Starting phenix.real_space_refine
on Wed Jul 30 02:39:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xhe_38348/07_2025/8xhe_38348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xhe_38348/07_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_38348/07_2025/8xhe_38348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xhe_38348/07_2025/8xhe_38348.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xhe_38348/07_2025/8xhe_38348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xhe_38348/07_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-5711/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: 7.36, per 1000 atoms: 0.62
  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 1.4 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: 1.57
  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: 4.08

  Time building geometry restraints manager: 3.38 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:             2.130
  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:          0.430
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     29.360
  Find NCS groups from input model:        0.680
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   46.350
-------------------------------------------------------------------------------
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  : 1.401 
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: 1.2828
  time to fit residues: 528.8021
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  : 1.390 
-------------------------------------------------------------------------------
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 = 0.110515 restraints weight = 16358.317|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.93
r_work: 0.3388 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
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       1.79642 (    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  : 1.435 
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: 0.8771 (ttm-80) cc_final: 0.8552 (mtt-85)
REVERT: C  458 ASP cc_start: 0.7576 (t0) cc_final: 0.7068 (t0)
REVERT: C  473 LYS cc_start: 0.8682 (tptt) cc_final: 0.8393 (tppp)
REVERT: C  497 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7743 (ttpt)
REVERT: A  142 SER cc_start: 0.8233 (p) cc_final: 0.7968 (t)
REVERT: A  488 ASP cc_start: 0.7832 (t0) cc_final: 0.7590 (t0)
REVERT: A  491 LYS cc_start: 0.8435 (ttpp) cc_final: 0.8157 (ttpp)
REVERT: B  151 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8189 (mmt)
REVERT: B  451 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7997 (ttmm)
  outliers start: 77
  outliers final: 39
  residues processed: 378
  average time/residue: 1.5183
  time to fit residues: 617.2844
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  : 1.300 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 78 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0470
   chunk 79 optimal weight:    2.9990
   chunk 112 optimal weight:    0.8980
   overall best weight:    0.9082

-------------------------------------------------------------------------------
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 = 0.3703 r_free = 0.3703 target = 0.125199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.111077 restraints weight = 16600.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.94
r_work: 0.3387 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3236 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.0894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12205  Z= 0.166
  Angle     :  0.560   7.806  16558  Z= 0.291
  Chirality :  0.043   0.201   1830
  Planarity :  0.004   0.042   2110
  Dihedral  :  8.910 106.895   2050
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  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: -0.26 (0.22), residues: 1454
  helix:  2.47 (0.27), residues: 380
  sheet:  0.02 (0.33), residues: 276
  loop : -1.68 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  65 
 HIS   0.009   0.001   HIS A 472 
 PHE   0.022   0.001   PHE B 295 
 TYR   0.013   0.001   TYR C 424 
 ARG   0.004   0.000   ARG B  74 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00730 (    8)
  link_NAG-ASN         : angle       2.64148 (   24)
  link_BETA1-4         : bond        0.00087 (    3)
  link_BETA1-4         : angle       2.39880 (    9)
  hydrogen bonds       : bond        0.05776 (  448)
  hydrogen bonds       : angle       4.85363 ( 1338)
  SS BOND              : bond        0.00483 (   18)
  SS BOND              : angle       1.38924 (   36)
  glycosidic custom    : bond        0.00409 (    3)
  glycosidic custom    : angle       1.15994 (    9)
  link_BETA1-3         : bond        0.00104 (    3)
  link_BETA1-3         : angle       1.25933 (    9)
  covalent geometry    : bond        0.00386 (12170)
  covalent geometry    : angle       0.54385 (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
  401 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 328
  time to evaluate  : 1.326 
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: 0.8770 (ttm-80) cc_final: 0.8560 (mtt-85)
REVERT: C  306 CYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7269 (m)
REVERT: C  387 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7459 (pp20)
REVERT: C  458 ASP cc_start: 0.7547 (t0) cc_final: 0.7039 (t0)
REVERT: C  497 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7753 (ttpt)
REVERT: A  137 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8075 (mmt)
REVERT: A  142 SER cc_start: 0.8223 (p) cc_final: 0.7952 (t)
REVERT: A  458 ASP cc_start: 0.8083 (t0) cc_final: 0.7625 (t0)
REVERT: A  488 ASP cc_start: 0.7834 (t0) cc_final: 0.7578 (t0)
REVERT: A  491 LYS cc_start: 0.8450 (ttpp) cc_final: 0.7984 (ttpp)
REVERT: B  151 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8172 (mmt)
REVERT: B  362 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7723 (t)
REVERT: B  451 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8009 (ttmm)
REVERT: B  457 ARG cc_start: 0.7239 (mtm180) cc_final: 0.7017 (mtm180)
REVERT: B  491 LYS cc_start: 0.8472 (tttm) cc_final: 0.8093 (tttm)
  outliers start: 73
  outliers final: 37
  residues processed: 366
  average time/residue: 1.3075
  time to fit residues: 514.2197
Evaluate side-chains
  380 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 336
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
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  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:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 140 optimal weight:    1.9990
   chunk 135 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 89 optimal weight:    0.5980
   chunk 124 optimal weight:    0.6980
   overall best weight:    1.0586

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

Flipped N/Q/H residues before XYZ refinement:
C  43 ASN
C 360 GLN
A  16 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 = 0.3695 r_free = 0.3695 target = 0.124689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.110656 restraints weight = 16481.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.92
r_work: 0.3380 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:          0.0977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  12205  Z= 0.187
  Angle     :  0.576  10.569  16558  Z= 0.299
  Chirality :  0.043   0.195   1830
  Planarity :  0.004   0.042   2110
  Dihedral  :  8.428 108.002   2040
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 29.47 %
    Favored  : 64.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.29 (0.22), residues: 1454
  helix:  2.42 (0.27), residues: 380
  sheet:  0.07 (0.33), residues: 275
  loop : -1.70 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  65 
 HIS   0.010   0.002   HIS B 356 
 PHE   0.014   0.002   PHE C 440 
 TYR   0.012   0.001   TYR C 424 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00720 (    8)
  link_NAG-ASN         : angle       2.64300 (   24)
  link_BETA1-4         : bond        0.00108 (    3)
  link_BETA1-4         : angle       2.16165 (    9)
  hydrogen bonds       : bond        0.05769 (  448)
  hydrogen bonds       : angle       4.77365 ( 1338)
  SS BOND              : bond        0.00458 (   18)
  SS BOND              : angle       1.26142 (   36)
  glycosidic custom    : bond        0.00421 (    3)
  glycosidic custom    : angle       0.97315 (    9)
  link_BETA1-3         : bond        0.00183 (    3)
  link_BETA1-3         : angle       0.96659 (    9)
  covalent geometry    : bond        0.00440 (12170)
  covalent geometry    : angle       0.56249 (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
  396 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 320
  time to evaluate  : 1.376 
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: 0.8722 (OUTLIER) cc_final: 0.8465 (mttp)
REVERT: C  163 VAL cc_start: 0.8798 (t) cc_final: 0.8586 (p)
REVERT: C  192 ARG cc_start: 0.8766 (ttm-80) cc_final: 0.8547 (mtt-85)
REVERT: C  360 GLN cc_start: 0.7520 (pt0) cc_final: 0.6838 (pt0)
REVERT: C  387 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7490 (pp20)
REVERT: C  458 ASP cc_start: 0.7490 (t0) cc_final: 0.6984 (t0)
REVERT: C  476 ASP cc_start: 0.7018 (m-30) cc_final: 0.6812 (m-30)
REVERT: C  497 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7720 (ttpt)
REVERT: A  137 MET cc_start: 0.8581 (mmm) cc_final: 0.8205 (mmt)
REVERT: A  142 SER cc_start: 0.8234 (p) cc_final: 0.7964 (t)
REVERT: A  458 ASP cc_start: 0.8108 (t0) cc_final: 0.7648 (t0)
REVERT: A  488 ASP cc_start: 0.7830 (t0) cc_final: 0.7584 (t0)
REVERT: A  491 LYS cc_start: 0.8465 (ttpp) cc_final: 0.7974 (ttpp)
REVERT: B   27 ARG cc_start: 0.6812 (OUTLIER) cc_final: 0.6451 (mpt90)
REVERT: B  151 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8146 (mmt)
REVERT: B  187 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7529 (p0)
REVERT: B  362 SER cc_start: 0.8031 (OUTLIER) cc_final: 0.7727 (t)
REVERT: B  451 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8004 (ttmm)
REVERT: B  491 LYS cc_start: 0.8507 (tttm) cc_final: 0.8272 (tttm)
  outliers start: 76
  outliers final: 45
  residues processed: 366
  average time/residue: 1.3451
  time to fit residues: 530.0026
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  : 2.014 
-------------------------------------------------------------------------------
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  460 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  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  388 LYS
Chi-restraints excluded: chain A residue  416 ASP
Chi-restraints excluded: chain A residue  460 VAL
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  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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 101 optimal weight:    1.9990
   chunk 127 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 106 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A  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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.110556 restraints weight = 16438.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 1.93
r_work: 0.3377 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3226 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.1075

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= 0.186
  Angle     :  0.579   9.914  16558  Z= 0.300
  Chirality :  0.044   0.191   1830
  Planarity :  0.004   0.045   2110
  Dihedral  :  8.207 108.946   2039
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 30.09 %
    Favored  : 64.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.22), residues: 1454
  helix:  2.38 (0.27), residues: 380
  sheet:  0.04 (0.32), 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   0.009   0.002   HIS B 356 
 PHE   0.024   0.002   PHE B 295 
 TYR   0.012   0.002   TYR B  12 
 ARG   0.003   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00716 (    8)
  link_NAG-ASN         : angle       2.62656 (   24)
  link_BETA1-4         : bond        0.00081 (    3)
  link_BETA1-4         : angle       2.08011 (    9)
  hydrogen bonds       : bond        0.05774 (  448)
  hydrogen bonds       : angle       4.72656 ( 1338)
  SS BOND              : bond        0.00471 (   18)
  SS BOND              : angle       1.32733 (   36)
  glycosidic custom    : bond        0.00428 (    3)
  glycosidic custom    : angle       0.92411 (    9)
  link_BETA1-3         : bond        0.00225 (    3)
  link_BETA1-3         : angle       0.83394 (    9)
  covalent geometry    : bond        0.00439 (12170)
  covalent geometry    : angle       0.56523 (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
  395 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 73
    poor density    : 322
  time to evaluate  : 1.293 
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: 0.8723 (OUTLIER) cc_final: 0.8466 (mttp)
REVERT: C  269 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8211 (ttm)
REVERT: C  387 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7509 (pp20)
REVERT: C  458 ASP cc_start: 0.7494 (t0) cc_final: 0.6994 (t0)
REVERT: C  497 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7722 (ttpt)
REVERT: A  137 MET cc_start: 0.8571 (mmm) cc_final: 0.8196 (mmt)
REVERT: A  142 SER cc_start: 0.8255 (p) cc_final: 0.7971 (t)
REVERT: A  458 ASP cc_start: 0.8119 (t0) cc_final: 0.7657 (t0)
REVERT: A  491 LYS cc_start: 0.8478 (ttpp) cc_final: 0.8108 (ttpp)
REVERT: B  151 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8157 (mmt)
REVERT: B  187 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7499 (p0)
REVERT: B  276 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8166 (mt-10)
REVERT: B  311 LYS cc_start: 0.7312 (tmmt) cc_final: 0.7048 (tmmt)
REVERT: B  362 SER cc_start: 0.7995 (OUTLIER) cc_final: 0.7685 (t)
REVERT: B  451 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8011 (ttmm)
  outliers start: 73
  outliers final: 46
  residues processed: 363
  average time/residue: 1.3342
  time to fit residues: 520.3336
Evaluate side-chains
  376 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 321
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
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  269 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  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  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  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  276 GLU
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  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:    0.7980
   chunk 96 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0870
   chunk 74 optimal weight:    2.9990
   chunk 103 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 126 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
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 480 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.125946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.111804 restraints weight = 16593.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3504 rms_B_bonded: 1.93
r_work: 0.3394 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.1118

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= 0.125
  Angle     :  0.534   8.544  16558  Z= 0.278
  Chirality :  0.042   0.204   1830
  Planarity :  0.004   0.040   2110
  Dihedral  :  7.864 110.962   2036
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 31.17 %
    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: -0.14 (0.22), residues: 1454
  helix:  2.59 (0.27), residues: 378
  sheet:  0.19 (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 422 
 HIS   0.011   0.001   HIS B 296 
 PHE   0.012   0.001   PHE C 440 
 TYR   0.030   0.001   TYR C 489 
 ARG   0.003   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00698 (    8)
  link_NAG-ASN         : angle       2.51667 (   24)
  link_BETA1-4         : bond        0.00103 (    3)
  link_BETA1-4         : angle       1.84452 (    9)
  hydrogen bonds       : bond        0.05239 (  448)
  hydrogen bonds       : angle       4.58889 ( 1338)
  SS BOND              : bond        0.00420 (   18)
  SS BOND              : angle       1.08220 (   36)
  glycosidic custom    : bond        0.00203 (    3)
  glycosidic custom    : angle       0.74316 (    9)
  link_BETA1-3         : bond        0.00247 (    3)
  link_BETA1-3         : angle       0.67814 (    9)
  covalent geometry    : bond        0.00282 (12170)
  covalent geometry    : angle       0.52233 (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
  381 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 325
  time to evaluate  : 1.278 
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   40 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8431 (mttp)
REVERT: C  163 VAL cc_start: 0.8798 (t) cc_final: 0.8587 (p)
REVERT: C  280 THR cc_start: 0.8573 (p) cc_final: 0.8348 (t)
REVERT: C  457 ARG cc_start: 0.7258 (mtm180) cc_final: 0.6868 (mtm180)
REVERT: C  458 ASP cc_start: 0.7477 (t0) cc_final: 0.6995 (t0)
REVERT: C  497 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7717 (ttpt)
REVERT: A   26 GLU cc_start: 0.7430 (tp30) cc_final: 0.7210 (tp30)
REVERT: A  137 MET cc_start: 0.8548 (mmm) cc_final: 0.8238 (mmt)
REVERT: A  142 SER cc_start: 0.8222 (p) cc_final: 0.7938 (t)
REVERT: A  389 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7262 (mmt)
REVERT: A  458 ASP cc_start: 0.8168 (t0) cc_final: 0.7732 (t0)
REVERT: A  488 ASP cc_start: 0.7836 (t0) cc_final: 0.7581 (t0)
REVERT: A  491 LYS cc_start: 0.8486 (ttpp) cc_final: 0.8221 (ttpp)
REVERT: A  492 TYR cc_start: 0.6828 (m-80) cc_final: 0.6345 (m-80)
REVERT: B   27 ARG cc_start: 0.6777 (OUTLIER) cc_final: 0.6385 (mpt90)
REVERT: B  187 ASP cc_start: 0.7764 (OUTLIER) cc_final: 0.7431 (p0)
REVERT: B  311 LYS cc_start: 0.7250 (tmmt) cc_final: 0.7006 (tmmt)
REVERT: B  451 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7994 (ttmm)
REVERT: B  457 ARG cc_start: 0.7214 (mtm180) cc_final: 0.6935 (mtm180)
REVERT: B  491 LYS cc_start: 0.8458 (tttm) cc_final: 0.8128 (tttm)
  outliers start: 56
  outliers final: 32
  residues processed: 358
  average time/residue: 1.3173
  time to fit residues: 506.8747
Evaluate side-chains
  354 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 316
  time to evaluate  : 1.468 
-------------------------------------------------------------------------------
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   46 LEU
Chi-restraints excluded: chain C residue  117 GLU
Chi-restraints excluded: chain C residue  157 LYS
Chi-restraints excluded: chain C residue  176 MET
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  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  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  388 LYS
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   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  187 ASP
Chi-restraints excluded: chain B residue  313 GLU
Chi-restraints excluded: chain B residue  380 ASN
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:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 71 optimal weight:    0.4980
   chunk 121 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 119 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 106 optimal weight:    0.6980
   chunk 135 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 29 optimal weight:    0.2980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
** 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.125580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.111463 restraints weight = 16679.022|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 1.94
r_work: 0.3390 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3241 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.1184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12205  Z= 0.139
  Angle     :  0.556  13.149  16558  Z= 0.286
  Chirality :  0.042   0.205   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.617 111.179   2026
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 32.17 %
    Favored  : 63.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.22), residues: 1454
  helix:  2.52 (0.27), residues: 380
  sheet:  0.20 (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   0.023   0.001   PHE B 295 
 TYR   0.021   0.001   TYR C 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00688 (    8)
  link_NAG-ASN         : angle       2.51223 (   24)
  link_BETA1-4         : bond        0.00045 (    3)
  link_BETA1-4         : angle       1.82734 (    9)
  hydrogen bonds       : bond        0.05284 (  448)
  hydrogen bonds       : angle       4.55185 ( 1338)
  SS BOND              : bond        0.00464 (   18)
  SS BOND              : angle       1.18653 (   36)
  glycosidic custom    : bond        0.00158 (    3)
  glycosidic custom    : angle       0.78439 (    9)
  link_BETA1-3         : bond        0.00256 (    3)
  link_BETA1-3         : angle       0.69135 (    9)
  covalent geometry    : bond        0.00320 (12170)
  covalent geometry    : angle       0.54438 (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
  373 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 316
  time to evaluate  : 1.313 
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   40 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8453 (mttp)
REVERT: C  280 THR cc_start: 0.8576 (OUTLIER) cc_final: 0.8345 (t)
REVERT: C  387 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7519 (pp20)
REVERT: C  457 ARG cc_start: 0.7294 (mtm180) cc_final: 0.7032 (mtm180)
REVERT: C  458 ASP cc_start: 0.7478 (t0) cc_final: 0.7010 (t0)
REVERT: C  497 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7711 (ttpt)
REVERT: A   26 GLU cc_start: 0.7505 (tp30) cc_final: 0.7300 (tp30)
REVERT: A  137 MET cc_start: 0.8543 (mmm) cc_final: 0.8245 (mmt)
REVERT: A  142 SER cc_start: 0.8221 (p) cc_final: 0.7936 (t)
REVERT: A  389 MET cc_start: 0.7666 (OUTLIER) cc_final: 0.7280 (mmt)
REVERT: A  458 ASP cc_start: 0.8189 (t0) cc_final: 0.7754 (t0)
REVERT: A  488 ASP cc_start: 0.7855 (t0) cc_final: 0.7588 (t0)
REVERT: A  491 LYS cc_start: 0.8489 (ttpp) cc_final: 0.8217 (ttpp)
REVERT: A  492 TYR cc_start: 0.6839 (m-80) cc_final: 0.6343 (m-80)
REVERT: B   27 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6406 (mpt90)
REVERT: B  151 MET cc_start: 0.8842 (OUTLIER) cc_final: 0.8118 (mmt)
REVERT: B  187 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7454 (p0)
REVERT: B  311 LYS cc_start: 0.7252 (tmmt) cc_final: 0.7015 (tmmt)
REVERT: B  451 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7996 (ttmm)
REVERT: B  491 LYS cc_start: 0.8456 (tttm) cc_final: 0.8107 (tttm)
  outliers start: 57
  outliers final: 36
  residues processed: 350
  average time/residue: 1.3882
  time to fit residues: 520.9295
Evaluate side-chains
  363 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 318
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
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   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  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  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  388 LYS
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   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  262 LYS
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 101 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 64 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 484 ASN
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**
B 480 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.124813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.110719 restraints weight = 16617.988|
|-----------------------------------------------------------------------------|
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: 0.3227 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
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      :  0.004   0.037  12205  Z= 0.176
  Angle     :  0.578  11.813  16558  Z= 0.300
  Chirality :  0.043   0.195   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.541 111.313   2026
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 4.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 33.18 %
    Favored  : 62.88 %
  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: -0.20 (0.22), residues: 1454
  helix:  2.52 (0.26), residues: 378
  sheet:  0.17 (0.33), residues: 273
  loop : -1.66 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  65 
 HIS   0.010   0.002   HIS C 356 
 PHE   0.033   0.002   PHE B 339 
 TYR   0.015   0.001   TYR B 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00684 (    8)
  link_NAG-ASN         : angle       2.56729 (   24)
  link_BETA1-4         : bond        0.00044 (    3)
  link_BETA1-4         : angle       1.89570 (    9)
  hydrogen bonds       : bond        0.05585 (  448)
  hydrogen bonds       : angle       4.58620 ( 1338)
  SS BOND              : bond        0.00476 (   18)
  SS BOND              : angle       1.16954 (   36)
  glycosidic custom    : bond        0.00332 (    3)
  glycosidic custom    : angle       0.92275 (    9)
  link_BETA1-3         : bond        0.00129 (    3)
  link_BETA1-3         : angle       0.68653 (    9)
  covalent geometry    : bond        0.00415 (12170)
  covalent geometry    : angle       0.56634 (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
  368 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 317
  time to evaluate  : 1.391 
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   40 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8472 (mttp)
REVERT: C  387 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7539 (pp20)
REVERT: C  458 ASP cc_start: 0.7533 (t0) cc_final: 0.7069 (t0)
REVERT: A   26 GLU cc_start: 0.7675 (tp30) cc_final: 0.7431 (tp30)
REVERT: A  137 MET cc_start: 0.8591 (mmm) cc_final: 0.8300 (mmt)
REVERT: A  142 SER cc_start: 0.8242 (p) cc_final: 0.7953 (t)
REVERT: A  389 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7301 (mmt)
REVERT: A  458 ASP cc_start: 0.8136 (t0) cc_final: 0.7747 (t0)
REVERT: A  492 TYR cc_start: 0.6845 (m-80) cc_final: 0.6338 (m-80)
REVERT: B   27 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6475 (mpt90)
REVERT: B  151 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8164 (mmt)
REVERT: B  187 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7505 (p0)
REVERT: B  311 LYS cc_start: 0.7313 (tmmt) cc_final: 0.7041 (tmmt)
REVERT: B  451 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8004 (ttmm)
REVERT: B  491 LYS cc_start: 0.8446 (tttm) cc_final: 0.8091 (tttm)
  outliers start: 51
  outliers final: 33
  residues processed: 345
  average time/residue: 1.3551
  time to fit residues: 501.7573
Evaluate side-chains
  350 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 310
  time to evaluate  : 1.268 
-------------------------------------------------------------------------------
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  478 CYS
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  388 LYS
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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 138 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   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:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.5588

-------------------------------------------------------------------------------
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 224 ASN
** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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 = 0.3677 r_free = 0.3677 target = 0.123492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.109371 restraints weight = 16554.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.94
r_work: 0.3358 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  12205  Z= 0.259
  Angle     :  0.645  12.697  16558  Z= 0.334
  Chirality :  0.046   0.181   1830
  Planarity :  0.004   0.041   2110
  Dihedral  :  7.589 110.349   2026
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 33.10 %
    Favored  : 62.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.22), residues: 1454
  helix:  2.34 (0.26), residues: 380
  sheet:  0.08 (0.32), residues: 274
  loop : -1.72 (0.20), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  65 
 HIS   0.010   0.002   HIS C 356 
 PHE   0.025   0.002   PHE B 295 
 TYR   0.024   0.002   TYR C 489 
 ARG   0.006   0.001   ARG C 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00704 (    8)
  link_NAG-ASN         : angle       2.69230 (   24)
  link_BETA1-4         : bond        0.00178 (    3)
  link_BETA1-4         : angle       2.08411 (    9)
  hydrogen bonds       : bond        0.06136 (  448)
  hydrogen bonds       : angle       4.72167 ( 1338)
  SS BOND              : bond        0.00553 (   18)
  SS BOND              : angle       1.34911 (   36)
  glycosidic custom    : bond        0.00560 (    3)
  glycosidic custom    : angle       1.13826 (    9)
  link_BETA1-3         : bond        0.00118 (    3)
  link_BETA1-3         : angle       0.81236 (    9)
  covalent geometry    : bond        0.00622 (12170)
  covalent geometry    : angle       0.63313 (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
  382 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 326
  time to evaluate  : 1.411 
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  387 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7569 (pp20)
REVERT: C  458 ASP cc_start: 0.7568 (t0) cc_final: 0.7122 (t0)
REVERT: A   26 GLU cc_start: 0.7750 (tp30) cc_final: 0.7512 (tp30)
REVERT: A   80 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6969 (tm-30)
REVERT: A  137 MET cc_start: 0.8618 (mmm) cc_final: 0.8260 (mmt)
REVERT: A  142 SER cc_start: 0.8285 (p) cc_final: 0.7999 (t)
REVERT: A  278 CYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6524 (p)
REVERT: A  389 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7340 (mmt)
REVERT: A  458 ASP cc_start: 0.8125 (t0) cc_final: 0.7733 (t0)
REVERT: B   27 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6513 (mpt90)
REVERT: B  151 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8139 (mmt)
REVERT: B  187 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7475 (p0)
REVERT: B  311 LYS cc_start: 0.7327 (tmmt) cc_final: 0.7081 (tmmt)
REVERT: B  451 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7995 (ttmm)
REVERT: B  491 LYS cc_start: 0.8481 (tttm) cc_final: 0.8114 (tttm)
  outliers start: 56
  outliers final: 34
  residues processed: 355
  average time/residue: 1.3238
  time to fit residues: 505.3828
Evaluate side-chains
  367 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 325
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  478 CYS
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   80 GLU
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  388 LYS
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  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  429 LEU
Chi-restraints excluded: chain B residue  431 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:    1.9990
   chunk 142 optimal weight:    0.9980
   chunk 82 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 137 optimal weight:    0.5980
   chunk 51 optimal weight:    2.9990
   chunk 121 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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
** A 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3699 r_free = 0.3699 target = 0.125155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.111123 restraints weight = 16448.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.92
r_work: 0.3383 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12205  Z= 0.150
  Angle     :  0.586  11.306  16558  Z= 0.303
  Chirality :  0.043   0.194   1830
  Planarity :  0.004   0.039   2110
  Dihedral  :  7.355 112.157   2024
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 34.26 %
    Favored  : 62.57 %
  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: -0.19 (0.22), residues: 1454
  helix:  2.54 (0.26), residues: 378
  sheet:  0.16 (0.33), residues: 273
  loop : -1.65 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  81 
 HIS   0.011   0.001   HIS C 356 
 PHE   0.026   0.001   PHE B 295 
 TYR   0.024   0.002   TYR C 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00716 (    8)
  link_NAG-ASN         : angle       2.53505 (   24)
  link_BETA1-4         : bond        0.00047 (    3)
  link_BETA1-4         : angle       1.86287 (    9)
  hydrogen bonds       : bond        0.05519 (  448)
  hydrogen bonds       : angle       4.61413 ( 1338)
  SS BOND              : bond        0.00460 (   18)
  SS BOND              : angle       1.14318 (   36)
  glycosidic custom    : bond        0.00267 (    3)
  glycosidic custom    : angle       0.86726 (    9)
  link_BETA1-3         : bond        0.00201 (    3)
  link_BETA1-3         : angle       0.66348 (    9)
  covalent geometry    : bond        0.00350 (12170)
  covalent geometry    : angle       0.57521 (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
  356 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 315
  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: symmetry clash
REVERT: C  280 THR cc_start: 0.8549 (p) cc_final: 0.8340 (t)
REVERT: C  458 ASP cc_start: 0.7568 (t0) cc_final: 0.7105 (t0)
REVERT: A   26 GLU cc_start: 0.7682 (tp30) cc_final: 0.7446 (tp30)
REVERT: A  137 MET cc_start: 0.8596 (mmm) cc_final: 0.8234 (mmt)
REVERT: A  142 SER cc_start: 0.8264 (p) cc_final: 0.7976 (t)
REVERT: A  389 MET cc_start: 0.7673 (OUTLIER) cc_final: 0.7294 (mmt)
REVERT: A  458 ASP cc_start: 0.8124 (t0) cc_final: 0.7691 (t0)
REVERT: B   27 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6484 (mpt90)
REVERT: B  151 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8143 (mmt)
REVERT: B  187 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7439 (p0)
REVERT: B  311 LYS cc_start: 0.7274 (tmmt) cc_final: 0.7043 (tmmt)
REVERT: B  451 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7985 (ttmm)
REVERT: B  491 LYS cc_start: 0.8445 (tttm) cc_final: 0.8067 (tttm)
REVERT: B  497 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8053 (tmtm)
  outliers start: 41
  outliers final: 29
  residues processed: 336
  average time/residue: 1.3355
  time to fit residues: 481.5415
Evaluate side-chains
  352 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 317
  time to evaluate  : 1.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  478 CYS
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  139 CYS
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  388 LYS
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  110 LEU
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  262 LYS
Chi-restraints excluded: chain B residue  321 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:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 58 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 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 356 HIS
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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.124842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.110849 restraints weight = 16554.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 1.92
r_work: 0.3380 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: 0.8074
moved from start:          0.1320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12205  Z= 0.171
  Angle     :  0.597  11.156  16558  Z= 0.309
  Chirality :  0.043   0.193   1830
  Planarity :  0.004   0.040   2110
  Dihedral  :  7.304 112.594   2024
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 4.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 34.18 %
    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: -0.19 (0.22), residues: 1454
  helix:  2.54 (0.26), residues: 378
  sheet:  0.15 (0.33), residues: 273
  loop : -1.65 (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   0.021   0.001   PHE A 339 
 TYR   0.029   0.002   TYR C 489 
 ARG   0.004   0.000   ARG C 212 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00692 (    8)
  link_NAG-ASN         : angle       2.57004 (   24)
  link_BETA1-4         : bond        0.00050 (    3)
  link_BETA1-4         : angle       1.89345 (    9)
  hydrogen bonds       : bond        0.05607 (  448)
  hydrogen bonds       : angle       4.59628 ( 1338)
  SS BOND              : bond        0.00454 (   18)
  SS BOND              : angle       1.15780 (   36)
  glycosidic custom    : bond        0.00279 (    3)
  glycosidic custom    : angle       0.93812 (    9)
  link_BETA1-3         : bond        0.00178 (    3)
  link_BETA1-3         : angle       0.69230 (    9)
  covalent geometry    : bond        0.00403 (12170)
  covalent geometry    : angle       0.58521 (16471)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10863.34 seconds
wall clock time: 186 minutes 31.37 seconds (11191.37 seconds total)