Starting phenix.real_space_refine
on Wed May 14 12:45:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xr8_38598/05_2025/8xr8_38598.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xr8_38598/05_2025/8xr8_38598.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xr8_38598/05_2025/8xr8_38598.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xr8_38598/05_2025/8xr8_38598.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xr8_38598/05_2025/8xr8_38598.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xr8_38598/05_2025/8xr8_38598.cif"
  }
  resolution = 2.53
  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=   0.001 sd=   0.024
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      72      5.16       5
     C    7372      2.51       5
     N    2006      2.21       5
     O    2359      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 11809
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 3871
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 3871
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 19, 'TRANS': 469}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 485, 3840
          Classifications: {'peptide': 485}
          Link IDs: {'PTRANS': 19, 'TRANS': 465}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3831
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 484, 3831
          Classifications: {'peptide': 484}
          Link IDs: {'PTRANS': 19, 'TRANS': 464}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'GAL': 1, 'SIA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "H"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {'GAL': 1, 'SIA': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 49
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 49
          Unusual residues: {'NAG': 2, 'SIA': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 8.14, per 1000 atoms: 0.69
  Number of scatterers: 11809
  At special positions: 0
  Unit cell: (91.8, 87.55, 150.45, 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      72     16.00
     O    2359      8.00
     N    2006      7.00
     C    7372      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   9 " - pdb=" SG  CYS A 467 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  47 " - pdb=" SG  CYS A 278 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 282 " - pdb=" SG  CYS A 306 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 478 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   9 " - pdb=" SG  CYS B 467 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  47 " - pdb=" SG  CYS B 278 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  60 " - pdb=" SG  CYS B  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  95 " - pdb=" SG  CYS B 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 282 " - pdb=" SG  CYS B 306 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 474 " - pdb=" SG  CYS B 478 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   9 " - pdb=" SG  CYS C 467 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  47 " - pdb=" SG  CYS C 278 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C  60 " - pdb=" SG  CYS C  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  95 " - pdb=" SG  CYS C 139 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 282 " - pdb=" SG  CYS C 306 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 474 " - pdb=" SG  CYS C 478 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    BETA2-3
      " GAL G   1 " - " SIA G   2 "
       ~> Even though SIA is an alpha isomer, a beta linkage is required...
      " GAL H   1 " - " SIA H   2 "
    NAG-ASN
      " NAG A 701 " - " ASN A  28 "
      " NAG A 702 " - " ASN A 290 "
      " NAG A 703 " - " ASN A  16 "
      " NAG B 701 " - " ASN B  28 "
      " NAG B 702 " - " ASN B 290 "
      " NAG C 701 " - " ASN C  28 "
      " NAG C 702 " - " ASN C 290 "
      " NAG D   1 " - " ASN A 169 "
      " NAG E   1 " - " ASN B 169 "
      " NAG F   1 " - " ASN C 169 "
  Time building additional restraints: 3.33
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2664

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 34 sheets defined
      27.5% alpha, 20.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.79
  Creating SS restraints...
    Processing helix  chain 'A' and resid 61 through 68
    Processing helix  chain 'A' and resid 72 through 76
      removed outlier: 3.759A  pdb=" N   LEU A  75 " --> pdb=" O   CYS A  72 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU A  76 " --> pdb=" O   ASP A  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 72 through 76'
    Processing helix  chain 'A' and resid 102 through 111
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 3.819A  pdb=" N   TRP A 127 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 195
      removed outlier: 3.568A  pdb=" N   GLN A 191 " --> pdb=" O   ASP A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 388
      removed outlier: 3.507A  pdb=" N   LYS A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 457
    Processing helix  chain 'A' and resid 475 through 485
    Processing helix  chain 'A' and resid 489 through 492
    Processing helix  chain 'A' and resid 493 through 501
    Processing helix  chain 'B' and resid 61 through 68
    Processing helix  chain 'B' and resid 72 through 76
      removed outlier: 3.707A  pdb=" N   LEU B  75 " --> pdb=" O   CYS B  72 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU B  76 " --> pdb=" O   ASP B  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 72 through 76'
    Processing helix  chain 'B' and resid 102 through 111
    Processing helix  chain 'B' and resid 123 through 127
      removed outlier: 3.540A  pdb=" N   TRP B 127 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 369 through 388
      removed outlier: 3.695A  pdb=" N   LYS B 373 " --> pdb=" O   GLU B 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 456
    Processing helix  chain 'B' and resid 475 through 484
    Processing helix  chain 'B' and resid 493 through 502
    Processing helix  chain 'C' and resid 61 through 68
    Processing helix  chain 'C' and resid 72 through 76
      removed outlier: 3.531A  pdb=" N   LEU C  75 " --> pdb=" O   CYS C  72 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   LEU C  76 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 72 through 76'
    Processing helix  chain 'C' and resid 102 through 111
    Processing helix  chain 'C' and resid 123 through 127
      removed outlier: 3.781A  pdb=" N   TRP C 127 " --> pdb=" O   LYS C 124 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 187 through 196
      removed outlier: 3.512A  pdb=" N   GLN C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 367 through 389
      removed outlier: 3.848A  pdb=" N   THR C 371 " --> pdb=" O   ASP C 367 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   GLN C 372 " --> pdb=" O   LYS C 368 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   MET C 389 " --> pdb=" O   VAL C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 457
    Processing helix  chain 'C' and resid 475 through 484
    Processing helix  chain 'C' and resid 493 through 501
      removed outlier: 3.822A  pdb=" N   ASN C 501 " --> pdb=" O   LYS C 497 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 357
      removed outlier: 4.426A  pdb=" N   ILE A   8 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   PHE A 468 " --> pdb=" O   ILE A   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 21
    Processing sheet with id=AA4, first strand: chain 'A' and resid 34 through 36
    Processing sheet with id=AA5, first strand: chain 'A' and resid 38 through 39
    Processing sheet with id=AA6, first strand: chain 'A' and resid 55 through 56
      removed outlier: 6.517A  pdb=" N   LEU A  55 " --> pdb=" O   MET A  85 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   ILE A  84 " --> pdb=" O   MET A 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 100
      removed outlier: 5.500A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   TYR A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 98 through 100
      removed outlier: 7.949A  pdb=" N   ILE A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141
      removed outlier: 7.456A  pdb=" N   ALA A 138 " --> pdb=" O   SER A 144 " (cutoff:3.500A)
      removed outlier: 9.983A  pdb=" N   SER A 144 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 289
      removed outlier: 3.505A  pdb=" N   ILE A 289 " --> pdb=" O   CYS A 282 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   CYS A 282 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 7 through 8
    Processing sheet with id=AB4, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.731A  pdb=" N   GLY B  11 " --> pdb=" O   GLY B 353 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 19 through 21
      removed outlier: 4.267A  pdb=" N   GLU B  19 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 34 through 36
    Processing sheet with id=AB7, first strand: chain 'B' and resid 38 through 39
    Processing sheet with id=AB8, first strand: chain 'B' and resid 55 through 56
      removed outlier: 6.872A  pdb=" N   LEU B  55 " --> pdb=" O   MET B  85 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE B  84 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 98 through 100
      removed outlier: 6.801A  pdb=" N   SER B  99 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   TRP B 234 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   ILE B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   TYR B 256 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 98 through 100
      removed outlier: 6.801A  pdb=" N   SER B  99 " --> pdb=" O   PHE B 232 " (cutoff:3.500A)
      removed outlier: 8.979A  pdb=" N   TRP B 234 " --> pdb=" O   SER B  99 " (cutoff:3.500A)
      removed outlier: 7.989A  pdb=" N   ILE B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 136 through 141
      removed outlier: 7.212A  pdb=" N   ALA B 138 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
      removed outlier: 10.057A  pdb=" N   SER B 144 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 164 through 169
    Processing sheet with id=AC4, first strand: chain 'B' and resid 287 through 289
      removed outlier: 3.558A  pdb=" N   ILE B 289 " --> pdb=" O   CYS B 282 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   CYS B 282 " --> pdb=" O   ILE B 289 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 460 through 462
    Processing sheet with id=AC6, first strand: chain 'C' and resid 356 through 357
      removed outlier: 4.542A  pdb=" N   ILE C   8 " --> pdb=" O   PHE C 468 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   PHE C 468 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.543A  pdb=" N   GLY C  11 " --> pdb=" O   GLY C 353 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'C' and resid 19 through 21
      removed outlier: 4.177A  pdb=" N   GLU C  19 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 34 through 36
    Processing sheet with id=AD1, first strand: chain 'C' and resid 38 through 39
    Processing sheet with id=AD2, first strand: chain 'C' and resid 55 through 56
      removed outlier: 6.939A  pdb=" N   LEU C  55 " --> pdb=" O   MET C  85 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE C  84 " --> pdb=" O   MET C 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'C' and resid 98 through 100
      removed outlier: 5.369A  pdb=" N   ILE C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   TYR C 256 " --> pdb=" O   ILE C 179 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 98 through 100
      removed outlier: 7.960A  pdb=" N   ILE C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 136 through 141
      removed outlier: 7.522A  pdb=" N   ALA C 138 " --> pdb=" O   SER C 144 " (cutoff:3.500A)
      removed outlier: 10.539A  pdb=" N   SER C 144 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 164 through 169
    Processing sheet with id=AD7, first strand: chain 'C' and resid 288 through 289
      removed outlier: 4.262A  pdb=" N   CYS C 282 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)

    470 hydrogen bonds defined for protein.
    1299 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.78

  Time building geometry restraints manager: 3.83 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: 3880
        1.34 -     1.46: 2756
        1.46 -     1.58: 5314
        1.58 -     1.71: 0
        1.71 -     1.83: 108
  Bond restraints: 12058
  Sorted by residual:
  bond pdb=" CB  CYS C 278 "
       pdb=" SG  CYS C 278 "
    ideal  model  delta    sigma   weight residual
    1.808  1.746  0.062 3.30e-02 9.18e+02 3.52e+00
  bond pdb=" CB  CYS B 278 "
       pdb=" SG  CYS B 278 "
    ideal  model  delta    sigma   weight residual
    1.808  1.755  0.053 3.30e-02 9.18e+02 2.57e+00
  bond pdb=" C3  GAL G   1 "
       pdb=" O3  GAL G   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.375  0.031 2.00e-02 2.50e+03 2.46e+00
  bond pdb=" C3  GAL H   1 "
       pdb=" O3  GAL H   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.375  0.031 2.00e-02 2.50e+03 2.44e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.35e+00
  ... (remaining 12053 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.25: 16269
        4.25 -     8.51: 39
        8.51 -    12.76: 3
       12.76 -    17.01: 0
       17.01 -    21.26: 2
  Bond angle restraints: 16313
  Sorted by residual:
  angle pdb=" C2  GAL G   1 "
        pdb=" C3  GAL G   1 "
        pdb=" O3  GAL G   1 "
      ideal   model   delta    sigma   weight residual
     107.49  128.75  -21.26 3.00e+00 1.11e-01 5.02e+01
  angle pdb=" C2  GAL H   1 "
        pdb=" C3  GAL H   1 "
        pdb=" O3  GAL H   1 "
      ideal   model   delta    sigma   weight residual
     107.49  125.90  -18.41 3.00e+00 1.11e-01 3.77e+01
  angle pdb=" CA  CYS C 278 "
        pdb=" CB  CYS C 278 "
        pdb=" SG  CYS C 278 "
      ideal   model   delta    sigma   weight residual
     114.40  124.99  -10.59 2.30e+00 1.89e-01 2.12e+01
  angle pdb=" C   CYS C 278 "
        pdb=" CA  CYS C 278 "
        pdb=" CB  CYS C 278 "
      ideal   model   delta    sigma   weight residual
     112.44  103.13    9.31 2.07e+00 2.33e-01 2.02e+01
  angle pdb=" CA  LYS C 368 "
        pdb=" CB  LYS C 368 "
        pdb=" CG  LYS C 368 "
      ideal   model   delta    sigma   weight residual
     114.10  121.28   -7.18 2.00e+00 2.50e-01 1.29e+01
  ... (remaining 16308 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.99: 6713
       27.99 -    55.99: 705
       55.99 -    83.98: 80
       83.98 -   111.98: 11
      111.98 -   139.97: 8
  Dihedral angle restraints: 7517
    sinusoidal: 3344
      harmonic: 4173
  Sorted by residual:
  dihedral pdb=" CB  CYS A 474 "
           pdb=" SG  CYS A 474 "
           pdb=" SG  CYS A 478 "
           pdb=" CB  CYS A 478 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   27.37   65.63     1      1.00e+01 1.00e-02 5.64e+01
  dihedral pdb=" CB  CYS B 474 "
           pdb=" SG  CYS B 474 "
           pdb=" SG  CYS B 478 "
           pdb=" CB  CYS B 478 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.04   55.96     1      1.00e+01 1.00e-02 4.23e+01
  dihedral pdb=" CB  CYS C 282 "
           pdb=" SG  CYS C 282 "
           pdb=" SG  CYS C 306 "
           pdb=" CB  CYS C 306 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   37.44   55.56     1      1.00e+01 1.00e-02 4.17e+01
  ... (remaining 7514 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.162: 1800
       0.162 -    0.325: 2
       0.325 -    0.487: 0
       0.487 -    0.650: 1
       0.650 -    0.812: 1
  Chirality restraints: 1804
  Sorted by residual:
  chirality pdb=" C2  SIA H   2 "
            pdb=" O3  GAL H   1 "
            pdb=" C1  SIA H   2 "
            pdb=" O6  SIA H   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.69    0.19 2.00e-02 2.50e+03 8.78e+01
  chirality pdb=" C2  SIA G   2 "
            pdb=" O3  GAL G   1 "
            pdb=" C1  SIA G   2 "
            pdb=" O6  SIA G   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.64    0.14 2.00e-02 2.50e+03 5.00e+01
  chirality pdb=" C3  GAL H   1 "
            pdb=" C2  GAL H   1 "
            pdb=" C4  GAL H   1 "
            pdb=" O3  GAL H   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.41    1.59    0.81 2.00e-01 2.50e+01 1.65e+01
  ... (remaining 1801 not shown)

  Planarity restraints: 2112
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C  16 "   -0.012 2.00e-02 2.50e+03   2.29e-02 5.26e+00
        pdb=" C   ASN C  16 "    0.040 2.00e-02 2.50e+03
        pdb=" O   ASN C  16 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   SER C  17 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 293 "   -0.037 5.00e-02 4.00e+02   5.66e-02 5.13e+00
        pdb=" N   PRO C 294 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO C 294 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C 294 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B  78 "    0.027 5.00e-02 4.00e+02   4.14e-02 2.74e+00
        pdb=" N   PRO B  79 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B  79 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  79 "    0.023 5.00e-02 4.00e+02
  ... (remaining 2109 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1393
        2.75 -     3.28: 10505
        3.28 -     3.82: 19411
        3.82 -     4.36: 22475
        4.36 -     4.90: 39215
  Nonbonded interactions: 92999
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 458 "
            pdb=" NH2 ARG B 500 "
     model   vdw
     2.208 3.120
  nonbonded pdb=" O   SER B 159 "
            pdb=" OG  SER B 159 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   SER C 112 "
            pdb=" OG  SER C 112 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   TYR A 492 "
            pdb=" OG  SER A 496 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   SER A 112 "
            pdb=" OG  SER A 112 "
     model   vdw
     2.250 3.040
  ... (remaining 92994 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' and (resid 6 through 325 or resid 338 through 501 or resid 701 throug \ 
h 702))
  selection = (chain 'B' and (resid 6 through 501 or resid 701 through 702))
  selection = (chain 'C' and (resid 6 through 501 or resid 701 through 702))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.460
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     30.580
  Find NCS groups from input model:        0.640
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
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      :  0.005   0.062  12091  Z= 0.208
  Angle     :  0.829  41.979  16394  Z= 0.372
  Chirality :  0.051   0.812   1804
  Planarity :  0.004   0.057   2102
  Dihedral  : 20.794 139.972   4799
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 30.71 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.75 %
    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: -0.58 (0.22), residues: 1446
  helix:  2.03 (0.27), residues: 366
  sheet: -0.30 (0.30), residues: 331
  loop : -1.74 (0.20), residues: 749

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 422 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.015   0.002   PHE C 148 
 TYR   0.009   0.001   TYR C 364 
 ARG   0.007   0.001   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.05709 (    2)
  link_BETA2-3         : angle      23.45757 (    6)
  link_NAG-ASN         : bond        0.00221 (   10)
  link_NAG-ASN         : angle       1.87743 (   30)
  link_BETA1-4         : bond        0.00419 (    3)
  link_BETA1-4         : angle       0.93059 (    9)
  hydrogen bonds       : bond        0.15226 (  436)
  hydrogen bonds       : angle       7.05096 ( 1299)
  SS BOND              : bond        0.00546 (   18)
  SS BOND              : angle       3.10648 (   36)
  covalent geometry    : bond        0.00474 (12058)
  covalent geometry    : angle       0.67841 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  385 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 309
  time to evaluate  : 1.406 
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  348 VAL cc_start: 0.8819 (m) cc_final: 0.8465 (t)
  outliers start: 76
  outliers final: 70
  residues processed: 376
  average time/residue: 1.2496
  time to fit residues: 506.5131
Evaluate side-chains
  374 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 304
  time to evaluate  : 1.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue   82 SER
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue   99 SER
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  146 SER
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  266 SER
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain A residue  461 LYS
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  496 SER
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   32 THR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain B residue  109 LEU
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  125 ASP
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  167 SER
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  357 SER
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  437 THR
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  461 LYS
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain C residue   32 THR
Chi-restraints excluded: chain C residue   35 GLN
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  111 SER
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  142 SER
Chi-restraints excluded: chain C residue  167 SER
Chi-restraints excluded: chain C residue  171 THR
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  243 ILE
Chi-restraints excluded: chain C residue  262 LYS
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  446 LYS
Chi-restraints excluded: chain C residue  457 ARG
Chi-restraints excluded: chain C residue  461 LYS
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  471 TYR
Chi-restraints excluded: chain C residue  496 SER
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain C residue  501 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0870
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   overall best weight:    1.5764

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

Flipped N/Q/H residues before XYZ refinement:
A   7 GLN
** A 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B  33 HIS
B  50 ASN
B 196 GLN
B 383 ASN
C 196 GLN
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.140532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.113833 restraints weight = 15643.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 1.91
r_work: 0.3408 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3267 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.0585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12091  Z= 0.258
  Angle     :  0.690  14.637  16394  Z= 0.347
  Chirality :  0.048   0.333   1804
  Planarity :  0.005   0.063   2102
  Dihedral  : 13.801 141.129   2112
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  7.17 %
    Allowed  : 27.36 %
    Favored  : 65.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.69 (0.22), residues: 1446
  helix:  1.94 (0.26), residues: 373
  sheet: -0.50 (0.29), residues: 341
  loop : -1.79 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  81 
 HIS   0.006   0.001   HIS A 296 
 PHE   0.016   0.002   PHE C 295 
 TYR   0.013   0.002   TYR B 103 
 ARG   0.004   0.001   ARG C 137 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.02903 (    2)
  link_BETA2-3         : angle       8.20609 (    6)
  link_NAG-ASN         : bond        0.00313 (   10)
  link_NAG-ASN         : angle       1.96524 (   30)
  link_BETA1-4         : bond        0.00520 (    3)
  link_BETA1-4         : angle       0.72529 (    9)
  hydrogen bonds       : bond        0.06238 (  436)
  hydrogen bonds       : angle       5.36898 ( 1299)
  SS BOND              : bond        0.00551 (   18)
  SS BOND              : angle       2.75147 (   36)
  covalent geometry    : bond        0.00627 (12058)
  covalent geometry    : angle       0.65559 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  401 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 92
    poor density    : 309
  time to evaluate  : 1.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 VAL cc_start: 0.8905 (m) cc_final: 0.8523 (t)
REVERT: B  196 GLN cc_start: 0.8571 (tp40) cc_final: 0.8189 (tp40)
REVERT: B  454 MET cc_start: 0.6074 (tmm) cc_final: 0.5810 (tmm)
REVERT: B  479 MET cc_start: 0.7453 (tmm) cc_final: 0.7083 (ttp)
  outliers start: 92
  outliers final: 57
  residues processed: 371
  average time/residue: 1.2693
  time to fit residues: 507.8952
Evaluate side-chains
  352 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 295
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  372 GLN
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   99 SER
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  146 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  379 THR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  448 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue   35 GLN
Chi-restraints excluded: chain C residue   74 ARG
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  206 THR
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  235 THR
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  371 THR
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  457 ARG
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  471 TYR
Chi-restraints excluded: chain C residue  496 SER
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 15 optimal weight:    0.0270
   chunk 42 optimal weight:    2.9990
   chunk 143 optimal weight:    7.9990
   chunk 80 optimal weight:    0.0170
   chunk 110 optimal weight:    0.2980
   chunk 45 optimal weight:    5.9990
   chunk 13 optimal weight:    0.8980
   chunk 70 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 47 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
B  16 ASN
B  33 HIS
B  50 ASN
B 323 ASN
B 383 ASN
B 455 GLN
C 196 GLN
C 358 ASN
C 444 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.142438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.115699 restraints weight = 15841.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.92
r_work: 0.3440 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.0741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060  12091  Z= 0.141
  Angle     :  0.617  14.961  16394  Z= 0.307
  Chirality :  0.044   0.286   1804
  Planarity :  0.004   0.054   2102
  Dihedral  : 11.935 143.878   2038
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 29.31 %
    Favored  : 64.77 %
  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: -0.50 (0.22), residues: 1446
  helix:  2.25 (0.27), residues: 373
  sheet: -0.51 (0.30), residues: 345
  loop : -1.70 (0.20), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 422 
 HIS   0.003   0.001   HIS A 296 
 PHE   0.011   0.001   PHE C 148 
 TYR   0.020   0.001   TYR A  12 
 ARG   0.005   0.000   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.02412 (    2)
  link_BETA2-3         : angle       7.74052 (    6)
  link_NAG-ASN         : bond        0.00221 (   10)
  link_NAG-ASN         : angle       1.76212 (   30)
  link_BETA1-4         : bond        0.00374 (    3)
  link_BETA1-4         : angle       0.82302 (    9)
  hydrogen bonds       : bond        0.05429 (  436)
  hydrogen bonds       : angle       4.99466 ( 1299)
  SS BOND              : bond        0.00634 (   18)
  SS BOND              : angle       2.75604 (   36)
  covalent geometry    : bond        0.00325 (12058)
  covalent geometry    : angle       0.58138 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  378 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 302
  time to evaluate  : 1.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 VAL cc_start: 0.8796 (m) cc_final: 0.8428 (t)
REVERT: B  454 MET cc_start: 0.5910 (tmm) cc_final: 0.5621 (tmm)
REVERT: B  479 MET cc_start: 0.7389 (tmm) cc_final: 0.7122 (ttp)
REVERT: B  500 ARG cc_start: 0.6619 (OUTLIER) cc_final: 0.6211 (ptm160)
REVERT: C  219 THR cc_start: 0.8441 (OUTLIER) cc_final: 0.8197 (p)
REVERT: C  345 GLN cc_start: 0.7746 (mp10) cc_final: 0.7538 (mp10)
REVERT: C  454 MET cc_start: 0.6746 (tmm) cc_final: 0.6498 (tmm)
  outliers start: 76
  outliers final: 41
  residues processed: 354
  average time/residue: 1.2490
  time to fit residues: 476.3628
Evaluate side-chains
  337 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 294
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   32 THR
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  109 LEU
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  446 LYS
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 57 optimal weight:    0.4980
   chunk 89 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 96 optimal weight:    5.9990
   chunk 116 optimal weight:    0.0010
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
A   7 GLN
A 210 ASN
A 283 GLN
B  16 ASN
B  50 ASN
B 196 GLN
B 383 ASN
B 455 GLN
C 196 GLN
C 402 ASN
C 444 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.143944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.117207 restraints weight = 15643.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 1.89
r_work: 0.3453 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3306 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12091  Z= 0.132
  Angle     :  0.593  14.690  16394  Z= 0.297
  Chirality :  0.043   0.271   1804
  Planarity :  0.004   0.052   2102
  Dihedral  : 10.915 143.635   2020
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  6.70 %
    Allowed  : 28.37 %
    Favored  : 64.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.39 (0.22), residues: 1446
  helix:  2.39 (0.27), residues: 373
  sheet: -0.41 (0.30), residues: 345
  loop : -1.67 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 422 
 HIS   0.003   0.001   HIS C 355 
 PHE   0.010   0.001   PHE B 339 
 TYR   0.010   0.001   TYR C 492 
 ARG   0.006   0.000   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.02201 (    2)
  link_BETA2-3         : angle       7.24618 (    6)
  link_NAG-ASN         : bond        0.00228 (   10)
  link_NAG-ASN         : angle       1.63176 (   30)
  link_BETA1-4         : bond        0.00388 (    3)
  link_BETA1-4         : angle       0.79637 (    9)
  hydrogen bonds       : bond        0.05175 (  436)
  hydrogen bonds       : angle       4.79801 ( 1299)
  SS BOND              : bond        0.00418 (   18)
  SS BOND              : angle       2.26735 (   36)
  covalent geometry    : bond        0.00305 (12058)
  covalent geometry    : angle       0.56393 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  395 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 86
    poor density    : 309
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8119 (t)
REVERT: A  348 VAL cc_start: 0.8882 (m) cc_final: 0.8515 (t)
REVERT: A  455 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7493 (tp40)
REVERT: B  196 GLN cc_start: 0.8553 (tp40) cc_final: 0.8210 (tp40)
REVERT: B  454 MET cc_start: 0.5991 (tmm) cc_final: 0.5689 (tmm)
REVERT: B  479 MET cc_start: 0.7434 (tmm) cc_final: 0.7184 (ttp)
REVERT: B  500 ARG cc_start: 0.6425 (OUTLIER) cc_final: 0.6040 (ptm160)
REVERT: C  219 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8198 (p)
REVERT: C  345 GLN cc_start: 0.7753 (mp10) cc_final: 0.7510 (mp10)
REVERT: C  454 MET cc_start: 0.6706 (tmm) cc_final: 0.6430 (tmm)
  outliers start: 86
  outliers final: 54
  residues processed: 364
  average time/residue: 1.2696
  time to fit residues: 497.8077
Evaluate side-chains
  360 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 302
  time to evaluate  : 1.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  455 GLN
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  305 GLU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue   13 HIS
Chi-restraints excluded: chain C residue  116 PHE
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  446 LYS
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 125 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 93 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
A 392 GLN
B  16 ASN
B  50 ASN
B 191 GLN
B 383 ASN
B 455 GLN
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.143445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.116520 restraints weight = 15664.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 1.92
r_work: 0.3440 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3291 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12091  Z= 0.168
  Angle     :  0.622  14.616  16394  Z= 0.313
  Chirality :  0.044   0.254   1804
  Planarity :  0.004   0.053   2102
  Dihedral  : 10.552 143.014   2014
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 29.70 %
    Favored  : 64.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.42 (0.22), residues: 1446
  helix:  2.36 (0.27), residues: 373
  sheet: -0.49 (0.30), residues: 347
  loop : -1.67 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 422 
 HIS   0.015   0.001   HIS C  13 
 PHE   0.011   0.002   PHE C 148 
 TYR   0.021   0.001   TYR A  12 
 ARG   0.005   0.000   ARG C 126 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.02110 (    2)
  link_BETA2-3         : angle       7.00413 (    6)
  link_NAG-ASN         : bond        0.00242 (   10)
  link_NAG-ASN         : angle       1.65240 (   30)
  link_BETA1-4         : bond        0.00419 (    3)
  link_BETA1-4         : angle       0.80195 (    9)
  hydrogen bonds       : bond        0.05321 (  436)
  hydrogen bonds       : angle       4.77754 ( 1299)
  SS BOND              : bond        0.00668 (   18)
  SS BOND              : angle       2.79252 (   36)
  covalent geometry    : bond        0.00398 (12058)
  covalent geometry    : angle       0.59050 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 304
  time to evaluate  : 1.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 VAL cc_start: 0.8872 (m) cc_final: 0.8498 (t)
REVERT: B  196 GLN cc_start: 0.8576 (tp40) cc_final: 0.8274 (tp40)
REVERT: B  454 MET cc_start: 0.5794 (tmm) cc_final: 0.5476 (tmm)
REVERT: B  479 MET cc_start: 0.7324 (tmm) cc_final: 0.7119 (ttp)
REVERT: B  500 ARG cc_start: 0.6565 (OUTLIER) cc_final: 0.6177 (ptm160)
REVERT: C  182 VAL cc_start: 0.8911 (p) cc_final: 0.8681 (t)
REVERT: C  219 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8192 (p)
REVERT: C  454 MET cc_start: 0.6730 (tmm) cc_final: 0.6462 (tmm)
  outliers start: 80
  outliers final: 52
  residues processed: 353
  average time/residue: 1.3352
  time to fit residues: 507.4123
Evaluate side-chains
  351 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 297
  time to evaluate  : 1.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  457 ARG
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  446 LYS
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 44 optimal weight:    9.9990
   chunk 122 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 125 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 127 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
A 455 GLN
B  16 ASN
B  50 ASN
B 383 ASN
B 455 GLN
B 499 ASN
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.142874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.116003 restraints weight = 15779.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 1.93
r_work: 0.3428 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3279 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.0982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  12091  Z= 0.191
  Angle     :  0.647  14.596  16394  Z= 0.326
  Chirality :  0.045   0.234   1804
  Planarity :  0.004   0.055   2102
  Dihedral  : 10.293 142.264   2011
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  6.24 %
    Allowed  : 29.31 %
    Favored  : 64.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.47 (0.22), residues: 1446
  helix:  2.29 (0.26), residues: 373
  sheet: -0.44 (0.30), residues: 340
  loop : -1.71 (0.20), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  81 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.013   0.002   PHE C 148 
 TYR   0.011   0.001   TYR C 487 
 ARG   0.007   0.000   ARG C 126 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.02066 (    2)
  link_BETA2-3         : angle       6.75824 (    6)
  link_NAG-ASN         : bond        0.00284 (   10)
  link_NAG-ASN         : angle       1.90332 (   30)
  link_BETA1-4         : bond        0.00394 (    3)
  link_BETA1-4         : angle       0.79439 (    9)
  hydrogen bonds       : bond        0.05484 (  436)
  hydrogen bonds       : angle       4.76171 ( 1299)
  SS BOND              : bond        0.00599 (   18)
  SS BOND              : angle       3.22587 (   36)
  covalent geometry    : bond        0.00460 (12058)
  covalent geometry    : angle       0.61187 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  380 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 80
    poor density    : 300
  time to evaluate  : 1.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 VAL cc_start: 0.8880 (m) cc_final: 0.8503 (t)
REVERT: B  500 ARG cc_start: 0.6572 (OUTLIER) cc_final: 0.6194 (ptm160)
REVERT: C  182 VAL cc_start: 0.8907 (p) cc_final: 0.8679 (t)
REVERT: C  219 THR cc_start: 0.8449 (OUTLIER) cc_final: 0.8196 (p)
REVERT: C  454 MET cc_start: 0.6786 (tmm) cc_final: 0.6510 (tmm)
  outliers start: 80
  outliers final: 49
  residues processed: 352
  average time/residue: 1.2301
  time to fit residues: 467.9499
Evaluate side-chains
  347 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 296
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  340 ILE
Chi-restraints excluded: chain A residue  372 GLN
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 101 optimal weight:    0.0870
   chunk 88 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 113 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 109 optimal weight:    0.8980
   chunk 93 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   chunk 130 optimal weight:    6.9990
   chunk 19 optimal weight:    2.9990
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
A 455 GLN
B  16 ASN
B  50 ASN
B 196 GLN
B 383 ASN
B 455 GLN
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.143058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.116002 restraints weight = 15990.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 1.94
r_work: 0.3448 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3300 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3300
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12091  Z= 0.139
  Angle     :  0.614  14.306  16394  Z= 0.309
  Chirality :  0.043   0.215   1804
  Planarity :  0.004   0.051   2102
  Dihedral  :  9.880 142.299   2007
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  5.92 %
    Allowed  : 30.16 %
    Favored  : 63.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.37 (0.22), residues: 1446
  helix:  2.44 (0.27), residues: 373
  sheet: -0.42 (0.30), residues: 340
  loop : -1.67 (0.21), residues: 733

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 422 
 HIS   0.003   0.001   HIS C 472 
 PHE   0.011   0.001   PHE C 148 
 TYR   0.019   0.001   TYR A  12 
 ARG   0.006   0.000   ARG C 126 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.01912 (    2)
  link_BETA2-3         : angle       6.47643 (    6)
  link_NAG-ASN         : bond        0.00357 (   10)
  link_NAG-ASN         : angle       1.73271 (   30)
  link_BETA1-4         : bond        0.00373 (    3)
  link_BETA1-4         : angle       0.80283 (    9)
  hydrogen bonds       : bond        0.05112 (  436)
  hydrogen bonds       : angle       4.64436 ( 1299)
  SS BOND              : bond        0.00415 (   18)
  SS BOND              : angle       2.77628 (   36)
  covalent geometry    : bond        0.00326 (12058)
  covalent geometry    : angle       0.58313 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  389 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 313
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7572 (tm-30)
REVERT: A  348 VAL cc_start: 0.8867 (m) cc_final: 0.8482 (t)
REVERT: B  454 MET cc_start: 0.5948 (tmm) cc_final: 0.5576 (tmm)
REVERT: B  455 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6274 (tt0)
REVERT: B  457 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.4990 (mpp-170)
REVERT: B  479 MET cc_start: 0.6740 (ttp) cc_final: 0.6500 (ttt)
REVERT: B  500 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.6098 (ptm160)
REVERT: C  182 VAL cc_start: 0.8910 (p) cc_final: 0.8679 (t)
REVERT: C  219 THR cc_start: 0.8415 (OUTLIER) cc_final: 0.8196 (p)
REVERT: C  305 GLU cc_start: 0.7664 (pm20) cc_final: 0.7443 (pp20)
REVERT: C  454 MET cc_start: 0.6684 (tmm) cc_final: 0.6396 (tmm)
REVERT: C  455 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7066 (tt0)
  outliers start: 76
  outliers final: 49
  residues processed: 363
  average time/residue: 1.2030
  time to fit residues: 471.6950
Evaluate side-chains
  360 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 305
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  340 ILE
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  496 SER
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  116 PHE
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  455 GLN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   chunk 136 optimal weight:    1.9990
   chunk 15 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9980
   chunk 73 optimal weight:    2.9990
   chunk 129 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
A 392 GLN
A 455 GLN
B  16 ASN
B  50 ASN
B 383 ASN
B 455 GLN
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.142014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.114974 restraints weight = 15820.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.93
r_work: 0.3436 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.1085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  12091  Z= 0.186
  Angle     :  0.644  14.338  16394  Z= 0.327
  Chirality :  0.045   0.189   1804
  Planarity :  0.004   0.053   2102
  Dihedral  :  9.746 141.087   2006
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 31.41 %
    Favored  : 63.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.45 (0.22), residues: 1446
  helix:  2.30 (0.27), residues: 374
  sheet: -0.46 (0.30), residues: 345
  loop : -1.68 (0.21), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 422 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.012   0.002   PHE C 148 
 TYR   0.012   0.001   TYR C 487 
 ARG   0.007   0.000   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.01947 (    2)
  link_BETA2-3         : angle       6.50692 (    6)
  link_NAG-ASN         : bond        0.00340 (   10)
  link_NAG-ASN         : angle       1.75618 (   30)
  link_BETA1-4         : bond        0.00391 (    3)
  link_BETA1-4         : angle       0.78809 (    9)
  hydrogen bonds       : bond        0.05372 (  436)
  hydrogen bonds       : angle       4.67701 ( 1299)
  SS BOND              : bond        0.00576 (   18)
  SS BOND              : angle       2.93518 (   36)
  covalent geometry    : bond        0.00448 (12058)
  covalent geometry    : angle       0.61365 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 302
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  246 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7524 (tm-30)
REVERT: A  348 VAL cc_start: 0.8871 (m) cc_final: 0.8480 (t)
REVERT: B  454 MET cc_start: 0.5893 (tmm) cc_final: 0.5502 (tmm)
REVERT: B  455 GLN cc_start: 0.6986 (OUTLIER) cc_final: 0.6771 (tt0)
REVERT: B  457 ARG cc_start: 0.5505 (OUTLIER) cc_final: 0.5233 (mpp-170)
REVERT: B  479 MET cc_start: 0.6789 (ttp) cc_final: 0.6561 (ttt)
REVERT: B  500 ARG cc_start: 0.6507 (OUTLIER) cc_final: 0.6130 (ptm160)
REVERT: C  182 VAL cc_start: 0.8913 (p) cc_final: 0.8690 (t)
REVERT: C  187 ASP cc_start: 0.7458 (p0) cc_final: 0.7224 (p0)
REVERT: C  219 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.8193 (p)
REVERT: C  305 GLU cc_start: 0.7725 (pm20) cc_final: 0.7474 (pp20)
REVERT: C  454 MET cc_start: 0.6737 (tmm) cc_final: 0.6455 (tmm)
  outliers start: 67
  outliers final: 52
  residues processed: 345
  average time/residue: 1.3666
  time to fit residues: 505.5709
Evaluate side-chains
  350 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 293
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  246 GLU
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLN
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  455 GLN
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  455 GLN
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  262 LYS
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 125 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 63 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** A   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 392 GLN
A 455 GLN
B  16 ASN
B  50 ASN
B 226 GLN
B 383 ASN
** B 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.142456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.115396 restraints weight = 15826.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 1.92
r_work: 0.3444 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3295 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  12091  Z= 0.154
  Angle     :  0.629  14.063  16394  Z= 0.319
  Chirality :  0.044   0.167   1804
  Planarity :  0.004   0.053   2102
  Dihedral  :  9.638 141.129   2005
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 31.10 %
    Favored  : 63.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.43 (0.22), residues: 1446
  helix:  2.32 (0.27), residues: 374
  sheet: -0.45 (0.30), residues: 340
  loop : -1.68 (0.20), residues: 732

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C 422 
 HIS   0.004   0.001   HIS A 296 
 PHE   0.011   0.001   PHE C 148 
 TYR   0.015   0.001   TYR A  12 
 ARG   0.007   0.000   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.01839 (    2)
  link_BETA2-3         : angle       6.34088 (    6)
  link_NAG-ASN         : bond        0.00327 (   10)
  link_NAG-ASN         : angle       1.70682 (   30)
  link_BETA1-4         : bond        0.00425 (    3)
  link_BETA1-4         : angle       0.79059 (    9)
  hydrogen bonds       : bond        0.05225 (  436)
  hydrogen bonds       : angle       4.64161 ( 1299)
  SS BOND              : bond        0.00485 (   18)
  SS BOND              : angle       2.69658 (   36)
  covalent geometry    : bond        0.00364 (12058)
  covalent geometry    : angle       0.60058 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 296
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 VAL cc_start: 0.8862 (m) cc_final: 0.8475 (t)
REVERT: B  457 ARG cc_start: 0.5546 (OUTLIER) cc_final: 0.5283 (mpp-170)
REVERT: B  500 ARG cc_start: 0.6501 (OUTLIER) cc_final: 0.6114 (ptm160)
REVERT: C  182 VAL cc_start: 0.8905 (p) cc_final: 0.8682 (t)
REVERT: C  187 ASP cc_start: 0.7448 (p0) cc_final: 0.7212 (p0)
REVERT: C  219 THR cc_start: 0.8421 (OUTLIER) cc_final: 0.8192 (p)
REVERT: C  305 GLU cc_start: 0.7742 (pm20) cc_final: 0.7488 (pp20)
REVERT: C  454 MET cc_start: 0.6728 (tmm) cc_final: 0.6440 (tmm)
REVERT: C  455 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7062 (tt0)
  outliers start: 64
  outliers final: 50
  residues processed: 337
  average time/residue: 1.3222
  time to fit residues: 479.5756
Evaluate side-chains
  347 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 293
  time to evaluate  : 1.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLN
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  455 GLN
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue    8 ILE
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  305 GLU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  208 THR
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  262 LYS
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  455 GLN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 92 optimal weight:    9.9990
   chunk 122 optimal weight:    3.9990
   chunk 119 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 66 optimal weight:    0.0370
   chunk 8 optimal weight:    0.9980
   chunk 95 optimal weight:    1.9990
   chunk 140 optimal weight:    9.9990
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.0262

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

Flipped N/Q/H residues before XYZ refinement:
A   7 GLN
A 392 GLN
A 455 GLN
B  16 ASN
B  50 ASN
B 383 ASN
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.142142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.115221 restraints weight = 15737.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3551 rms_B_bonded: 1.91
r_work: 0.3437 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.3288 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12091  Z= 0.184
  Angle     :  0.656  13.864  16394  Z= 0.332
  Chirality :  0.045   0.173   1804
  Planarity :  0.004   0.053   2102
  Dihedral  :  9.583 141.067   2005
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 5.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 31.57 %
    Favored  : 63.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.47 (0.22), residues: 1446
  helix:  2.26 (0.27), residues: 374
  sheet: -0.48 (0.30), residues: 345
  loop : -1.69 (0.21), residues: 727

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 422 
 HIS   0.005   0.001   HIS A 296 
 PHE   0.012   0.002   PHE C 148 
 TYR   0.028   0.001   TYR A 492 
 ARG   0.007   0.000   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.01815 (    2)
  link_BETA2-3         : angle       6.31164 (    6)
  link_NAG-ASN         : bond        0.00331 (   10)
  link_NAG-ASN         : angle       1.72708 (   30)
  link_BETA1-4         : bond        0.00393 (    3)
  link_BETA1-4         : angle       0.81228 (    9)
  hydrogen bonds       : bond        0.05413 (  436)
  hydrogen bonds       : angle       4.67672 ( 1299)
  SS BOND              : bond        0.00540 (   18)
  SS BOND              : angle       2.96462 (   36)
  covalent geometry    : bond        0.00442 (12058)
  covalent geometry    : angle       0.62650 (16313)

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

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

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2892 Ramachandran restraints generated.
    1446 Oldfield, 0 Emsley, 1446 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  359 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 297
  time to evaluate  : 1.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  348 VAL cc_start: 0.8866 (m) cc_final: 0.8475 (t)
REVERT: B  196 GLN cc_start: 0.8613 (tp40) cc_final: 0.8298 (tp40)
REVERT: B  457 ARG cc_start: 0.5570 (OUTLIER) cc_final: 0.5306 (mpp-170)
REVERT: B  500 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.6122 (ptm160)
REVERT: C  182 VAL cc_start: 0.8908 (p) cc_final: 0.8680 (t)
REVERT: C  187 ASP cc_start: 0.7464 (p0) cc_final: 0.7231 (p0)
REVERT: C  219 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8191 (p)
REVERT: C  454 MET cc_start: 0.6735 (tmm) cc_final: 0.6448 (tmm)
  outliers start: 62
  outliers final: 49
  residues processed: 333
  average time/residue: 1.2838
  time to fit residues: 459.6905
Evaluate side-chains
  342 residues out of total 1283 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 290
  time to evaluate  : 1.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  125 ASP
Chi-restraints excluded: chain A residue  174 GLU
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  275 LEU
Chi-restraints excluded: chain A residue  279 GLU
Chi-restraints excluded: chain A residue  315 LEU
Chi-restraints excluded: chain A residue  372 GLN
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  468 PHE
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   23 THR
Chi-restraints excluded: chain B residue   24 ILE
Chi-restraints excluded: chain B residue   26 GLU
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  117 GLU
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  208 THR
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  247 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  305 GLU
Chi-restraints excluded: chain B residue  315 LEU
Chi-restraints excluded: chain B residue  324 VAL
Chi-restraints excluded: chain B residue  354 TYR
Chi-restraints excluded: chain B residue  364 TYR
Chi-restraints excluded: chain B residue  399 GLU
Chi-restraints excluded: chain B residue  402 ASN
Chi-restraints excluded: chain B residue  410 LEU
Chi-restraints excluded: chain B residue  419 LEU
Chi-restraints excluded: chain B residue  457 ARG
Chi-restraints excluded: chain B residue  468 PHE
Chi-restraints excluded: chain B residue  495 GLU
Chi-restraints excluded: chain B residue  497 LYS
Chi-restraints excluded: chain B residue  500 ARG
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  120 LYS
Chi-restraints excluded: chain C residue  139 CYS
Chi-restraints excluded: chain C residue  198 VAL
Chi-restraints excluded: chain C residue  209 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  262 LYS
Chi-restraints excluded: chain C residue  356 HIS
Chi-restraints excluded: chain C residue  403 LEU
Chi-restraints excluded: chain C residue  447 ASN
Chi-restraints excluded: chain C residue  468 PHE
Chi-restraints excluded: chain C residue  497 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 123 optimal weight:    0.1980
   chunk 78 optimal weight:    0.3980
   chunk 86 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 103 optimal weight:    0.1980
   chunk 87 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 126 optimal weight:    0.7980
   chunk 121 optimal weight:    2.9990
   chunk 96 optimal weight:    4.9990
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
A 392 GLN
A 455 GLN
B  16 ASN
B  50 ASN
B 383 ASN
C 196 GLN
** C 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 444 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.143885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.116851 restraints weight = 15687.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3572 rms_B_bonded: 1.91
r_work: 0.3462 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12091  Z= 0.124
  Angle     :  0.608  12.850  16394  Z= 0.309
  Chirality :  0.043   0.152   1804
  Planarity :  0.004   0.053   2102
  Dihedral  :  9.295 141.191   2005
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 32.19 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

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: -0.34 (0.22), residues: 1446
  helix:  2.41 (0.27), residues: 374
  sheet: -0.42 (0.30), residues: 338
  loop : -1.60 (0.21), residues: 734

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 422 
 HIS   0.004   0.001   HIS C 355 
 PHE   0.008   0.001   PHE B 339 
 TYR   0.026   0.001   TYR A 492 
 ARG   0.007   0.000   ARG C  27 

Details of bonding type rmsd
  link_BETA2-3         : bond        0.01590 (    2)
  link_BETA2-3         : angle       5.93928 (    6)
  link_NAG-ASN         : bond        0.00343 (   10)
  link_NAG-ASN         : angle       1.57694 (   30)
  link_BETA1-4         : bond        0.00370 (    3)
  link_BETA1-4         : angle       0.86837 (    9)
  hydrogen bonds       : bond        0.04900 (  436)
  hydrogen bonds       : angle       4.55065 ( 1299)
  SS BOND              : bond        0.00401 (   18)
  SS BOND              : angle       2.37069 (   36)
  covalent geometry    : bond        0.00284 (12058)
  covalent geometry    : angle       0.58452 (16313)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 11811.09 seconds
wall clock time: 203 minutes 20.90 seconds (12200.90 seconds total)