Starting phenix.real_space_refine
on Wed May 14 14:49:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xhe_38348/05_2025/8xhe_38348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xhe_38348/05_2025/8xhe_38348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.64
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xhe_38348/05_2025/8xhe_38348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xhe_38348/05_2025/8xhe_38348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xhe_38348/05_2025/8xhe_38348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xhe_38348/05_2025/8xhe_38348.cif"
  }
  resolution = 2.64
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.026
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      75      5.16       5
     C    7450      2.51       5
     N    2011      2.21       5
     O    2376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 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: 11912
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "C"
      Number of atoms: 3878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 3878
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 19, 'TRANS': 469}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 488, 3873
          Classifications: {'peptide': 488}
          Link IDs: {'PTRANS': 19, 'TRANS': 468}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3878
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 489, 3878
          Classifications: {'peptide': 489}
          Link IDs: {'PTRANS': 19, 'TRANS': 469}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 57
          Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 57
          Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 3
    Chain: "F"
      Number of atoms: 57
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 57
          Unusual residues: {'GAL': 2, 'NAG': 1, 'SIA': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 10
          Unresolved non-hydrogen chiralities: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 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: 7.20, per 1000 atoms: 0.60
  Number of scatterers: 11912
  At special positions: 0
  Unit cell: (87.55, 86.7, 150.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      75     16.00
     O    2376      8.00
     N    2011      7.00
     C    7450      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-3
      " GAL D   1 " - " NAG D   2 "
      " GAL E   1 " - " NAG E   2 "
      " GAL F   1 " - " NAG F   2 "
    BETA1-4
      " NAG D   2 " - " GAL D   3 "
      " NAG E   2 " - " GAL E   3 "
      " NAG F   2 " - " GAL F   3 "
    BETA2-6
      " GAL D   3 " - " SIA D   4 "
       ~> Even though SIA is an alpha isomer, a beta linkage is required...
      " GAL E   3 " - " SIA E   4 "
      " GAL F   3 " - " SIA F   4 "
    NAG-ASN
      " NAG A 601 " - " ASN A 169 "
      " NAG A 602 " - " ASN A 484 "
      " NAG A 603 " - " ASN A  28 "
      " NAG B 601 " - " ASN B 169 "
      " NAG B 602 " - " ASN B 484 "
      " NAG B 603 " - " ASN B  28 "
      " NAG C 601 " - " ASN C 169 "
      " NAG C 602 " - " ASN C  28 "
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2686

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 33 sheets defined
      27.6% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.49
  Creating SS restraints...
    Processing helix  chain 'C' and resid 61 through 68
    Processing helix  chain 'C' and resid 72 through 76
      removed outlier: 3.557A  pdb=" N   LEU C  75 " --> pdb=" O   CYS C  72 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU C  76 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 72 through 76'
    Processing helix  chain 'C' and resid 102 through 111
    Processing helix  chain 'C' and resid 187 through 196
    Processing helix  chain 'C' and resid 367 through 388
      removed outlier: 3.788A  pdb=" N   LYS C 388 " --> pdb=" O   SER C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 457
      removed outlier: 3.852A  pdb=" N   ASP C 442 " --> pdb=" O   LEU C 438 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 475 through 485
    Processing helix  chain 'C' and resid 489 through 491
      No H-bonds generated for 'chain 'C' and resid 489 through 491'
    Processing helix  chain 'C' and resid 492 through 501
      removed outlier: 3.803A  pdb=" N   ASN C 501 " --> pdb=" O   LYS C 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 68
    Processing helix  chain 'A' and resid 102 through 111
    Processing helix  chain 'A' and resid 123 through 127
      removed outlier: 3.845A  pdb=" N   TRP A 127 " --> pdb=" O   LYS A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 196
    Processing helix  chain 'A' and resid 368 through 387
    Processing helix  chain 'A' and resid 404 through 457
      removed outlier: 3.841A  pdb=" N   ASP A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 485
    Processing helix  chain 'A' and resid 489 through 491
      No H-bonds generated for 'chain 'A' and resid 489 through 491'
    Processing helix  chain 'A' and resid 492 through 501
      removed outlier: 3.841A  pdb=" N   SER A 496 " --> pdb=" O   TYR A 492 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A 498 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 68
    Processing helix  chain 'B' and resid 69 through 76
      removed outlier: 3.957A  pdb=" N   ASP B  73 " --> pdb=" O   PRO B  70 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   ARG B  74 " --> pdb=" O   GLU B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 111
    Processing helix  chain 'B' and resid 123 through 127
      removed outlier: 3.519A  pdb=" N   TRP B 127 " --> pdb=" O   LYS B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 196
    Processing helix  chain 'B' and resid 367 through 388
      removed outlier: 3.659A  pdb=" N   THR B 371 " --> pdb=" O   ASP B 367 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 457
      removed outlier: 3.875A  pdb=" N   GLU B 435 " --> pdb=" O   LEU B 431 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 475 through 483
    Processing helix  chain 'B' and resid 488 through 501
      removed outlier: 4.205A  pdb=" N   TYR B 492 " --> pdb=" O   ASP B 488 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   GLU B 494 " --> pdb=" O   PRO B 490 " (cutoff:3.500A)
      removed outlier: 6.112A  pdb=" N   GLU B 495 " --> pdb=" O   LYS B 491 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LYS B 497 " --> pdb=" O   GLU B 493 " (cutoff:3.500A)
      removed outlier: 4.425A  pdb=" N   LEU B 498 " --> pdb=" O   GLU B 494 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASN B 499 " --> pdb=" O   GLU B 495 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 361 through 364
      removed outlier: 3.666A  pdb=" N   GLY C 361 " --> pdb=" O   ASN C 358 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE C 468 " --> pdb=" O   ILE C   8 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 19 through 21
      removed outlier: 4.308A  pdb=" N   GLU C  19 " --> pdb=" O   VAL C  31 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 36
    Processing sheet with id=AA4, first strand: chain 'C' and resid 38 through 39
    Processing sheet with id=AA5, first strand: chain 'C' and resid 46 through 49
      removed outlier: 9.097A  pdb=" N   LEU C  46 " --> pdb=" O   CYS C 278 " (cutoff:3.500A)
      removed outlier: 8.507A  pdb=" N   THR C 280 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
      removed outlier: 6.419A  pdb=" N   LYS C  48 " --> pdb=" O   THR C 280 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 55 through 56
      removed outlier: 6.813A  pdb=" N   LEU C  55 " --> pdb=" O   MET C  85 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE C  84 " --> pdb=" O   MET C 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 98 through 100
      removed outlier: 6.696A  pdb=" N   SER C  99 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   TRP C 234 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 5.456A  pdb=" N   ILE C 179 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   TYR C 256 " --> pdb=" O   ILE C 179 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100
      removed outlier: 6.696A  pdb=" N   SER C  99 " --> pdb=" O   PHE C 232 " (cutoff:3.500A)
      removed outlier: 8.713A  pdb=" N   TRP C 234 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   ILE C 179 " --> pdb=" O   PRO C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 130 through 131
    Processing sheet with id=AB1, first strand: chain 'C' and resid 136 through 141
      removed outlier: 4.990A  pdb=" N   CYS C 139 " --> pdb=" O   SER C 146 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 164 through 169
    Processing sheet with id=AB3, first strand: chain 'C' and resid 288 through 289
      removed outlier: 3.515A  pdb=" N   ILE C 289 " --> pdb=" O   CYS C 282 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   CYS C 282 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 8 through 12
      removed outlier: 3.788A  pdb=" N   HIS A 356 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   GLY A 363 " --> pdb=" O   HIS A 356 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 19 through 21
      removed outlier: 3.938A  pdb=" N   GLU A  19 " --> pdb=" O   VAL A  31 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 34 through 36
    Processing sheet with id=AB7, first strand: chain 'A' and resid 46 through 49
      removed outlier: 7.938A  pdb=" N   LEU A  46 " --> pdb=" O   CYS A 278 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   THR A 280 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   LYS A  48 " --> pdb=" O   THR A 280 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7
    Processing sheet with id=AB8, first strand: chain 'A' and resid 55 through 56
      removed outlier: 6.556A  pdb=" N   LEU A  55 " --> pdb=" O   MET A  85 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ILE A  84 " --> pdb=" O   MET A 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'A' and resid 98 through 100
      removed outlier: 6.606A  pdb=" N   SER A  99 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   TRP A 234 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 256 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   TYR A 256 " --> pdb=" O   ILE A 179 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   HIS A 115 " --> pdb=" O   SER A 261 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ARG A 263 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   VAL A 113 " --> pdb=" O   ARG A 263 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 98 through 100
      removed outlier: 6.606A  pdb=" N   SER A  99 " --> pdb=" O   PHE A 232 " (cutoff:3.500A)
      removed outlier: 8.748A  pdb=" N   TRP A 234 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
      removed outlier: 8.067A  pdb=" N   ILE A 179 " --> pdb=" O   PRO A 254 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 136 through 141
      removed outlier: 7.504A  pdb=" N   ALA A 138 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
      removed outlier: 10.091A  pdb=" N   ASN A 144 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'A' and resid 164 through 169
    Processing sheet with id=AC4, first strand: chain 'A' and resid 288 through 289
      removed outlier: 4.189A  pdb=" N   CYS A 282 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'A' and resid 460 through 462
    Processing sheet with id=AC6, first strand: chain 'B' and resid 363 through 366
    Processing sheet with id=AC7, first strand: chain 'B' and resid 19 through 21
      removed outlier: 4.296A  pdb=" N   GLU B  19 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'B' and resid 34 through 36
    Processing sheet with id=AC9, first strand: chain 'B' and resid 38 through 39
    Processing sheet with id=AD1, first strand: chain 'B' and resid 48 through 49
      removed outlier: 6.091A  pdb=" N   LYS B  48 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD1
    Processing sheet with id=AD2, first strand: chain 'B' and resid 55 through 56
      removed outlier: 6.763A  pdb=" N   LEU B  55 " --> pdb=" O   MET B  85 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   ILE B  84 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD2
    Processing sheet with id=AD3, first strand: chain 'B' and resid 98 through 100
      removed outlier: 5.364A  pdb=" N   ILE B 179 " --> pdb=" O   TYR B 256 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   TYR B 256 " --> pdb=" O   ILE B 179 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'B' and resid 98 through 100
      removed outlier: 7.877A  pdb=" N   ILE B 179 " --> pdb=" O   PRO B 254 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'B' and resid 136 through 141
      removed outlier: 7.420A  pdb=" N   ALA B 138 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
      removed outlier: 9.909A  pdb=" N   ASN B 144 " --> pdb=" O   ALA B 138 " (cutoff:3.500A)
    Processing sheet with id=AD6, first strand: chain 'B' and resid 164 through 169

    480 hydrogen bonds defined for protein.
    1338 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.68

  Time building geometry restraints manager: 3.33 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: 3890
        1.34 -     1.47: 2929
        1.47 -     1.59: 5237
        1.59 -     1.72: 0
        1.72 -     1.84: 114
  Bond restraints: 12170
  Sorted by residual:
  bond pdb=" C1  NAG C 602 "
       pdb=" O5  NAG C 602 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.16e+00
  bond pdb=" C4  NAG E   2 "
       pdb=" O4  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.409  1.374  0.035 2.00e-02 2.50e+03 3.11e+00
  bond pdb=" C4  NAG F   2 "
       pdb=" O4  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.409  1.374  0.035 2.00e-02 2.50e+03 3.09e+00
  bond pdb=" C4  NAG D   2 "
       pdb=" O4  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.409  1.375  0.034 2.00e-02 2.50e+03 2.98e+00
  bond pdb=" C6  GAL F   3 "
       pdb=" O6  GAL F   3 "
    ideal  model  delta    sigma   weight residual
    1.407  1.374  0.033 2.00e-02 2.50e+03 2.76e+00
  ... (remaining 12165 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.75: 16456
        6.75 -    13.51: 5
       13.51 -    20.26: 5
       20.26 -    27.01: 4
       27.01 -    33.76: 1
  Bond angle restraints: 16471
  Sorted by residual:
  angle pdb=" C2  GAL F   1 "
        pdb=" C3  GAL F   1 "
        pdb=" O3  GAL F   1 "
      ideal   model   delta    sigma   weight residual
     107.49  141.25  -33.76 3.00e+00 1.11e-01 1.27e+02
  angle pdb=" C4  GAL F   1 "
        pdb=" C3  GAL F   1 "
        pdb=" O3  GAL F   1 "
      ideal   model   delta    sigma   weight residual
     113.26   86.62   26.64 3.00e+00 1.11e-01 7.89e+01
  angle pdb=" C3  NAG F   2 "
        pdb=" C4  NAG F   2 "
        pdb=" O4  NAG F   2 "
      ideal   model   delta    sigma   weight residual
     107.29  132.32  -25.03 3.00e+00 1.11e-01 6.96e+01
  angle pdb=" C4  GAL E   1 "
        pdb=" C3  GAL E   1 "
        pdb=" O3  GAL E   1 "
      ideal   model   delta    sigma   weight residual
     113.26   89.33   23.93 3.00e+00 1.11e-01 6.36e+01
  angle pdb=" C5  NAG D   2 "
        pdb=" C4  NAG D   2 "
        pdb=" O4  NAG D   2 "
      ideal   model   delta    sigma   weight residual
     111.70   89.93   21.77 3.00e+00 1.11e-01 5.27e+01
  ... (remaining 16466 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.55: 6541
       22.55 -    45.10: 831
       45.10 -    67.64: 176
       67.64 -    90.19: 37
       90.19 -   112.74: 5
  Dihedral angle restraints: 7590
    sinusoidal: 3387
      harmonic: 4203
  Sorted by residual:
  dihedral pdb=" CB  CYS C 282 "
           pdb=" SG  CYS C 282 "
           pdb=" SG  CYS C 306 "
           pdb=" CB  CYS C 306 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   36.17   56.83     1      1.00e+01 1.00e-02 4.35e+01
  dihedral pdb=" CB  CYS A   9 "
           pdb=" SG  CYS A   9 "
           pdb=" SG  CYS A 467 "
           pdb=" CB  CYS A 467 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.77   42.23     1      1.00e+01 1.00e-02 2.49e+01
  dihedral pdb=" CA  CYS C 467 "
           pdb=" C   CYS C 467 "
           pdb=" N   PHE C 468 "
           pdb=" CA  PHE C 468 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.02  -23.98     0      5.00e+00 4.00e-02 2.30e+01
  ... (remaining 7587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1817
       0.127 -    0.254: 11
       0.254 -    0.381: 0
       0.381 -    0.507: 0
       0.507 -    0.634: 2
  Chirality restraints: 1830
  Sorted by residual:
  chirality pdb=" C2  SIA E   4 "
            pdb=" O6  GAL E   3 "
            pdb=" C1  SIA E   4 "
            pdb=" O6  SIA E   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.67    0.17 2.00e-02 2.50e+03 7.42e+01
  chirality pdb=" C2  SIA F   4 "
            pdb=" O6  GAL F   3 "
            pdb=" C1  SIA F   4 "
            pdb=" O6  SIA F   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.66    0.16 2.00e-02 2.50e+03 6.43e+01
  chirality pdb=" C2  SIA D   4 "
            pdb=" O6  GAL D   3 "
            pdb=" C1  SIA D   4 "
            pdb=" O6  SIA D   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.64    0.14 2.00e-02 2.50e+03 4.97e+01
  ... (remaining 1827 not shown)

  Planarity restraints: 2118
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 306 "   -0.028 5.00e-02 4.00e+02   4.29e-02 2.95e+00
        pdb=" N   PRO B 307 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 307 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 307 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 306 "    0.028 5.00e-02 4.00e+02   4.20e-02 2.82e+00
        pdb=" N   PRO C 307 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO C 307 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 307 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 293 "    0.025 5.00e-02 4.00e+02   3.81e-02 2.32e+00
        pdb=" N   PRO A 294 "   -0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO A 294 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 294 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2115 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 704
        2.73 -     3.27: 10770
        3.27 -     3.81: 19032
        3.81 -     4.36: 23043
        4.36 -     4.90: 40315
  Nonbonded interactions: 93864
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 190 "
            pdb=" O9  SIA F   4 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OG1 THR B 284 "
            pdb=" O   GLY B 287 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O6  SIA F   4 "
            pdb=" O8  SIA F   4 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" N   GLU A 313 "
            pdb=" OE1 GLU A 313 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" O   THR A 486 "
            pdb=" OG1 THR A 486 "
     model   vdw
     2.273 3.040
  ... (remaining 93859 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 6 through 501 or resid 601 through 602))
  selection = (chain 'B' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ 
h 602))
  selection = (chain 'C' and (resid 6 through 327 or resid 336 through 501 or resid 601 throug \ 
h 602))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     28.180
  Find NCS groups from input model:        0.590
  Set up NCS constraints:                  0.040
  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:10.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12205  Z= 0.184
  Angle     :  0.882  33.763  16558  Z= 0.377
  Chirality :  0.048   0.634   1830
  Planarity :  0.004   0.043   2110
  Dihedral  : 19.715 112.738   4850
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 33.64 %
    Favored  : 61.56 %
  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: 1454
  helix:  2.40 (0.27), residues: 367
  sheet:  0.09 (0.35), residues: 252
  loop : -1.74 (0.19), residues: 835

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  81 
 HIS   0.012   0.001   HIS B 356 
 PHE   0.018   0.001   PHE A 339 
 TYR   0.012   0.001   TYR A 492 
 ARG   0.007   0.001   ARG B 126 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00702 (    8)
  link_NAG-ASN         : angle       2.70142 (   24)
  link_BETA1-4         : bond        0.03942 (    3)
  link_BETA1-4         : angle       8.39704 (    9)
  hydrogen bonds       : bond        0.18805 (  448)
  hydrogen bonds       : angle       6.95406 ( 1338)
  SS BOND              : bond        0.00405 (   18)
  SS BOND              : angle       1.17300 (   36)
  glycosidic custom    : bond        0.06057 (    3)
  glycosidic custom    : angle       5.33463 (    9)
  link_BETA1-3         : bond        0.04923 (    3)
  link_BETA1-3         : angle       9.34155 (    9)
  covalent geometry    : bond        0.00368 (12170)
  covalent geometry    : angle       0.81641 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 329
  time to evaluate  : 1.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  159 SER cc_start: 0.8569 (OUTLIER) cc_final: 0.8256 (t)
REVERT: C  458 ASP cc_start: 0.7202 (t0) cc_final: 0.6701 (t0)
REVERT: C  473 LYS cc_start: 0.8556 (tptt) cc_final: 0.8324 (tppp)
REVERT: A  142 SER cc_start: 0.8221 (p) cc_final: 0.7958 (t)
REVERT: B  295 PHE cc_start: 0.7899 (m-80) cc_final: 0.7677 (m-80)
  outliers start: 62
  outliers final: 53
  residues processed: 382
  average time/residue: 1.2051
  time to fit residues: 497.8299
Evaluate side-chains
  376 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 322
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 SER
Chi-restraints excluded: chain C residue   18 THR
Chi-restraints excluded: chain C residue   23 THR
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  144 ASN
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  262 LYS
Chi-restraints excluded: chain C residue  278 CYS
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  306 CYS
Chi-restraints excluded: chain C residue  336 ILE
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  384 SER
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  399 GLU
Chi-restraints excluded: chain C residue  460 VAL
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  111 SER
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  368 LYS
Chi-restraints excluded: chain A residue  486 THR
Chi-restraints excluded: chain A residue  497 LYS
Chi-restraints excluded: chain B residue   18 THR
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  111 SER
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  128 THR
Chi-restraints excluded: chain B residue  207 SER
Chi-restraints excluded: chain B residue  228 SER
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  390 ASN
Chi-restraints excluded: chain B residue  437 THR
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  494 GLU
Chi-restraints excluded: chain B residue  497 LYS
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:    6.9990
   chunk 60 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
C 480 ASN
A 210 ASN
A 224 ASN
A 472 HIS
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.124736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.110516 restraints weight = 16358.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.93
r_work: 0.3388 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3237 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.0723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12205  Z= 0.171
  Angle     :  0.587   8.363  16558  Z= 0.301
  Chirality :  0.043   0.219   1830
  Planarity :  0.004   0.043   2110
  Dihedral  : 10.238 106.563   2106
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 29.85 %
    Favored  : 64.19 %
  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: 1454
  helix:  2.37 (0.27), residues: 382
  sheet:  0.14 (0.32), residues: 280
  loop : -1.69 (0.20), residues: 792

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 127 
 HIS   0.011   0.002   HIS B 356 
 PHE   0.015   0.001   PHE C 440 
 TYR   0.013   0.002   TYR C 364 
 ARG   0.007   0.001   ARG B 126 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00814 (    8)
  link_NAG-ASN         : angle       2.67858 (   24)
  link_BETA1-4         : bond        0.00682 (    3)
  link_BETA1-4         : angle       2.41881 (    9)
  hydrogen bonds       : bond        0.06044 (  448)
  hydrogen bonds       : angle       5.13233 ( 1338)
  SS BOND              : bond        0.00441 (   18)
  SS BOND              : angle       1.24340 (   36)
  glycosidic custom    : bond        0.00412 (    3)
  glycosidic custom    : angle       1.79641 (    9)
  link_BETA1-3         : bond        0.00291 (    3)
  link_BETA1-3         : angle       1.62555 (    9)
  covalent geometry    : bond        0.00396 (12170)
  covalent geometry    : angle       0.57103 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  414 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 337
  time to evaluate  : 1.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  192 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8547 (mtt-85)
REVERT: C  458 ASP cc_start: 0.7573 (t0) cc_final: 0.7062 (t0)
REVERT: C  473 LYS cc_start: 0.8679 (tptt) cc_final: 0.8387 (tppp)
REVERT: C  497 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7743 (ttpt)
REVERT: A  142 SER cc_start: 0.8228 (p) cc_final: 0.7964 (t)
REVERT: A  488 ASP cc_start: 0.7841 (t0) cc_final: 0.7594 (t0)
REVERT: A  491 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8152 (ttpp)
REVERT: B  151 MET cc_start: 0.8857 (OUTLIER) cc_final: 0.8189 (mmt)
REVERT: B  451 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7998 (ttmm)
  outliers start: 77
  outliers final: 39
  residues processed: 378
  average time/residue: 1.3040
  time to fit residues: 531.9287
Evaluate side-chains
  370 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 328
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  187 ASP
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  306 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  460 VAL
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  136 SER
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  125 ASP
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  494 GLU
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0870
   chunk 78 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.9562

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

Flipped N/Q/H residues before XYZ refinement:
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  16 ASN
A  50 ASN
A 210 ASN
A 224 ASN
A 299 HIS
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.125029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.110917 restraints weight = 16600.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 1.93
r_work: 0.3386 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3234 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.0893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12205  Z= 0.173
  Angle     :  0.564   7.874  16558  Z= 0.294
  Chirality :  0.043   0.201   1830
  Planarity :  0.004   0.043   2110
  Dihedral  :  8.933 106.917   2050
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 29.85 %
    Favored  : 64.50 %
  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: -0.28 (0.22), residues: 1454
  helix:  2.46 (0.27), residues: 380
  sheet:  0.01 (0.33), residues: 276
  loop : -1.68 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  65 
 HIS   0.010   0.002   HIS A 472 
 PHE   0.022   0.002   PHE B 295 
 TYR   0.013   0.001   TYR C 424 
 ARG   0.004   0.000   ARG C  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00730 (    8)
  link_NAG-ASN         : angle       2.65039 (   24)
  link_BETA1-4         : bond        0.00076 (    3)
  link_BETA1-4         : angle       2.42445 (    9)
  hydrogen bonds       : bond        0.05828 (  448)
  hydrogen bonds       : angle       4.86849 ( 1338)
  SS BOND              : bond        0.00466 (   18)
  SS BOND              : angle       1.36067 (   36)
  glycosidic custom    : bond        0.00469 (    3)
  glycosidic custom    : angle       1.12894 (    9)
  link_BETA1-3         : bond        0.00194 (    3)
  link_BETA1-3         : angle       1.28770 (    9)
  covalent geometry    : bond        0.00404 (12170)
  covalent geometry    : angle       0.54881 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 330
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  192 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8559 (mtt-85)
REVERT: C  306 CYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7267 (m)
REVERT: C  387 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7466 (pp20)
REVERT: C  436 ARG cc_start: 0.7737 (mpp80) cc_final: 0.7484 (mpp80)
REVERT: C  458 ASP cc_start: 0.7549 (t0) cc_final: 0.7040 (t0)
REVERT: C  497 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7754 (ttpt)
REVERT: A  137 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.8065 (mmt)
REVERT: A  142 SER cc_start: 0.8222 (p) cc_final: 0.7955 (t)
REVERT: A  458 ASP cc_start: 0.8084 (t0) cc_final: 0.7625 (t0)
REVERT: A  488 ASP cc_start: 0.7839 (t0) cc_final: 0.7582 (t0)
REVERT: A  491 LYS cc_start: 0.8462 (ttpp) cc_final: 0.7989 (ttpp)
REVERT: B  151 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8172 (mmt)
REVERT: B  362 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7722 (t)
REVERT: B  451 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8005 (ttmm)
REVERT: B  457 ARG cc_start: 0.7249 (mtm180) cc_final: 0.7033 (mtm180)
REVERT: B  491 LYS cc_start: 0.8460 (tttm) cc_final: 0.8076 (tttm)
  outliers start: 73
  outliers final: 38
  residues processed: 369
  average time/residue: 1.3238
  time to fit residues: 526.2693
Evaluate side-chains
  382 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 337
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  306 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  137 MET
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  292 THR
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 100 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 140 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    0.0470
   chunk 1 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 124 optimal weight:    0.6980
   overall best weight:    0.5878

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

Flipped N/Q/H residues before XYZ refinement:
C  43 ASN
** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  16 ASN
A  50 ASN
A 210 ASN
A 224 ASN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.126046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.112023 restraints weight = 16509.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.92
r_work: 0.3400 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.0960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12205  Z= 0.126
  Angle     :  0.537   9.855  16558  Z= 0.278
  Chirality :  0.042   0.205   1830
  Planarity :  0.004   0.042   2110
  Dihedral  :  8.328 109.191   2040
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 30.09 %
    Favored  : 64.58 %
  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: -0.17 (0.22), residues: 1454
  helix:  2.54 (0.27), residues: 380
  sheet:  0.13 (0.33), residues: 275
  loop : -1.64 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 422 
 HIS   0.010   0.001   HIS B 356 
 PHE   0.012   0.001   PHE C 440 
 TYR   0.011   0.001   TYR B 354 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00730 (    8)
  link_NAG-ASN         : angle       2.56670 (   24)
  link_BETA1-4         : bond        0.00080 (    3)
  link_BETA1-4         : angle       2.01933 (    9)
  hydrogen bonds       : bond        0.05342 (  448)
  hydrogen bonds       : angle       4.69774 ( 1338)
  SS BOND              : bond        0.00464 (   18)
  SS BOND              : angle       1.15268 (   36)
  glycosidic custom    : bond        0.00174 (    3)
  glycosidic custom    : angle       0.87537 (    9)
  link_BETA1-3         : bond        0.00230 (    3)
  link_BETA1-3         : angle       0.86906 (    9)
  covalent geometry    : bond        0.00283 (12170)
  covalent geometry    : angle       0.52373 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  391 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 322
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8450 (mttp)
REVERT: C  192 ARG cc_start: 0.8755 (ttm-80) cc_final: 0.8539 (mtt-85)
REVERT: C  306 CYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7406 (m)
REVERT: C  387 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7457 (pp20)
REVERT: C  432 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7155 (mpp)
REVERT: C  436 ARG cc_start: 0.7759 (OUTLIER) cc_final: 0.7442 (mpp80)
REVERT: C  458 ASP cc_start: 0.7480 (t0) cc_final: 0.6971 (t0)
REVERT: C  497 LYS cc_start: 0.7973 (OUTLIER) cc_final: 0.7716 (ttpt)
REVERT: A  137 MET cc_start: 0.8563 (mmm) cc_final: 0.8113 (mmt)
REVERT: A  142 SER cc_start: 0.8215 (p) cc_final: 0.7945 (t)
REVERT: A  458 ASP cc_start: 0.8179 (t0) cc_final: 0.7726 (t0)
REVERT: A  488 ASP cc_start: 0.7814 (t0) cc_final: 0.7577 (t0)
REVERT: A  491 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8241 (tmmm)
REVERT: B   27 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6383 (mpt90)
REVERT: B  187 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7531 (p0)
REVERT: B  362 SER cc_start: 0.8016 (OUTLIER) cc_final: 0.7704 (t)
REVERT: B  451 LYS cc_start: 0.8427 (OUTLIER) cc_final: 0.8006 (ttmm)
REVERT: B  457 ARG cc_start: 0.7204 (mtm180) cc_final: 0.6969 (mtm180)
REVERT: B  491 LYS cc_start: 0.8484 (tttm) cc_final: 0.8253 (tttm)
  outliers start: 69
  outliers final: 34
  residues processed: 364
  average time/residue: 1.2997
  time to fit residues: 508.7873
Evaluate side-chains
  363 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 319
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  146 SER
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  306 CYS
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  460 VAL
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 142 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 32 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 127 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 106 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 ASN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 480 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.124852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.110720 restraints weight = 16447.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3491 rms_B_bonded: 1.93
r_work: 0.3379 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3230 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12205  Z= 0.186
  Angle     :  0.576   8.547  16558  Z= 0.299
  Chirality :  0.044   0.195   1830
  Planarity :  0.004   0.042   2110
  Dihedral  :  8.094 108.824   2031
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 30.55 %
    Favored  : 63.81 %
  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: -0.24 (0.22), residues: 1454
  helix:  2.44 (0.26), residues: 380
  sheet:  0.11 (0.33), residues: 275
  loop : -1.67 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  65 
 HIS   0.010   0.002   HIS B 356 
 PHE   0.023   0.002   PHE B 295 
 TYR   0.013   0.002   TYR C 424 
 ARG   0.003   0.000   ARG A  91 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00697 (    8)
  link_NAG-ASN         : angle       2.61839 (   24)
  link_BETA1-4         : bond        0.00093 (    3)
  link_BETA1-4         : angle       2.07674 (    9)
  hydrogen bonds       : bond        0.05705 (  448)
  hydrogen bonds       : angle       4.69137 ( 1338)
  SS BOND              : bond        0.00531 (   18)
  SS BOND              : angle       1.38353 (   36)
  glycosidic custom    : bond        0.00394 (    3)
  glycosidic custom    : angle       0.95001 (    9)
  link_BETA1-3         : bond        0.00172 (    3)
  link_BETA1-3         : angle       0.83258 (    9)
  covalent geometry    : bond        0.00438 (12170)
  covalent geometry    : angle       0.56273 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  393 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 320
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8474 (mttp)
REVERT: C  387 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7508 (pp20)
REVERT: C  432 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7165 (mpp)
REVERT: C  436 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7440 (mpp80)
REVERT: C  458 ASP cc_start: 0.7501 (t0) cc_final: 0.7007 (t0)
REVERT: C  497 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7721 (ttpt)
REVERT: A  137 MET cc_start: 0.8563 (mmm) cc_final: 0.8196 (mmt)
REVERT: A  142 SER cc_start: 0.8242 (p) cc_final: 0.7974 (t)
REVERT: A  458 ASP cc_start: 0.8122 (t0) cc_final: 0.7669 (t0)
REVERT: A  488 ASP cc_start: 0.7833 (t0) cc_final: 0.7595 (t0)
REVERT: A  491 LYS cc_start: 0.8475 (ttpp) cc_final: 0.8090 (ttpp)
REVERT: B  151 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8165 (mmt)
REVERT: B  187 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7506 (p0)
REVERT: B  311 LYS cc_start: 0.7293 (tmmt) cc_final: 0.7081 (tmmt)
REVERT: B  362 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7721 (t)
REVERT: B  451 LYS cc_start: 0.8435 (OUTLIER) cc_final: 0.8017 (ttmm)
REVERT: B  491 LYS cc_start: 0.8510 (tttm) cc_final: 0.8113 (tttm)
  outliers start: 73
  outliers final: 44
  residues processed: 360
  average time/residue: 1.2967
  time to fit residues: 502.1138
Evaluate side-chains
  370 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 317
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  402 ASN
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  460 VAL
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain A residue   10 ILE
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  362 SER
Chi-restraints excluded: chain B residue  388 LYS
Chi-restraints excluded: chain B residue  389 MET
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 96 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0040
   chunk 74 optimal weight:    2.9990
   chunk 103 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 126 optimal weight:    0.9980
   chunk 24 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A  16 ASN
A 224 ASN
** A 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.125831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.111678 restraints weight = 16543.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 1.93
r_work: 0.3393 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3242 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12205  Z= 0.136
  Angle     :  0.540   8.752  16558  Z= 0.282
  Chirality :  0.042   0.201   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.860 110.435   2029
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 31.40 %
    Favored  : 64.04 %
  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: -0.14 (0.22), residues: 1454
  helix:  2.55 (0.27), residues: 380
  sheet:  0.19 (0.33), residues: 273
  loop : -1.61 (0.20), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 422 
 HIS   0.010   0.001   HIS B 296 
 PHE   0.013   0.001   PHE C 440 
 TYR   0.013   0.001   TYR B 354 
 ARG   0.004   0.000   ARG B  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00699 (    8)
  link_NAG-ASN         : angle       2.53083 (   24)
  link_BETA1-4         : bond        0.00054 (    3)
  link_BETA1-4         : angle       1.87362 (    9)
  hydrogen bonds       : bond        0.05335 (  448)
  hydrogen bonds       : angle       4.59232 ( 1338)
  SS BOND              : bond        0.00431 (   18)
  SS BOND              : angle       1.10520 (   36)
  glycosidic custom    : bond        0.00189 (    3)
  glycosidic custom    : angle       0.80795 (    9)
  link_BETA1-3         : bond        0.00212 (    3)
  link_BETA1-3         : angle       0.69600 (    9)
  covalent geometry    : bond        0.00312 (12170)
  covalent geometry    : angle       0.52825 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  384 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 325
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8442 (mttp)
REVERT: C  280 THR cc_start: 0.8570 (p) cc_final: 0.8338 (t)
REVERT: C  432 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7185 (mpp)
REVERT: C  436 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7442 (mpp80)
REVERT: C  458 ASP cc_start: 0.7466 (t0) cc_final: 0.6981 (t0)
REVERT: C  497 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7702 (ttpt)
REVERT: A   26 GLU cc_start: 0.7427 (tp30) cc_final: 0.7213 (tp30)
REVERT: A  137 MET cc_start: 0.8550 (mmm) cc_final: 0.8237 (mmt)
REVERT: A  142 SER cc_start: 0.8222 (p) cc_final: 0.7951 (t)
REVERT: A  458 ASP cc_start: 0.8176 (t0) cc_final: 0.7740 (t0)
REVERT: A  488 ASP cc_start: 0.7845 (t0) cc_final: 0.7606 (t0)
REVERT: A  491 LYS cc_start: 0.8487 (ttpp) cc_final: 0.8269 (ttpp)
REVERT: B   27 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6394 (mpt90)
REVERT: B  151 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8114 (mmt)
REVERT: B  187 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7446 (p0)
REVERT: B  311 LYS cc_start: 0.7263 (tmmt) cc_final: 0.7019 (tmmt)
REVERT: B  451 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8008 (ttmm)
  outliers start: 59
  outliers final: 36
  residues processed: 355
  average time/residue: 1.3144
  time to fit residues: 501.7335
Evaluate side-chains
  365 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 321
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  396 VAL
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  110 LEU
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  388 LYS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 71 optimal weight:    0.6980
   chunk 121 optimal weight:    2.9990
   chunk 69 optimal weight:    0.0870
   chunk 119 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 106 optimal weight:    0.8980
   chunk 135 optimal weight:    0.4980
   chunk 58 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 224 ASN
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 ASN
B 480 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.126146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.112031 restraints weight = 16637.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3508 rms_B_bonded: 1.93
r_work: 0.3398 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12205  Z= 0.125
  Angle     :  0.534   6.966  16558  Z= 0.278
  Chirality :  0.042   0.206   1830
  Planarity :  0.004   0.038   2110
  Dihedral  :  7.671 111.415   2029
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 32.48 %
    Favored  : 63.11 %
  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: -0.07 (0.22), residues: 1454
  helix:  2.66 (0.27), residues: 378
  sheet:  0.22 (0.33), residues: 273
  loop : -1.58 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 422 
 HIS   0.010   0.001   HIS B 296 
 PHE   0.024   0.001   PHE B 295 
 TYR   0.029   0.001   TYR C 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00686 (    8)
  link_NAG-ASN         : angle       2.49101 (   24)
  link_BETA1-4         : bond        0.00077 (    3)
  link_BETA1-4         : angle       1.78468 (    9)
  hydrogen bonds       : bond        0.05161 (  448)
  hydrogen bonds       : angle       4.52551 ( 1338)
  SS BOND              : bond        0.00460 (   18)
  SS BOND              : angle       1.08967 (   36)
  glycosidic custom    : bond        0.00118 (    3)
  glycosidic custom    : angle       0.75443 (    9)
  link_BETA1-3         : bond        0.00220 (    3)
  link_BETA1-3         : angle       0.65632 (    9)
  covalent geometry    : bond        0.00283 (12170)
  covalent geometry    : angle       0.52210 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 318
  time to evaluate  : 1.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8427 (mttp)
REVERT: C  159 SER cc_start: 0.8549 (OUTLIER) cc_final: 0.8232 (t)
REVERT: C  387 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7486 (pp20)
REVERT: C  432 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7192 (mpp)
REVERT: C  436 ARG cc_start: 0.7812 (OUTLIER) cc_final: 0.7443 (mpp80)
REVERT: C  457 ARG cc_start: 0.7269 (mtm180) cc_final: 0.7063 (mtm180)
REVERT: C  458 ASP cc_start: 0.7491 (t0) cc_final: 0.7030 (t0)
REVERT: C  497 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7708 (ttpt)
REVERT: A   26 GLU cc_start: 0.7469 (tp30) cc_final: 0.7268 (tp30)
REVERT: A  137 MET cc_start: 0.8538 (mmm) cc_final: 0.8239 (mmt)
REVERT: A  142 SER cc_start: 0.8229 (p) cc_final: 0.7956 (t)
REVERT: A  389 MET cc_start: 0.7693 (OUTLIER) cc_final: 0.7365 (mmt)
REVERT: A  458 ASP cc_start: 0.8160 (t0) cc_final: 0.7737 (t0)
REVERT: A  488 ASP cc_start: 0.7828 (t0) cc_final: 0.7572 (t0)
REVERT: A  491 LYS cc_start: 0.8575 (ttpp) cc_final: 0.8256 (ttpp)
REVERT: B   27 ARG cc_start: 0.6796 (OUTLIER) cc_final: 0.6390 (mpt90)
REVERT: B  151 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8122 (mmt)
REVERT: B  187 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7483 (p0)
REVERT: B  311 LYS cc_start: 0.7239 (tmmt) cc_final: 0.7014 (tmmt)
REVERT: B  451 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8010 (ttmm)
REVERT: B  491 LYS cc_start: 0.8443 (tttm) cc_final: 0.8099 (tttm)
  outliers start: 57
  outliers final: 35
  residues processed: 350
  average time/residue: 1.2765
  time to fit residues: 481.6871
Evaluate side-chains
  359 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 313
  time to evaluate  : 1.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   24 ILE
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  497 LYS
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  388 LYS
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 101 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    0.4980
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 484 ASN
A  16 ASN
A 224 ASN
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.125109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.110567 restraints weight = 16530.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.3486 rms_B_bonded: 1.99
r_work: 0.3376 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12205  Z= 0.179
  Angle     :  0.571   8.171  16558  Z= 0.300
  Chirality :  0.043   0.195   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.570 111.161   2026
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 32.79 %
    Favored  : 62.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.16 (0.22), residues: 1454
  helix:  2.56 (0.26), residues: 378
  sheet:  0.16 (0.33), residues: 273
  loop : -1.63 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  65 
 HIS   0.009   0.001   HIS B 356 
 PHE   0.022   0.002   PHE A 339 
 TYR   0.022   0.002   TYR C 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00682 (    8)
  link_NAG-ASN         : angle       2.56713 (   24)
  link_BETA1-4         : bond        0.00054 (    3)
  link_BETA1-4         : angle       1.88673 (    9)
  hydrogen bonds       : bond        0.05585 (  448)
  hydrogen bonds       : angle       4.58097 ( 1338)
  SS BOND              : bond        0.00477 (   18)
  SS BOND              : angle       1.19087 (   36)
  glycosidic custom    : bond        0.00322 (    3)
  glycosidic custom    : angle       0.90883 (    9)
  link_BETA1-3         : bond        0.00190 (    3)
  link_BETA1-3         : angle       0.71990 (    9)
  covalent geometry    : bond        0.00424 (12170)
  covalent geometry    : angle       0.55893 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  383 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 326
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  159 SER cc_start: 0.8570 (OUTLIER) cc_final: 0.8240 (t)
REVERT: C  276 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7174 (mp0)
REVERT: C  387 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7532 (pp20)
REVERT: C  432 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7175 (mpp)
REVERT: C  436 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7463 (mpp80)
REVERT: C  458 ASP cc_start: 0.7517 (t0) cc_final: 0.7069 (t0)
REVERT: A   26 GLU cc_start: 0.7644 (tp30) cc_final: 0.7388 (tp30)
REVERT: A  137 MET cc_start: 0.8561 (mmm) cc_final: 0.8265 (mmt)
REVERT: A  142 SER cc_start: 0.8238 (p) cc_final: 0.7965 (t)
REVERT: A  389 MET cc_start: 0.7718 (OUTLIER) cc_final: 0.7395 (mmt)
REVERT: A  458 ASP cc_start: 0.8161 (t0) cc_final: 0.7776 (t0)
REVERT: A  488 ASP cc_start: 0.7840 (t0) cc_final: 0.7590 (t0)
REVERT: A  491 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8247 (ttpp)
REVERT: B   27 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6476 (mpt90)
REVERT: B  151 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8171 (mmt)
REVERT: B  187 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7510 (p0)
REVERT: B  311 LYS cc_start: 0.7292 (tmmt) cc_final: 0.7033 (tmmt)
REVERT: B  387 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7818 (mm-30)
REVERT: B  451 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8009 (ttmm)
REVERT: B  479 MET cc_start: 0.7484 (mmt) cc_final: 0.7045 (mmt)
REVERT: B  491 LYS cc_start: 0.8436 (tttm) cc_final: 0.8103 (tttm)
  outliers start: 57
  outliers final: 34
  residues processed: 355
  average time/residue: 1.2926
  time to fit residues: 493.5894
Evaluate side-chains
  365 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 321
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  461 LYS
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  403 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 138 optimal weight:    0.8980
   chunk 112 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 356 HIS
** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  50 ASN
A 224 ASN
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 480 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.125567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.111056 restraints weight = 16487.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.98
r_work: 0.3382 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.1299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12205  Z= 0.165
  Angle     :  0.569   8.083  16558  Z= 0.298
  Chirality :  0.043   0.197   1830
  Planarity :  0.004   0.038   2110
  Dihedral  :  7.481 111.860   2026
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 33.18 %
    Favored  : 62.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.15 (0.22), residues: 1454
  helix:  2.55 (0.27), residues: 380
  sheet:  0.17 (0.33), residues: 273
  loop : -1.62 (0.20), residues: 801

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  65 
 HIS   0.011   0.001   HIS C 356 
 PHE   0.032   0.002   PHE B 339 
 TYR   0.012   0.001   TYR C 424 
 ARG   0.005   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00696 (    8)
  link_NAG-ASN         : angle       2.52765 (   24)
  link_BETA1-4         : bond        0.00034 (    3)
  link_BETA1-4         : angle       1.85491 (    9)
  hydrogen bonds       : bond        0.05508 (  448)
  hydrogen bonds       : angle       4.59462 ( 1338)
  SS BOND              : bond        0.00453 (   18)
  SS BOND              : angle       1.09603 (   36)
  glycosidic custom    : bond        0.00308 (    3)
  glycosidic custom    : angle       0.89085 (    9)
  link_BETA1-3         : bond        0.00203 (    3)
  link_BETA1-3         : angle       0.69530 (    9)
  covalent geometry    : bond        0.00389 (12170)
  covalent geometry    : angle       0.55729 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  379 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 323
  time to evaluate  : 1.453 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8443 (mttp)
REVERT: C  159 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8235 (t)
REVERT: C  276 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7178 (mp0)
REVERT: C  280 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8369 (t)
REVERT: C  387 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7546 (pp20)
REVERT: C  432 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7195 (mpp)
REVERT: C  436 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.7473 (mpp80)
REVERT: C  458 ASP cc_start: 0.7570 (t0) cc_final: 0.7111 (t0)
REVERT: C  476 ASP cc_start: 0.6901 (m-30) cc_final: 0.6659 (m-30)
REVERT: A   26 GLU cc_start: 0.7665 (tp30) cc_final: 0.7430 (tp30)
REVERT: A  137 MET cc_start: 0.8576 (mmm) cc_final: 0.8212 (mmt)
REVERT: A  142 SER cc_start: 0.8235 (p) cc_final: 0.7965 (t)
REVERT: A  389 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7359 (mmt)
REVERT: A  458 ASP cc_start: 0.8172 (t0) cc_final: 0.7785 (t0)
REVERT: A  491 LYS cc_start: 0.8606 (ttpp) cc_final: 0.8331 (ttpp)
REVERT: B   27 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6492 (mpt90)
REVERT: B  151 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8100 (mmt)
REVERT: B  187 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7490 (p0)
REVERT: B  311 LYS cc_start: 0.7317 (tmmt) cc_final: 0.7093 (tmmt)
REVERT: B  403 LEU cc_start: 0.8594 (mp) cc_final: 0.8394 (mm)
REVERT: B  451 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8013 (ttmm)
REVERT: B  479 MET cc_start: 0.7465 (mmt) cc_final: 0.7054 (mmt)
REVERT: B  491 LYS cc_start: 0.8452 (tttm) cc_final: 0.8112 (tttm)
  outliers start: 56
  outliers final: 37
  residues processed: 350
  average time/residue: 1.3169
  time to fit residues: 495.5839
Evaluate side-chains
  362 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 313
  time to evaluate  : 1.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  461 LYS
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  262 LYS
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 120 optimal weight:    0.9980
   chunk 142 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 86 optimal weight:    2.9990
   chunk 137 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 356 HIS
** C 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  50 ASN
A 224 ASN
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.125313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.110814 restraints weight = 16380.010|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 1.98
r_work: 0.3384 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.1305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  12205  Z= 0.153
  Angle     :  0.568   7.958  16558  Z= 0.297
  Chirality :  0.043   0.199   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.365 112.546   2026
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 33.49 %
    Favored  : 62.10 %
  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: -0.10 (0.22), residues: 1454
  helix:  2.65 (0.26), residues: 378
  sheet:  0.21 (0.33), residues: 273
  loop : -1.62 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  65 
 HIS   0.011   0.001   HIS C 356 
 PHE   0.020   0.001   PHE A 339 
 TYR   0.012   0.001   TYR C 424 
 ARG   0.004   0.000   ARG B 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00692 (    8)
  link_NAG-ASN         : angle       2.50525 (   24)
  link_BETA1-4         : bond        0.00030 (    3)
  link_BETA1-4         : angle       1.81916 (    9)
  hydrogen bonds       : bond        0.05412 (  448)
  hydrogen bonds       : angle       4.56340 ( 1338)
  SS BOND              : bond        0.00439 (   18)
  SS BOND              : angle       1.13231 (   36)
  glycosidic custom    : bond        0.00250 (    3)
  glycosidic custom    : angle       0.85588 (    9)
  link_BETA1-3         : bond        0.00189 (    3)
  link_BETA1-3         : angle       0.67058 (    9)
  covalent geometry    : bond        0.00356 (12170)
  covalent geometry    : angle       0.55694 (16471)

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

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

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2908 Ramachandran restraints generated.
    1454 Oldfield, 0 Emsley, 1454 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  369 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 312
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   40 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8446 (mttp)
REVERT: C  159 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8233 (t)
REVERT: C  280 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8341 (t)
REVERT: C  387 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7555 (pp20)
REVERT: C  432 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7192 (mpp)
REVERT: C  436 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7461 (mpp80)
REVERT: C  452 VAL cc_start: 0.8436 (t) cc_final: 0.8206 (p)
REVERT: C  458 ASP cc_start: 0.7556 (t0) cc_final: 0.7109 (t0)
REVERT: C  476 ASP cc_start: 0.6920 (m-30) cc_final: 0.6647 (m-30)
REVERT: A   26 GLU cc_start: 0.7647 (tp30) cc_final: 0.7413 (tp30)
REVERT: A  137 MET cc_start: 0.8584 (mmm) cc_final: 0.8239 (mmt)
REVERT: A  142 SER cc_start: 0.8234 (p) cc_final: 0.7960 (t)
REVERT: A  389 MET cc_start: 0.7712 (OUTLIER) cc_final: 0.7360 (mmt)
REVERT: A  458 ASP cc_start: 0.8199 (t0) cc_final: 0.7805 (t0)
REVERT: A  491 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8325 (ttpp)
REVERT: B   27 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6477 (mpt90)
REVERT: B  151 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8093 (mmt)
REVERT: B  187 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7462 (p0)
REVERT: B  311 LYS cc_start: 0.7263 (tmmt) cc_final: 0.7040 (tmmt)
REVERT: B  387 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7841 (mm-30)
REVERT: B  451 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8017 (ttmm)
REVERT: B  491 LYS cc_start: 0.8446 (tttm) cc_final: 0.8101 (tttm)
REVERT: B  497 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8061 (tmtm)
  outliers start: 57
  outliers final: 37
  residues processed: 340
  average time/residue: 1.3167
  time to fit residues: 480.5157
Evaluate side-chains
  358 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 309
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  125 ASP
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  159 SER
Chi-restraints excluded: chain C residue  176 MET
Chi-restraints excluded: chain C residue  197 ASN
Chi-restraints excluded: chain C residue  230 MET
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  284 THR
Chi-restraints excluded: chain C residue  321 LEU
Chi-restraints excluded: chain C residue  348 VAL
Chi-restraints excluded: chain C residue  387 GLU
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  432 MET
Chi-restraints excluded: chain C residue  436 ARG
Chi-restraints excluded: chain C residue  478 CYS
Chi-restraints excluded: chain C residue  494 GLU
Chi-restraints excluded: chain A residue   40 LYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
Chi-restraints excluded: chain A residue  213 SER
Chi-restraints excluded: chain A residue  274 THR
Chi-restraints excluded: chain A residue  278 CYS
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  292 THR
Chi-restraints excluded: chain A residue  310 VAL
Chi-restraints excluded: chain A residue  324 VAL
Chi-restraints excluded: chain A residue  388 LYS
Chi-restraints excluded: chain A residue  389 MET
Chi-restraints excluded: chain A residue  419 LEU
Chi-restraints excluded: chain A residue  461 LYS
Chi-restraints excluded: chain B residue   20 THR
Chi-restraints excluded: chain B residue   27 ARG
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  116 PHE
Chi-restraints excluded: chain B residue  139 CYS
Chi-restraints excluded: chain B residue  151 MET
Chi-restraints excluded: chain B residue  187 ASP
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  262 LYS
Chi-restraints excluded: chain B residue  321 LEU
Chi-restraints excluded: chain B residue  428 LEU
Chi-restraints excluded: chain B residue  429 LEU
Chi-restraints excluded: chain B residue  451 LYS
Chi-restraints excluded: chain B residue  456 LEU
Chi-restraints excluded: chain B residue  481 SER
Chi-restraints excluded: chain B residue  497 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 84 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 136 optimal weight:    0.9990
   chunk 5 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** C 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 356 HIS
A  16 ASN
A  50 ASN
A 224 ASN
B 283 GLN
B 296 HIS
** B 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 480 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.125652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.111249 restraints weight = 16489.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 1.98
r_work: 0.3385 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12205  Z= 0.158
  Angle     :  0.574   7.881  16558  Z= 0.300
  Chirality :  0.043   0.199   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.336 112.864   2026
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 33.64 %
    Favored  : 61.95 %
  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: -0.12 (0.22), residues: 1454
  helix:  2.62 (0.26), residues: 378
  sheet:  0.20 (0.33), residues: 273
  loop : -1.63 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  65 
 HIS   0.012   0.001   HIS C 356 
 PHE   0.022   0.002   PHE B 295 
 TYR   0.029   0.001   TYR C 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00689 (    8)
  link_NAG-ASN         : angle       2.51384 (   24)
  link_BETA1-4         : bond        0.00028 (    3)
  link_BETA1-4         : angle       1.82458 (    9)
  hydrogen bonds       : bond        0.05438 (  448)
  hydrogen bonds       : angle       4.56068 ( 1338)
  SS BOND              : bond        0.00442 (   18)
  SS BOND              : angle       1.13883 (   36)
  glycosidic custom    : bond        0.00245 (    3)
  glycosidic custom    : angle       0.88902 (    9)
  link_BETA1-3         : bond        0.00197 (    3)
  link_BETA1-3         : angle       0.67998 (    9)
  covalent geometry    : bond        0.00370 (12170)
  covalent geometry    : angle       0.56245 (16471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10705.69 seconds
wall clock time: 184 minutes 38.56 seconds (11078.56 seconds total)