk 290 optimal weight:    0.0170
   chunk 174 optimal weight:    2.9990
   chunk 135 optimal weight:    7.9990
   chunk 212 optimal weight:   20.0000
   chunk 125 optimal weight:    0.0870
   overall best weight:    1.0800

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

Flipped N/Q/H residues before XYZ refinement:
** A 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1005 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.090631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.063331 restraints weight = 94985.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.065851 restraints weight = 57172.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.066729 restraints weight = 34131.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  26447  Z= 0.122
  Angle     :  0.687  14.814  36109  Z= 0.325
  Chirality :  0.048   0.617   4220
  Planarity :  0.004   0.052   4554
  Dihedral  :  6.981  98.419   4651
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.19 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 25.69 %
    Favored  : 70.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.03 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.13 (0.15), residues: 3159
  helix:  1.44 (0.20), residues: 711
  sheet: -0.67 (0.20), residues: 650
  loop : -1.77 (0.15), residues: 1798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP C 104 
 HIS   0.007   0.001   HIS C 339 
 PHE   0.025   0.001   PHE B  92 
 TYR   0.023   0.001   TYR C 636 
 ARG   0.002   0.000   ARG B 319 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00659 (   44)
  link_NAG-ASN         : angle       4.06831 (  132)
  link_BETA1-4         : bond        0.00347 (   15)
  link_BETA1-4         : angle       2.10820 (   45)
  hydrogen bonds       : bond        0.03593 (  887)
  hydrogen bonds       : angle       4.98309 ( 2466)
  SS BOND              : bond        0.00405 (   38)
  SS BOND              : angle       1.88058 (   76)
  covalent geometry    : bond        0.00283 (26349)
  covalent geometry    : angle       0.63383 (35856)
  Misc. bond           : bond        0.00024 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7276.27 seconds
wall clock time: 130 minutes 16.23 seconds (7816.23 seconds total)