Starting phenix.real_space_refine
on Wed May 14 18:23:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jn0_61617/05_2025/9jn0_61617.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jn0_61617/05_2025/9jn0_61617.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jn0_61617/05_2025/9jn0_61617.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jn0_61617/05_2025/9jn0_61617.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jn0_61617/05_2025/9jn0_61617.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jn0_61617/05_2025/9jn0_61617.cif"
  }
  resolution = 2.84
  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=  -0.000 sd=   0.028
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      69      5.16       5
     C    7520      2.51       5
     N    2054      2.21       5
     O    2358      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 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: 12001
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 3897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 487, 3897
          Classifications: {'peptide': 487}
          Link IDs: {'PTRANS': 19, 'TRANS': 467}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 486, 3892
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 19, 'TRANS': 466}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3892
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 486, 3892
          Classifications: {'peptide': 486}
          Link IDs: {'PTRANS': 19, 'TRANS': 466}
          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: "K"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 46
          Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
    Chain: "L"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 46
          Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 46
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 46
          Unusual residues: {'GAL': 1, 'NAG': 1, 'SIA': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 7
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 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: 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
  Time building chain proxies: 8.12, per 1000 atoms: 0.68
  Number of scatterers: 12001
  At special positions: 0
  Unit cell: (89.7, 86.25, 153.18, 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      69     16.00
     O    2358      8.00
     N    2054      7.00
     C    7520      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   4 " - pdb=" SG  CYS A 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  55 " - pdb=" SG  CYS A  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  90 " - pdb=" SG  CYS A 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 473 " - pdb=" SG  CYS A 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B   4 " - pdb=" SG  CYS B 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  42 " - pdb=" SG  CYS B 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  55 " - pdb=" SG  CYS B  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  90 " - pdb=" SG  CYS B 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 278 " - pdb=" SG  CYS B 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 473 " - pdb=" SG  CYS B 477 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   4 " - pdb=" SG  CYS C 466 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  42 " - pdb=" SG  CYS C 274 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  55 " - pdb=" SG  CYS C  67 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  90 " - pdb=" SG  CYS C 135 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 278 " - pdb=" SG  CYS C 302 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 473 " - pdb=" SG  CYS C 477 " 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 " - " GAL F   2 "
      " NAG K   1 " - " GAL K   2 "
      " NAG L   1 " - " GAL L   2 "
    BETA2-6
      " GAL F   2 " - " SIA F   3 "
       ~> Even though SIA is an alpha isomer, a beta linkage is required...
      " GAL K   2 " - " SIA K   3 "
      " GAL L   2 " - " SIA L   3 "
    NAG-ASN
      " NAG A 601 " - " ASN A 165 "
      " NAG A 602 " - " ASN A  11 "
      " NAG A 603 " - " ASN A  23 "
      " NAG A 604 " - " ASN A 286 "
      " NAG B 601 " - " ASN B  11 "
      " NAG B 602 " - " ASN B 286 "
      " NAG C 601 " - " ASN C 165 "
      " NAG C 602 " - " ASN C  23 "
      " NAG C 603 " - " ASN C 286 "
      " NAG D   1 " - " ASN B 165 "
      " NAG E   1 " - " ASN B  23 "
  Time building additional restraints: 3.24
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2720

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 33 sheets defined
      26.7% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 63
    Processing helix  chain 'A' and resid 97 through 105
    Processing helix  chain 'A' and resid 118 through 122
      removed outlier: 3.527A  pdb=" N   TRP A 122 " --> pdb=" O   LYS A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 192
    Processing helix  chain 'A' and resid 366 through 387
      removed outlier: 3.622A  pdb=" N   THR A 370 " --> pdb=" O   ASP A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 452
      removed outlier: 3.512A  pdb=" N   GLU A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   ASP A 438 " --> pdb=" O   GLU A 434 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A 439 " --> pdb=" O   ARG A 435 " (cutoff:3.500A)
      removed outlier: 4.292A  pdb=" N   HIS A 440 " --> pdb=" O   THR A 436 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   ASP A 441 " --> pdb=" O   LEU A 437 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 484
    Processing helix  chain 'A' and resid 487 through 499
      removed outlier: 3.867A  pdb=" N   TYR A 491 " --> pdb=" O   ASP A 487 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   GLU A 493 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
      removed outlier: 5.258A  pdb=" N   GLU A 494 " --> pdb=" O   GLN A 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 97 through 105
    Processing helix  chain 'B' and resid 118 through 122
      removed outlier: 3.553A  pdb=" N   TRP B 122 " --> pdb=" O   LYS B 119 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 191
    Processing helix  chain 'B' and resid 337 through 341
      removed outlier: 3.721A  pdb=" N   GLU B 340 " --> pdb=" O   GLY B 337 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLY B 341 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 337 through 341'
    Processing helix  chain 'B' and resid 366 through 387
      removed outlier: 3.566A  pdb=" N   THR B 370 " --> pdb=" O   ASP B 366 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 456
      removed outlier: 3.597A  pdb=" N   ASP B 438 " --> pdb=" O   GLU B 434 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   HIS B 440 " --> pdb=" O   THR B 436 " (cutoff:3.500A)
      removed outlier: 5.242A  pdb=" N   ASP B 441 " --> pdb=" O   LEU B 437 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   SER B 442 " --> pdb=" O   ASP B 438 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ASN B 443 " --> pdb=" O   PHE B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 474 through 484
    Processing helix  chain 'B' and resid 487 through 499
      removed outlier: 4.128A  pdb=" N   TYR B 491 " --> pdb=" O   ASP B 487 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   GLU B 493 " --> pdb=" O   PRO B 489 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   GLU B 494 " --> pdb=" O   GLN B 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 56 through 63
    Processing helix  chain 'C' and resid 97 through 106
    Processing helix  chain 'C' and resid 118 through 122
      removed outlier: 3.738A  pdb=" N   TRP C 122 " --> pdb=" O   LYS C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 192
    Processing helix  chain 'C' and resid 366 through 387
      removed outlier: 3.759A  pdb=" N   LYS C 372 " --> pdb=" O   GLU C 368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 403 through 452
      removed outlier: 3.595A  pdb=" N   GLU C 407 " --> pdb=" O   GLU C 403 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU C 434 " --> pdb=" O   LEU C 430 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 474 through 484
    Processing helix  chain 'C' and resid 491 through 499
    Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 365
      removed outlier: 3.582A  pdb=" N   SER A 356 " --> pdb=" O   GLN A   2 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16
      removed outlier: 3.999A  pdb=" N   GLU A  14 " --> pdb=" O   VAL A  26 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31
    Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34
    Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 44
      removed outlier: 6.761A  pdb=" N   LEU A  41 " --> pdb=" O   GLY A 272 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   CYS A 274 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51
      removed outlier: 6.731A  pdb=" N   LEU A  50 " --> pdb=" O   VAL A  80 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ILE A  79 " --> pdb=" O   MET A 265 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 93 through 95
      removed outlier: 6.935A  pdb=" N   SER A  94 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   TRP A 230 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 225 " --> pdb=" O   HIS A 180 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ASP A 171 " --> pdb=" O   ILE A 256 " (cutoff:3.500A)
      removed outlier: 5.421A  pdb=" N   LEU A 175 " --> pdb=" O   TYR A 252 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   TYR A 252 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   HIS A 110 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 93 through 95
      removed outlier: 6.935A  pdb=" N   SER A  94 " --> pdb=" O   PHE A 228 " (cutoff:3.500A)
      removed outlier: 8.921A  pdb=" N   TRP A 230 " --> pdb=" O   SER A  94 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A 225 " --> pdb=" O   HIS A 180 " (cutoff:3.500A)
      removed outlier: 7.960A  pdb=" N   LEU A 175 " --> pdb=" O   PRO A 250 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY A 177 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 132 through 137
      removed outlier: 4.775A  pdb=" N   CYS A 135 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 160 through 165
    Processing sheet with id=AB2, first strand: chain 'A' and resid 283 through 285
      removed outlier: 4.113A  pdb=" N   CYS A 278 " --> pdb=" O   ILE A 285 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   GLU A 393 " --> pdb=" O   GLY A 300 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 361 through 365
      removed outlier: 3.690A  pdb=" N   GLY B 352 " --> pdb=" O   GLY B   6 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLY B   6 " --> pdb=" O   GLY B 352 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER B 356 " --> pdb=" O   GLN B   2 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE B   3 " --> pdb=" O   PHE B 467 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 15 through 16
    Processing sheet with id=AB5, first strand: chain 'B' and resid 29 through 31
    Processing sheet with id=AB6, first strand: chain 'B' and resid 33 through 34
    Processing sheet with id=AB7, first strand: chain 'B' and resid 41 through 44
      removed outlier: 7.044A  pdb=" N   LEU B  41 " --> pdb=" O   GLY B 272 " (cutoff:3.500A)
      removed outlier: 4.983A  pdb=" N   CYS B 274 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 50 through 51
      removed outlier: 6.524A  pdb=" N   LEU B  50 " --> pdb=" O   VAL B  80 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   ILE B  79 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 93 through 95
      removed outlier: 6.923A  pdb=" N   SER B  94 " --> pdb=" O   PHE B 228 " (cutoff:3.500A)
      removed outlier: 8.928A  pdb=" N   TRP B 230 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG B 225 " --> pdb=" O   HIS B 180 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ASP B 171 " --> pdb=" O   ILE B 256 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   LEU B 175 " --> pdb=" O   TYR B 252 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   TYR B 252 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL B 257 " --> pdb=" O   HIS B 110 " (cutoff:3.500A)
      removed outlier: 4.945A  pdb=" N   HIS B 110 " --> pdb=" O   VAL B 257 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 93 through 95
      removed outlier: 6.923A  pdb=" N   SER B  94 " --> pdb=" O   PHE B 228 " (cutoff:3.500A)
      removed outlier: 8.928A  pdb=" N   TRP B 230 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG B 225 " --> pdb=" O   HIS B 180 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   LEU B 175 " --> pdb=" O   PRO B 250 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 132 through 137
      removed outlier: 4.887A  pdb=" N   CYS B 135 " --> pdb=" O   SER B 142 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'B' and resid 160 through 165
    Processing sheet with id=AC4, first strand: chain 'B' and resid 283 through 285
      removed outlier: 3.775A  pdb=" N   CYS B 278 " --> pdb=" O   ILE B 285 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU B 393 " --> pdb=" O   GLY B 300 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'C' and resid 361 through 365
      removed outlier: 3.698A  pdb=" N   GLY C 352 " --> pdb=" O   GLY C   6 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   CYS C   4 " --> pdb=" O   HIS C 354 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   SER C 356 " --> pdb=" O   GLN C   2 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'C' and resid 14 through 16
      removed outlier: 4.093A  pdb=" N   GLU C  14 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'C' and resid 29 through 31
    Processing sheet with id=AC8, first strand: chain 'C' and resid 33 through 34
    Processing sheet with id=AC9, first strand: chain 'C' and resid 41 through 44
      removed outlier: 6.960A  pdb=" N   LEU C  41 " --> pdb=" O   GLY C 272 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   CYS C 274 " --> pdb=" O   LEU C  41 " (cutoff:3.500A)
    Processing sheet with id=AD1, first strand: chain 'C' and resid 50 through 51
      removed outlier: 6.545A  pdb=" N   LEU C  50 " --> pdb=" O   VAL C  80 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'C' and resid 93 through 95
      removed outlier: 6.921A  pdb=" N   SER C  94 " --> pdb=" O   PHE C 228 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   TRP C 230 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG C 225 " --> pdb=" O   HIS C 180 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASP C 171 " --> pdb=" O   ILE C 256 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   LEU C 175 " --> pdb=" O   TYR C 252 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   TYR C 252 " --> pdb=" O   LEU C 175 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'C' and resid 93 through 95
      removed outlier: 6.921A  pdb=" N   SER C  94 " --> pdb=" O   PHE C 228 " (cutoff:3.500A)
      removed outlier: 8.907A  pdb=" N   TRP C 230 " --> pdb=" O   SER C  94 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ARG C 225 " --> pdb=" O   HIS C 180 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   LEU C 175 " --> pdb=" O   PRO C 250 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'C' and resid 132 through 137
      removed outlier: 4.722A  pdb=" N   CYS C 135 " --> pdb=" O   SER C 142 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'C' and resid 160 through 165
      removed outlier: 3.553A  pdb=" N   ILE C 162 " --> pdb=" O   PHE C 241 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'C' and resid 283 through 285
      removed outlier: 4.062A  pdb=" N   CYS C 278 " --> pdb=" O   ILE C 285 " (cutoff:3.500A)

    485 hydrogen bonds defined for protein.
    1380 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: 4.09

  Time building geometry restraints manager: 3.78 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: 3952
        1.34 -     1.46: 2873
        1.46 -     1.58: 5338
        1.58 -     1.70: 3
        1.70 -     1.82: 102
  Bond restraints: 12268
  Sorted by residual:
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.61e+00
  bond pdb=" C1  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.445 -0.039 2.00e-02 2.50e+03 3.77e+00
  bond pdb=" C1  NAG A 602 "
       pdb=" O5  NAG A 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.25e+00
  bond pdb=" C1  NAG L   1 "
       pdb=" O5  NAG L   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.00e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.75e+00
  ... (remaining 12263 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.10: 16515
        3.10 -     6.19: 86
        6.19 -     9.29: 9
        9.29 -    12.39: 5
       12.39 -    15.48: 1
  Bond angle restraints: 16616
  Sorted by residual:
  angle pdb=" CA  LEU A 453 "
        pdb=" CB  LEU A 453 "
        pdb=" CG  LEU A 453 "
      ideal   model   delta    sigma   weight residual
     116.30  131.78  -15.48 3.50e+00 8.16e-02 1.96e+01
  angle pdb=" C   ASN A  10 "
        pdb=" N   ASN A  11 "
        pdb=" CA  ASN A  11 "
      ideal   model   delta    sigma   weight residual
     122.67  129.35   -6.68 1.59e+00 3.96e-01 1.77e+01
  angle pdb=" CB  MET A 388 "
        pdb=" CG  MET A 388 "
        pdb=" SD  MET A 388 "
      ideal   model   delta    sigma   weight residual
     112.70  124.48  -11.78 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" CA  ARG C  72 "
        pdb=" CB  ARG C  72 "
        pdb=" CG  ARG C  72 "
      ideal   model   delta    sigma   weight residual
     114.10  121.61   -7.51 2.00e+00 2.50e-01 1.41e+01
  angle pdb=" CB  MET A  66 "
        pdb=" CG  MET A  66 "
        pdb=" SD  MET A  66 "
      ideal   model   delta    sigma   weight residual
     112.70  122.63   -9.93 3.00e+00 1.11e-01 1.10e+01
  ... (remaining 16611 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 6958
       17.91 -    35.82: 562
       35.82 -    53.74: 118
       53.74 -    71.65: 46
       71.65 -    89.56: 11
  Dihedral angle restraints: 7695
    sinusoidal: 3456
      harmonic: 4239
  Sorted by residual:
  dihedral pdb=" CB  CYS B  55 "
           pdb=" SG  CYS B  55 "
           pdb=" SG  CYS B  67 "
           pdb=" CB  CYS B  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.52  -52.52     1      1.00e+01 1.00e-02 3.76e+01
  dihedral pdb=" CA  ASN B  23 "
           pdb=" C   ASN B  23 "
           pdb=" N   VAL B  24 "
           pdb=" CA  VAL B  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.29   24.71     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  LYS A 255 "
           pdb=" C   LYS A 255 "
           pdb=" N   ILE A 256 "
           pdb=" CA  ILE A 256 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.18  -19.82     0      5.00e+00 4.00e-02 1.57e+01
  ... (remaining 7692 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.136: 1822
       0.136 -    0.272: 8
       0.272 -    0.408: 2
       0.408 -    0.545: 0
       0.545 -    0.681: 1
  Chirality restraints: 1833
  Sorted by residual:
  chirality pdb=" C2  SIA F   3 "
            pdb=" O6  GAL F   2 "
            pdb=" C1  SIA F   3 "
            pdb=" O6  SIA F   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.73    0.23 2.00e-02 2.50e+03 1.34e+02
  chirality pdb=" C2  SIA L   3 "
            pdb=" O6  GAL L   2 "
            pdb=" C1  SIA L   3 "
            pdb=" O6  SIA L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.71    0.21 2.00e-02 2.50e+03 1.12e+02
  chirality pdb=" C2  SIA K   3 "
            pdb=" O6  GAL K   2 "
            pdb=" C1  SIA K   3 "
            pdb=" O6  SIA K   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.71    0.21 2.00e-02 2.50e+03 1.08e+02
  ... (remaining 1830 not shown)

  Planarity restraints: 2155
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A  11 "    0.034 2.00e-02 2.50e+03   3.15e-02 1.24e+01
        pdb=" CG  ASN A  11 "   -0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A  11 "   -0.005 2.00e-02 2.50e+03
        pdb=" ND2 ASN A  11 "   -0.037 2.00e-02 2.50e+03
        pdb=" C1  NAG A 602 "    0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C  23 "    0.021 2.00e-02 2.50e+03   1.90e-02 4.53e+00
        pdb=" CG  ASN C  23 "   -0.028 2.00e-02 2.50e+03
        pdb=" OD1 ASN C  23 "    0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN C  23 "   -0.016 2.00e-02 2.50e+03
        pdb=" C1  NAG C 602 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  70 "   -0.013 2.00e-02 2.50e+03   1.45e-02 3.69e+00
        pdb=" CG  PHE A  70 "    0.034 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  70 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  70 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  70 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  70 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  70 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 2152 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 884
        2.74 -     3.28: 11161
        3.28 -     3.82: 18947
        3.82 -     4.36: 22066
        4.36 -     4.90: 39207
  Nonbonded interactions: 92265
  Sorted by model distance:
  nonbonded pdb=" N   GLU C 270 "
            pdb=" OE1 GLU C 270 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" N   GLU B 270 "
            pdb=" OE1 GLU B 270 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" NZ  LYS B 258 "
            pdb=" O   GLY B 260 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OE2 GLU C 126 "
            pdb=" OG  SER C 128 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OG1 THR B 280 "
            pdb=" O   GLY B 283 "
     model   vdw
     2.287 3.040
  ... (remaining 92260 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 1 through 320 or resid 335 through 500 or resid 601 throug \ 
h 602))
  selection = chain 'B'
  selection = (chain 'C' and (resid 1 through 500 or resid 601 through 602))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'F'
  selection = chain 'K'
  selection = chain 'L'
}

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:             2.430
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     31.380
  Find NCS groups from input model:        0.650
  Set up NCS constraints:                  0.060
  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:12.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
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      :  0.003   0.051  12305  Z= 0.145
  Angle     :  0.714  21.904  16709  Z= 0.315
  Chirality :  0.047   0.681   1833
  Planarity :  0.003   0.039   2144
  Dihedral  : 14.138  89.559   4921
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 14.80 %
    Favored  : 84.50 %
  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:  0.44 (0.22), residues: 1447
  helix:  2.30 (0.27), residues: 370
  sheet:  0.64 (0.32), residues: 228
  loop : -0.76 (0.21), residues: 849

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP B 343 
 HIS   0.002   0.000   HIS B 355 
 PHE   0.034   0.001   PHE A  70 
 TYR   0.010   0.001   TYR C 164 
 ARG   0.003   0.000   ARG A 456 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00897 (   11)
  link_NAG-ASN         : angle       6.44810 (   33)
  link_BETA1-4         : bond        0.00397 (    5)
  link_BETA1-4         : angle       1.78157 (   15)
  hydrogen bonds       : bond        0.18549 (  458)
  hydrogen bonds       : angle       6.89190 ( 1380)
  SS BOND              : bond        0.00113 (   18)
  SS BOND              : angle       0.71382 (   36)
  glycosidic custom    : bond        0.00574 (    3)
  glycosidic custom    : angle       9.42988 (    9)
  covalent geometry    : bond        0.00293 (12268)
  covalent geometry    : angle       0.61487 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 8
  residues processed: 74
  average time/residue: 1.0845
  time to fit residues: 89.2079
Evaluate side-chains
  71 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  193 ASN
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
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:    0.5980
   chunk 60 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 73 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 112 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0670
   chunk 84 optimal weight:    0.9980
   chunk 130 optimal weight:    0.6980
   overall best weight:    1.0720

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

Flipped N/Q/H residues before XYZ refinement:
A 454 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.063403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.044257 restraints weight = 36963.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2600 rms_B_bonded: 4.09
r_work: 0.2437 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.2437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.0688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12305  Z= 0.116
  Angle     :  0.587  18.174  16709  Z= 0.285
  Chirality :  0.043   0.315   1833
  Planarity :  0.003   0.037   2144
  Dihedral  :  8.090  83.314   2086
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.93 %
    Favored  : 85.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: 1447
  helix:  2.46 (0.28), residues: 373
  sheet:  0.67 (0.31), residues: 248
  loop : -0.82 (0.21), residues: 826

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 176 
 HIS   0.004   0.001   HIS A   8 
 PHE   0.014   0.001   PHE B  70 
 TYR   0.011   0.001   TYR C 353 
 ARG   0.008   0.000   ARG C 435 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00602 (   11)
  link_NAG-ASN         : angle       4.71406 (   33)
  link_BETA1-4         : bond        0.00451 (    5)
  link_BETA1-4         : angle       1.24566 (   15)
  hydrogen bonds       : bond        0.05622 (  458)
  hydrogen bonds       : angle       5.16049 ( 1380)
  SS BOND              : bond        0.00338 (   18)
  SS BOND              : angle       0.91958 (   36)
  glycosidic custom    : bond        0.00729 (    3)
  glycosidic custom    : angle       1.55067 (    9)
  covalent geometry    : bond        0.00248 (12268)
  covalent geometry    : angle       0.54584 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 1.468 
Fit side-chains
   revert: symmetry clash
  outliers start: 18
  outliers final: 7
  residues processed: 81
  average time/residue: 1.0281
  time to fit residues: 93.2387
Evaluate side-chains
  72 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 1.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  367 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 16 optimal weight:   10.0000
   chunk 15 optimal weight:    5.9990
   chunk 96 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 133 optimal weight:    2.9990
   chunk 127 optimal weight:    8.9990
   chunk 27 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0770
   chunk 89 optimal weight:    6.9990
   chunk 81 optimal weight:    9.9990
   chunk 125 optimal weight:    2.9990
   overall best weight:    3.8146

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

Flipped N/Q/H residues before XYZ refinement:
A   2 GLN
B 440 HIS
C 218 GLN
C 355 HIS
C 440 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.059726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2521 r_free = 0.2521 target = 0.040459 restraints weight = 37354.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2489 rms_B_bonded: 4.04
r_work: 0.2324 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  12305  Z= 0.258
  Angle     :  0.660  17.801  16709  Z= 0.330
  Chirality :  0.045   0.280   1833
  Planarity :  0.004   0.037   2144
  Dihedral  :  7.716  84.054   2077
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 12.23 %
    Favored  : 85.44 %
  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:  0.21 (0.22), residues: 1447
  helix:  2.21 (0.27), residues: 377
  sheet:  0.84 (0.33), residues: 238
  loop : -1.13 (0.20), residues: 832

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 350 
 HIS   0.008   0.001   HIS A   8 
 PHE   0.023   0.002   PHE A 439 
 TYR   0.011   0.001   TYR A 353 
 ARG   0.005   0.001   ARG C 435 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00497 (   11)
  link_NAG-ASN         : angle       4.31135 (   33)
  link_BETA1-4         : bond        0.00246 (    5)
  link_BETA1-4         : angle       1.43233 (   15)
  hydrogen bonds       : bond        0.06821 (  458)
  hydrogen bonds       : angle       5.03176 ( 1380)
  SS BOND              : bond        0.00309 (   18)
  SS BOND              : angle       0.89064 (   36)
  glycosidic custom    : bond        0.00157 (    3)
  glycosidic custom    : angle       1.09834 (    9)
  covalent geometry    : bond        0.00621 (12268)
  covalent geometry    : angle       0.62968 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 70
  time to evaluate  : 1.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  449 ASP cc_start: 0.9609 (m-30) cc_final: 0.8962 (p0)
  outliers start: 30
  outliers final: 12
  residues processed: 95
  average time/residue: 0.9895
  time to fit residues: 104.6177
Evaluate side-chains
  75 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain C residue  367 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 130 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9980
   chunk 134 optimal weight:    7.9990
   chunk 116 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 141 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 127 optimal weight:    6.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 454 GLN
A 458 ASN
C 218 GLN
C 355 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.060771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.041795 restraints weight = 36374.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2520 rms_B_bonded: 3.96
r_work: 0.2354 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8756
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12305  Z= 0.158
  Angle     :  0.591  16.959  16709  Z= 0.291
  Chirality :  0.043   0.250   1833
  Planarity :  0.003   0.036   2144
  Dihedral  :  7.239  81.556   2077
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.24 %
    Favored  : 84.97 %
  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:  0.30 (0.22), residues: 1447
  helix:  2.36 (0.27), residues: 377
  sheet:  0.91 (0.33), residues: 237
  loop : -1.11 (0.20), residues: 833

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 421 
 HIS   0.004   0.001   HIS A   8 
 PHE   0.015   0.001   PHE A 469 
 TYR   0.015   0.001   TYR A 488 
 ARG   0.004   0.000   ARG C 435 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00458 (   11)
  link_NAG-ASN         : angle       4.08933 (   33)
  link_BETA1-4         : bond        0.00282 (    5)
  link_BETA1-4         : angle       1.22185 (   15)
  hydrogen bonds       : bond        0.06028 (  458)
  hydrogen bonds       : angle       4.86426 ( 1380)
  SS BOND              : bond        0.00239 (   18)
  SS BOND              : angle       0.82368 (   36)
  glycosidic custom    : bond        0.00316 (    3)
  glycosidic custom    : angle       0.93845 (    9)
  covalent geometry    : bond        0.00367 (12268)
  covalent geometry    : angle       0.56123 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 1.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  449 ASP cc_start: 0.9592 (m-30) cc_final: 0.8929 (p0)
  outliers start: 23
  outliers final: 13
  residues processed: 87
  average time/residue: 1.0267
  time to fit residues: 99.6178
Evaluate side-chains
  77 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 1.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  427 LEU
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain C residue  367 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 121 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 135 optimal weight:    4.9990
   chunk 76 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    8.9990
   chunk 87 optimal weight:    5.9990
   chunk 117 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 218 GLN
C 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.060061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2539 r_free = 0.2539 target = 0.041091 restraints weight = 36830.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.2503 rms_B_bonded: 4.01
r_work: 0.2337 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.1581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12305  Z= 0.204
  Angle     :  0.616  19.668  16709  Z= 0.300
  Chirality :  0.044   0.296   1833
  Planarity :  0.003   0.037   2144
  Dihedral  :  7.113  82.325   2077
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.40 %
    Favored  : 84.81 %
  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:  0.29 (0.22), residues: 1447
  helix:  2.36 (0.27), residues: 377
  sheet:  0.82 (0.32), residues: 258
  loop : -1.15 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 122 
 HIS   0.005   0.001   HIS A   8 
 PHE   0.017   0.002   PHE A  70 
 TYR   0.013   0.001   TYR B 491 
 ARG   0.003   0.000   ARG C 435 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00534 (   11)
  link_NAG-ASN         : angle       4.43803 (   33)
  link_BETA1-4         : bond        0.00250 (    5)
  link_BETA1-4         : angle       1.31766 (   15)
  hydrogen bonds       : bond        0.06106 (  458)
  hydrogen bonds       : angle       4.80076 ( 1380)
  SS BOND              : bond        0.00262 (   18)
  SS BOND              : angle       0.82814 (   36)
  glycosidic custom    : bond        0.00194 (    3)
  glycosidic custom    : angle       0.81709 (    9)
  covalent geometry    : bond        0.00485 (12268)
  covalent geometry    : angle       0.58176 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 67
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 PHE cc_start: 0.9169 (m-80) cc_final: 0.8582 (m-80)
REVERT: C  449 ASP cc_start: 0.9589 (m-30) cc_final: 0.8941 (p0)
  outliers start: 23
  outliers final: 15
  residues processed: 88
  average time/residue: 1.0460
  time to fit residues: 102.4897
Evaluate side-chains
  80 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 LYS
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  453 LEU
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  367 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 129 optimal weight:    8.9990
   chunk 93 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 67 optimal weight:    4.9990
   chunk 12 optimal weight:    0.1980
   chunk 72 optimal weight:    7.9990
   chunk 86 optimal weight:    0.5980
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 218 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.061670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.042710 restraints weight = 36809.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.2549 rms_B_bonded: 4.02
r_work: 0.2385 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12305  Z= 0.109
  Angle     :  0.570  17.923  16709  Z= 0.274
  Chirality :  0.043   0.249   1833
  Planarity :  0.003   0.033   2144
  Dihedral  :  6.752  80.758   2077
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 13.63 %
    Favored  : 84.42 %
  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:  0.49 (0.22), residues: 1447
  helix:  2.47 (0.27), residues: 377
  sheet:  1.01 (0.31), residues: 257
  loop : -1.01 (0.20), residues: 813

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 350 
 HIS   0.002   0.000   HIS A 354 
 PHE   0.019   0.001   PHE A 469 
 TYR   0.012   0.001   TYR B 491 
 ARG   0.007   0.000   ARG B 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00472 (   11)
  link_NAG-ASN         : angle       4.13142 (   33)
  link_BETA1-4         : bond        0.00345 (    5)
  link_BETA1-4         : angle       1.17339 (   15)
  hydrogen bonds       : bond        0.05311 (  458)
  hydrogen bonds       : angle       4.60504 ( 1380)
  SS BOND              : bond        0.00172 (   18)
  SS BOND              : angle       0.87714 (   36)
  glycosidic custom    : bond        0.00295 (    3)
  glycosidic custom    : angle       0.78011 (    9)
  covalent geometry    : bond        0.00235 (12268)
  covalent geometry    : angle       0.53839 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 70
  time to evaluate  : 1.353 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8673 (mp)
REVERT: B  469 PHE cc_start: 0.9178 (m-80) cc_final: 0.8581 (m-80)
REVERT: C  449 ASP cc_start: 0.9558 (OUTLIER) cc_final: 0.8882 (p0)
  outliers start: 25
  outliers final: 12
  residues processed: 87
  average time/residue: 1.0288
  time to fit residues: 99.7092
Evaluate side-chains
  81 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 1.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain C residue  449 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 138 optimal weight:    4.9990
   chunk 110 optimal weight:    6.9990
   chunk 1 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 105 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   chunk 41 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 218 GLN
C 355 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.059877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2520 r_free = 0.2520 target = 0.040670 restraints weight = 37261.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.2489 rms_B_bonded: 4.03
r_work: 0.2321 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.1783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  12305  Z= 0.229
  Angle     :  0.620  17.645  16709  Z= 0.306
  Chirality :  0.044   0.259   1833
  Planarity :  0.003   0.036   2144
  Dihedral  :  6.812  82.967   2077
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.64 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.26 (0.22), residues: 1447
  helix:  2.35 (0.27), residues: 377
  sheet:  0.82 (0.32), residues: 258
  loop : -1.18 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 421 
 HIS   0.005   0.001   HIS A   8 
 PHE   0.019   0.002   PHE A  70 
 TYR   0.009   0.001   TYR B 491 
 ARG   0.003   0.000   ARG B 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00477 (   11)
  link_NAG-ASN         : angle       4.12755 (   33)
  link_BETA1-4         : bond        0.00233 (    5)
  link_BETA1-4         : angle       1.18790 (   15)
  hydrogen bonds       : bond        0.06181 (  458)
  hydrogen bonds       : angle       4.74610 ( 1380)
  SS BOND              : bond        0.00304 (   18)
  SS BOND              : angle       0.85263 (   36)
  glycosidic custom    : bond        0.00073 (    3)
  glycosidic custom    : angle       0.67292 (    9)
  covalent geometry    : bond        0.00546 (12268)
  covalent geometry    : angle       0.59180 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 1.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 PHE cc_start: 0.9206 (m-80) cc_final: 0.8614 (m-80)
  outliers start: 17
  outliers final: 13
  residues processed: 81
  average time/residue: 1.0026
  time to fit residues: 91.1211
Evaluate side-chains
  75 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain C residue   19 ILE
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  355 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 2 optimal weight:    6.9990
   chunk 40 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9980
   chunk 119 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 96 optimal weight:   10.0000
   chunk 81 optimal weight:    0.1980
   chunk 21 optimal weight:    6.9990
   chunk 38 optimal weight:    6.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.061290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.042121 restraints weight = 37238.556|
|-----------------------------------------------------------------------------|
r_work (start): 0.2531 rms_B_bonded: 4.06
r_work: 0.2363 rms_B_bonded: 4.19 restraints_weight: 0.5000
r_work (final): 0.2363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12305  Z= 0.110
  Angle     :  0.585  16.838  16709  Z= 0.282
  Chirality :  0.043   0.239   1833
  Planarity :  0.003   0.033   2144
  Dihedral  :  6.576  81.295   2077
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.49 %
    Favored  : 83.96 %
  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:  0.40 (0.22), residues: 1447
  helix:  2.43 (0.27), residues: 377
  sheet:  0.91 (0.32), residues: 258
  loop : -1.07 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP B 149 
 HIS   0.014   0.001   HIS C 355 
 PHE   0.018   0.001   PHE A 469 
 TYR   0.010   0.001   TYR B 491 
 ARG   0.003   0.000   ARG B 452 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00446 (   11)
  link_NAG-ASN         : angle       4.02192 (   33)
  link_BETA1-4         : bond        0.00294 (    5)
  link_BETA1-4         : angle       1.15421 (   15)
  hydrogen bonds       : bond        0.05436 (  458)
  hydrogen bonds       : angle       4.61678 ( 1380)
  SS BOND              : bond        0.00171 (   18)
  SS BOND              : angle       0.81470 (   36)
  glycosidic custom    : bond        0.00296 (    3)
  glycosidic custom    : angle       0.73413 (    9)
  covalent geometry    : bond        0.00240 (12268)
  covalent geometry    : angle       0.55605 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 71
  time to evaluate  : 1.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 PHE cc_start: 0.9208 (m-80) cc_final: 0.8617 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 87
  average time/residue: 0.9750
  time to fit residues: 94.9430
Evaluate side-chains
  79 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  355 HIS
Chi-restraints excluded: chain C residue  449 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 58 optimal weight:    6.9990
   chunk 71 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 31 optimal weight:    0.0970
   chunk 136 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 120 optimal weight:    8.9990
   chunk 138 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    3.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.060003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.040872 restraints weight = 37337.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.2499 rms_B_bonded: 4.02
r_work: 0.2330 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12305  Z= 0.217
  Angle     :  0.637  21.425  16709  Z= 0.310
  Chirality :  0.045   0.394   1833
  Planarity :  0.003   0.035   2144
  Dihedral  :  6.709  82.279   2077
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.03 %
    Favored  : 83.72 %
  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:  0.21 (0.22), residues: 1447
  helix:  2.33 (0.27), residues: 377
  sheet:  0.56 (0.31), residues: 278
  loop : -1.18 (0.20), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 421 
 HIS   0.005   0.001   HIS A   8 
 PHE   0.020   0.002   PHE B  70 
 TYR   0.009   0.001   TYR B 271 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00441 (   11)
  link_NAG-ASN         : angle       4.72452 (   33)
  link_BETA1-4         : bond        0.00380 (    5)
  link_BETA1-4         : angle       1.31852 (   15)
  hydrogen bonds       : bond        0.05981 (  458)
  hydrogen bonds       : angle       4.71822 ( 1380)
  SS BOND              : bond        0.00278 (   18)
  SS BOND              : angle       0.85030 (   36)
  glycosidic custom    : bond        0.00167 (    3)
  glycosidic custom    : angle       0.69297 (    9)
  covalent geometry    : bond        0.00518 (12268)
  covalent geometry    : angle       0.60057 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  469 PHE cc_start: 0.9241 (m-80) cc_final: 0.8624 (m-80)
  outliers start: 16
  outliers final: 14
  residues processed: 80
  average time/residue: 1.0350
  time to fit residues: 92.4030
Evaluate side-chains
  76 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  269 VAL
Chi-restraints excluded: chain A residue  274 CYS
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  355 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 142 optimal weight:    3.9990
   chunk 79 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 62 optimal weight:    3.9990
   chunk 102 optimal weight:    0.5980
   chunk 130 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A   2 GLN
A 354 HIS
C 179 HIS
C 354 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.061486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.042420 restraints weight = 36579.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.2540 rms_B_bonded: 4.01
r_work: 0.2372 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.2372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8707
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12305  Z= 0.116
  Angle     :  0.606  18.876  16709  Z= 0.289
  Chirality :  0.043   0.313   1833
  Planarity :  0.003   0.034   2144
  Dihedral  :  6.553  80.912   2077
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 15.19 %
    Favored  : 83.64 %
  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:  0.33 (0.22), residues: 1447
  helix:  2.36 (0.27), residues: 377
  sheet:  0.68 (0.31), residues: 278
  loop : -1.07 (0.21), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 343 
 HIS   0.003   0.001   HIS A 354 
 PHE   0.020   0.001   PHE A  70 
 TYR   0.010   0.001   TYR B 271 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00492 (   11)
  link_NAG-ASN         : angle       4.33845 (   33)
  link_BETA1-4         : bond        0.00373 (    5)
  link_BETA1-4         : angle       1.18876 (   15)
  hydrogen bonds       : bond        0.05357 (  458)
  hydrogen bonds       : angle       4.60261 ( 1380)
  SS BOND              : bond        0.00169 (   18)
  SS BOND              : angle       0.83377 (   36)
  glycosidic custom    : bond        0.00197 (    3)
  glycosidic custom    : angle       0.66323 (    9)
  covalent geometry    : bond        0.00258 (12268)
  covalent geometry    : angle       0.57402 (16616)

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

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

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2894 Ramachandran restraints generated.
    1447 Oldfield, 0 Emsley, 1447 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 1.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  311 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8617 (mp)
REVERT: B  346 MET cc_start: 0.9258 (tmm) cc_final: 0.8989 (tmt)
REVERT: B  469 PHE cc_start: 0.9236 (m-80) cc_final: 0.8617 (m-80)
  outliers start: 15
  outliers final: 11
  residues processed: 79
  average time/residue: 1.0805
  time to fit residues: 94.6780
Evaluate side-chains
  78 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  280 THR
Chi-restraints excluded: chain A residue  477 CYS
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  269 VAL
Chi-restraints excluded: chain B residue  274 CYS
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  339 ILE
Chi-restraints excluded: chain B residue  437 LEU
Chi-restraints excluded: chain B residue  477 CYS
Chi-restraints excluded: chain C residue   73 VAL
Chi-restraints excluded: chain C residue  274 CYS
Chi-restraints excluded: chain C residue  355 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 56 optimal weight:    0.0770
   chunk 66 optimal weight:    9.9990
   chunk 73 optimal weight:    0.9990
   chunk 82 optimal weight:    9.9990
   chunk 74 optimal weight:    6.9990
   chunk 70 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0670
   chunk 113 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.8282

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

Flipped N/Q/H residues before XYZ refinement:
** A   2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.061154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.042069 restraints weight = 36756.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.2531 rms_B_bonded: 4.01
r_work: 0.2363 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.1855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12305  Z= 0.144
  Angle     :  0.607  17.935  16709  Z= 0.292
  Chirality :  0.043   0.280   1833
  Planarity :  0.003   0.033   2144
  Dihedral  :  6.512  80.914   2076
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 15.11 %
    Favored  : 83.64 %
  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: 1447
  helix:  2.35 (0.27), residues: 377
  sheet:  0.98 (0.32), residues: 258
  loop : -1.09 (0.20), residues: 812

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.000   TRP A 343 
 HIS   0.003   0.001   HIS A 354 
 PHE   0.021   0.001   PHE B  70 
 TYR   0.009   0.001   TYR B 491 
 ARG   0.004   0.000   ARG A 169 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00461 (   11)
  link_NAG-ASN         : angle       4.19030 (   33)
  link_BETA1-4         : bond        0.00316 (    5)
  link_BETA1-4         : angle       1.16480 (   15)
  hydrogen bonds       : bond        0.05425 (  458)
  hydrogen bonds       : angle       4.60033 ( 1380)
  SS BOND              : bond        0.00198 (   18)
  SS BOND              : angle       0.81192 (   36)
  glycosidic custom    : bond        0.00156 (    3)
  glycosidic custom    : angle       0.66315 (    9)
  covalent geometry    : bond        0.00336 (12268)
  covalent geometry    : angle       0.57700 (16616)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6429.23 seconds
wall clock time: 112 minutes 8.32 seconds (6728.32 seconds total)