Starting phenix.real_space_refine
on Sat May 17 06:11:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tvi_41643/05_2025/8tvi_41643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tvi_41643/05_2025/8tvi_41643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tvi_41643/05_2025/8tvi_41643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tvi_41643/05_2025/8tvi_41643.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tvi_41643/05_2025/8tvi_41643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tvi_41643/05_2025/8tvi_41643.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.083
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: 5
    Type Number    sf(0)   Gaussians
     Zn      4      6.06       5
     S      96      5.16       5
     C    9832      2.51       5
     N    2540      2.21       5
     O    2852      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 84 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 15324
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 513, 3816
          Classifications: {'peptide': 513}
          Incomplete info: {'truncation_to_alanine': 68}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 486}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 189
          Unresolved non-hydrogen angles: 233
          Unresolved non-hydrogen dihedrals: 147
          Unresolved non-hydrogen chiralities: 14
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 109
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {' ZN': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, B, D
  Time building chain proxies: 9.47, per 1000 atoms: 0.62
  Number of scatterers: 15324
  At special positions: 0
  Unit cell: (143.29, 143.29, 123.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      4     29.99
     S      96     16.00
     O    2852      8.00
     N    2540      7.00
     C    9832      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=28, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 188 " - pdb=" SG  CYS A 604 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 219 " - pdb=" SG  CYS A 243 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 285 " - pdb=" SG  CYS A 298 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 396 " distance=2.08
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS A 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 494 " - pdb=" SG  CYS A 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 568 " - pdb=" SG  CYS A 577 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 188 " - pdb=" SG  CYS C 604 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 188 " - pdb=" SG  CYS B 604 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 188 " - pdb=" SG  CYS D 604 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 219 " - pdb=" SG  CYS C 243 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 219 " - pdb=" SG  CYS B 243 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D 219 " - pdb=" SG  CYS D 243 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 285 " - pdb=" SG  CYS C 298 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 285 " - pdb=" SG  CYS B 298 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 285 " - pdb=" SG  CYS D 298 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 396 " distance=2.08
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 396 " distance=2.08
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 396 " distance=2.08
    Simple disulfide: pdb=" SG  CYS C 384 " - pdb=" SG  CYS C 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 384 " - pdb=" SG  CYS B 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 384 " - pdb=" SG  CYS D 502 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 494 " - pdb=" SG  CYS C 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 494 " - pdb=" SG  CYS B 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 494 " - pdb=" SG  CYS D 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 568 " - pdb=" SG  CYS C 577 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 568 " - pdb=" SG  CYS B 577 " distance=2.02
    Simple disulfide: pdb=" SG  CYS D 568 " - pdb=" SG  CYS D 577 " distance=2.02

  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
    NAG-ASN
      " NAG A 701 " - " ASN A 189 "
      " NAG B 701 " - " ASN B 189 "
      " NAG C 701 " - " ASN C 189 "
      " NAG D 701 " - " ASN D 189 "
  Time building additional restraints: 3.48
  Conformation dependent library (CDL) restraints added in 2.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 702 "
        pdb="ZN    ZN A 702 " - pdb=" ND1 HIS A 548 "
        pdb="ZN    ZN A 702 " - pdb=" NE2 HIS A 194 "
      pdb="  ZN B 702 "
        pdb="ZN    ZN B 702 " - pdb=" ND1 HIS B 548 "
        pdb="ZN    ZN B 702 " - pdb=" NE2 HIS B 194 "
      pdb="  ZN C 702 "
        pdb="ZN    ZN C 702 " - pdb=" ND1 HIS C 548 "
        pdb="ZN    ZN C 702 " - pdb=" NE2 HIS C 194 "
      pdb="  ZN D 702 "
        pdb="ZN    ZN D 702 " - pdb=" ND1 HIS D 548 "
        pdb="ZN    ZN D 702 " - pdb=" NE2 HIS D 194 "


  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3832

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 24 sheets defined
      19.3% alpha, 28.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 86
    Processing helix  chain 'A' and resid 86 through 99
      removed outlier: 3.514A  pdb=" N   VAL A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 113
      removed outlier: 3.936A  pdb=" N   LYS A 103 " --> pdb=" O   GLU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 141
    Processing helix  chain 'A' and resid 278 through 280
      No H-bonds generated for 'chain 'A' and resid 278 through 280'
    Processing helix  chain 'A' and resid 391 through 400
      removed outlier: 3.938A  pdb=" N   VAL A 400 " --> pdb=" O   CYS A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 423
    Processing helix  chain 'A' and resid 433 through 437
    Processing helix  chain 'B' and resid 69 through 86
    Processing helix  chain 'B' and resid 86 through 99
      removed outlier: 3.514A  pdb=" N   VAL B  90 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 113
      removed outlier: 3.936A  pdb=" N   LYS B 103 " --> pdb=" O   GLU B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 141
    Processing helix  chain 'B' and resid 278 through 280
      No H-bonds generated for 'chain 'B' and resid 278 through 280'
    Processing helix  chain 'B' and resid 391 through 400
      removed outlier: 3.938A  pdb=" N   VAL B 400 " --> pdb=" O   CYS B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 423
    Processing helix  chain 'B' and resid 433 through 437
    Processing helix  chain 'C' and resid 69 through 86
    Processing helix  chain 'C' and resid 86 through 99
      removed outlier: 3.514A  pdb=" N   VAL C  90 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 113
      removed outlier: 3.936A  pdb=" N   LYS C 103 " --> pdb=" O   GLU C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 141
    Processing helix  chain 'C' and resid 278 through 280
      No H-bonds generated for 'chain 'C' and resid 278 through 280'
    Processing helix  chain 'C' and resid 391 through 400
      removed outlier: 3.938A  pdb=" N   VAL C 400 " --> pdb=" O   CYS C 396 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 419 through 423
    Processing helix  chain 'C' and resid 433 through 437
    Processing helix  chain 'D' and resid 69 through 86
    Processing helix  chain 'D' and resid 86 through 99
      removed outlier: 3.514A  pdb=" N   VAL D  90 " --> pdb=" O   LEU D  86 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 99 through 113
      removed outlier: 3.936A  pdb=" N   LYS D 103 " --> pdb=" O   GLU D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 113 through 141
    Processing helix  chain 'D' and resid 278 through 280
      No H-bonds generated for 'chain 'D' and resid 278 through 280'
    Processing helix  chain 'D' and resid 391 through 400
      removed outlier: 3.938A  pdb=" N   VAL D 400 " --> pdb=" O   CYS D 396 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 419 through 423
    Processing helix  chain 'D' and resid 433 through 437
    Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 177 through 178
    current: chain 'A' and resid 574 through 584
      removed outlier: 4.582A  pdb=" N   ILE A 575 " --> pdb=" O   VAL A 600 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 218 through 227
      removed outlier: 5.442A  pdb=" N   TYR A 220 " --> pdb=" O   ARG A 239 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ARG A 239 " --> pdb=" O   TYR A 220 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ASN A 222 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU A 237 " --> pdb=" O   ASN A 222 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER A 250 " --> pdb=" O   ILE A 238 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS A 240 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   ILE A 248 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ILE A 251 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER A 275 " --> pdb=" O   ILE A 251 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ILE A 253 " --> pdb=" O   VAL A 273 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   VAL A 273 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU A 255 " --> pdb=" O   LEU A 271 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 289
      removed outlier: 6.848A  pdb=" N   SER A 299 " --> pdb=" O   ASN A 283 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   CYS A 285 " --> pdb=" O   LEU A 297 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU A 297 " --> pdb=" O   CYS A 285 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL A 287 " --> pdb=" O   TRP A 295 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP A 295 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 338 through 339
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 338 through 339
    current: chain 'A' and resid 360 through 370
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 360 through 370
    current: chain 'A' and resid 405 through 418
    Processing sheet with id=AA5, first strand: chain 'A' and resid 443 through 448
    Processing sheet with id=AA6, first strand: chain 'A' and resid 514 through 516
      removed outlier: 4.512A  pdb=" N   SER A 538 " --> pdb=" O   ILE A 554 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 177 through 178
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 177 through 178
    current: chain 'B' and resid 574 through 584
      removed outlier: 4.582A  pdb=" N   ILE B 575 " --> pdb=" O   VAL B 600 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 218 through 227
      removed outlier: 5.442A  pdb=" N   TYR B 220 " --> pdb=" O   ARG B 239 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ARG B 239 " --> pdb=" O   TYR B 220 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ASN B 222 " --> pdb=" O   GLU B 237 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU B 237 " --> pdb=" O   ASN B 222 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER B 250 " --> pdb=" O   ILE B 238 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS B 240 " --> pdb=" O   ILE B 248 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   ILE B 248 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ILE B 251 " --> pdb=" O   SER B 275 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER B 275 " --> pdb=" O   ILE B 251 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ILE B 253 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   VAL B 273 " --> pdb=" O   ILE B 253 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU B 255 " --> pdb=" O   LEU B 271 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 282 through 289
      removed outlier: 6.848A  pdb=" N   SER B 299 " --> pdb=" O   ASN B 283 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   CYS B 285 " --> pdb=" O   LEU B 297 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU B 297 " --> pdb=" O   CYS B 285 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL B 287 " --> pdb=" O   TRP B 295 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP B 295 " --> pdb=" O   VAL B 287 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 338 through 339
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 338 through 339
    current: chain 'B' and resid 360 through 370
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 360 through 370
    current: chain 'B' and resid 405 through 418
    Processing sheet with id=AB2, first strand: chain 'B' and resid 443 through 448
    Processing sheet with id=AB3, first strand: chain 'B' and resid 514 through 516
      removed outlier: 4.512A  pdb=" N   SER B 538 " --> pdb=" O   ILE B 554 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 177 through 178
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 177 through 178
    current: chain 'C' and resid 574 through 584
      removed outlier: 4.582A  pdb=" N   ILE C 575 " --> pdb=" O   VAL C 600 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 218 through 227
      removed outlier: 5.442A  pdb=" N   TYR C 220 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ARG C 239 " --> pdb=" O   TYR C 220 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ASN C 222 " --> pdb=" O   GLU C 237 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU C 237 " --> pdb=" O   ASN C 222 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER C 250 " --> pdb=" O   ILE C 238 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS C 240 " --> pdb=" O   ILE C 248 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   ILE C 248 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ILE C 251 " --> pdb=" O   SER C 275 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER C 275 " --> pdb=" O   ILE C 251 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ILE C 253 " --> pdb=" O   VAL C 273 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   VAL C 273 " --> pdb=" O   ILE C 253 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU C 255 " --> pdb=" O   LEU C 271 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 282 through 289
      removed outlier: 6.848A  pdb=" N   SER C 299 " --> pdb=" O   ASN C 283 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   CYS C 285 " --> pdb=" O   LEU C 297 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU C 297 " --> pdb=" O   CYS C 285 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL C 287 " --> pdb=" O   TRP C 295 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP C 295 " --> pdb=" O   VAL C 287 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 338 through 339
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 338 through 339
    current: chain 'C' and resid 360 through 370
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 360 through 370
    current: chain 'C' and resid 405 through 418
    Processing sheet with id=AB8, first strand: chain 'C' and resid 443 through 448
    Processing sheet with id=AB9, first strand: chain 'C' and resid 514 through 516
      removed outlier: 4.512A  pdb=" N   SER C 538 " --> pdb=" O   ILE C 554 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 177 through 178
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 177 through 178
    current: chain 'D' and resid 574 through 584
      removed outlier: 4.582A  pdb=" N   ILE D 575 " --> pdb=" O   VAL D 600 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 218 through 227
      removed outlier: 5.442A  pdb=" N   TYR D 220 " --> pdb=" O   ARG D 239 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ARG D 239 " --> pdb=" O   TYR D 220 " (cutoff:3.500A)
      removed outlier: 5.333A  pdb=" N   ASN D 222 " --> pdb=" O   GLU D 237 " (cutoff:3.500A)
      removed outlier: 4.193A  pdb=" N   GLU D 237 " --> pdb=" O   ASN D 222 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER D 250 " --> pdb=" O   ILE D 238 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   LYS D 240 " --> pdb=" O   ILE D 248 " (cutoff:3.500A)
      removed outlier: 7.050A  pdb=" N   ILE D 248 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   ILE D 251 " --> pdb=" O   SER D 275 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER D 275 " --> pdb=" O   ILE D 251 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   ILE D 253 " --> pdb=" O   VAL D 273 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   VAL D 273 " --> pdb=" O   ILE D 253 " (cutoff:3.500A)
      removed outlier: 6.850A  pdb=" N   LEU D 255 " --> pdb=" O   LEU D 271 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'D' and resid 282 through 289
      removed outlier: 6.848A  pdb=" N   SER D 299 " --> pdb=" O   ASN D 283 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   CYS D 285 " --> pdb=" O   LEU D 297 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   LEU D 297 " --> pdb=" O   CYS D 285 " (cutoff:3.500A)
      removed outlier: 4.598A  pdb=" N   VAL D 287 " --> pdb=" O   TRP D 295 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   TRP D 295 " --> pdb=" O   VAL D 287 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 338 through 339
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 338 through 339
    current: chain 'D' and resid 360 through 370
  WARNING: can't find start of bonding for strands!
    previous: chain 'D' and resid 360 through 370
    current: chain 'D' and resid 405 through 418
    Processing sheet with id=AC5, first strand: chain 'D' and resid 443 through 448
    Processing sheet with id=AC6, first strand: chain 'D' and resid 514 through 516
      removed outlier: 4.512A  pdb=" N   SER D 538 " --> pdb=" O   ILE D 554 " (cutoff:3.500A)

    553 hydrogen bonds defined for protein.
    1503 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: 4.92

  Time building geometry restraints manager: 4.20 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 2740
        1.32 -     1.45: 3940
        1.45 -     1.57: 8832
        1.57 -     1.70: 8
        1.70 -     1.82: 136
  Bond restraints: 15656
  Sorted by residual:
  bond pdb=" C   LYS D 103 "
       pdb=" O   LYS D 103 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.29e-02 6.01e+03 1.09e+01
  bond pdb=" C   LYS B 103 "
       pdb=" O   LYS B 103 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.29e-02 6.01e+03 1.09e+01
  bond pdb=" C   LYS A 103 "
       pdb=" O   LYS A 103 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.29e-02 6.01e+03 1.09e+01
  bond pdb=" C   LYS C 103 "
       pdb=" O   LYS C 103 "
    ideal  model  delta    sigma   weight residual
    1.236  1.193  0.043 1.29e-02 6.01e+03 1.09e+01
  bond pdb=" C5  NAG D 701 "
       pdb=" O5  NAG D 701 "
    ideal  model  delta    sigma   weight residual
    1.413  1.478 -0.065 2.00e-02 2.50e+03 1.07e+01
  ... (remaining 15651 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 18440
        1.63 -     3.26: 2368
        3.26 -     4.90: 300
        4.90 -     6.53: 148
        6.53 -     8.16: 80
  Bond angle restraints: 21336
  Sorted by residual:
  angle pdb=" C   PHE C 432 "
        pdb=" N   PRO C 433 "
        pdb=" CA  PRO C 433 "
      ideal   model   delta    sigma   weight residual
     119.66  126.07   -6.41 7.20e-01 1.93e+00 7.93e+01
  angle pdb=" C   PHE B 432 "
        pdb=" N   PRO B 433 "
        pdb=" CA  PRO B 433 "
      ideal   model   delta    sigma   weight residual
     119.66  126.07   -6.41 7.20e-01 1.93e+00 7.93e+01
  angle pdb=" C   PHE D 432 "
        pdb=" N   PRO D 433 "
        pdb=" CA  PRO D 433 "
      ideal   model   delta    sigma   weight residual
     119.66  126.07   -6.41 7.20e-01 1.93e+00 7.93e+01
  angle pdb=" C   PHE A 432 "
        pdb=" N   PRO A 433 "
        pdb=" CA  PRO A 433 "
      ideal   model   delta    sigma   weight residual
     119.66  126.07   -6.41 7.20e-01 1.93e+00 7.93e+01
  angle pdb=" C   LYS B 101 "
        pdb=" N   PRO B 102 "
        pdb=" CA  PRO B 102 "
      ideal   model   delta    sigma   weight residual
     119.24  127.40   -8.16 1.04e+00 9.25e-01 6.16e+01
  ... (remaining 21331 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.51: 9120
       17.51 -    35.02: 252
       35.02 -    52.53: 48
       52.53 -    70.05: 32
       70.05 -    87.56: 8
  Dihedral angle restraints: 9460
    sinusoidal: 3484
      harmonic: 5976
  Sorted by residual:
  dihedral pdb=" CB  CYS A 188 "
           pdb=" SG  CYS A 188 "
           pdb=" SG  CYS A 604 "
           pdb=" CB  CYS A 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.62   53.62     1      1.00e+01 1.00e-02 3.91e+01
  dihedral pdb=" CB  CYS C 188 "
           pdb=" SG  CYS C 188 "
           pdb=" SG  CYS C 604 "
           pdb=" CB  CYS C 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.62   53.62     1      1.00e+01 1.00e-02 3.91e+01
  dihedral pdb=" CB  CYS B 188 "
           pdb=" SG  CYS B 188 "
           pdb=" SG  CYS B 604 "
           pdb=" CB  CYS B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -139.62   53.62     1      1.00e+01 1.00e-02 3.91e+01
  ... (remaining 9457 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1712
       0.058 -    0.116: 624
       0.116 -    0.174: 136
       0.174 -    0.232: 8
       0.232 -    0.290: 4
  Chirality restraints: 2484
  Sorted by residual:
  chirality pdb=" C2  NAG A 701 "
            pdb=" C1  NAG A 701 "
            pdb=" C3  NAG A 701 "
            pdb=" N2  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.78    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C2  NAG D 701 "
            pdb=" C1  NAG D 701 "
            pdb=" C3  NAG D 701 "
            pdb=" N2  NAG D 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.78    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C2  NAG B 701 "
            pdb=" C1  NAG B 701 "
            pdb=" C3  NAG B 701 "
            pdb=" N2  NAG B 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.78    0.29 2.00e-01 2.50e+01 2.11e+00
  ... (remaining 2481 not shown)

  Planarity restraints: 2716
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 571 "    0.043 2.00e-02 2.50e+03   2.21e-02 9.74e+00
        pdb=" CG  TYR A 571 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 571 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 571 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 571 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 571 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 571 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 571 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D 571 "    0.043 2.00e-02 2.50e+03   2.21e-02 9.74e+00
        pdb=" CG  TYR D 571 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR D 571 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR D 571 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR D 571 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR D 571 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR D 571 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR D 571 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 571 "    0.043 2.00e-02 2.50e+03   2.21e-02 9.74e+00
        pdb=" CG  TYR C 571 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 571 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 571 "   -0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 571 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 571 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 571 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR C 571 "    0.029 2.00e-02 2.50e+03
  ... (remaining 2713 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 4
        2.47 -     3.08: 10244
        3.08 -     3.69: 21203
        3.69 -     4.29: 33243
        4.29 -     4.90: 55526
  Nonbonded interactions: 120220
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 544 "
            pdb="ZN    ZN C 702 "
     model   vdw
     1.868 2.230
  nonbonded pdb=" OD2 ASP D 544 "
            pdb="ZN    ZN D 702 "
     model   vdw
     1.868 2.230
  nonbonded pdb=" OD2 ASP A 544 "
            pdb="ZN    ZN A 702 "
     model   vdw
     1.868 2.230
  nonbonded pdb=" OD2 ASP B 544 "
            pdb="ZN    ZN B 702 "
     model   vdw
     1.868 2.230
  nonbonded pdb=" OG  SER A 230 "
            pdb=" NH1 ARG A 257 "
     model   vdw
     2.546 3.120
  ... (remaining 120215 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: 0.11
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'D'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             7.420
  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:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     38.820
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.320
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
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      :  0.012   0.134  15696  Z= 0.683
  Angle     :  1.288   8.550  21404  Z= 0.895
  Chirality :  0.060   0.290   2484
  Planarity :  0.008   0.126   2712
  Dihedral  : 10.007  87.557   5544
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 1.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.52 (0.17), residues: 2028
  helix:  1.39 (0.26), residues: 316
  sheet:  0.68 (0.17), residues: 780
  loop : -0.24 (0.19), residues: 932

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.005   TRP B 318 
 HIS   0.003   0.001   HIS C 596 
 PHE   0.020   0.005   PHE C 523 
 TYR   0.043   0.005   TYR A 571 
 ARG   0.005   0.001   ARG C 592 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05506 (    4)
  link_NAG-ASN         : angle       2.59730 (   12)
  hydrogen bonds       : bond        0.18282 (  553)
  hydrogen bonds       : angle       7.07807 ( 1503)
  metal coordination   : bond        0.11115 (    8)
  SS BOND              : bond        0.01945 (   28)
  SS BOND              : angle       4.06850 (   56)
  covalent geometry    : bond        0.01164 (15656)
  covalent geometry    : angle       1.27172 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 1.703 
Fit side-chains
REVERT: A  181 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7704 (mt-10)
REVERT: B  181 GLU cc_start: 0.7917 (mt-10) cc_final: 0.7689 (mt-10)
REVERT: C  181 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7683 (mt-10)
REVERT: D  181 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7691 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.3015
  time to fit residues: 115.2482
Evaluate side-chains
  140 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 1.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 172 optimal weight:    0.7980
   chunk 154 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 104 optimal weight:    0.7980
   chunk 82 optimal weight:    0.6980
   chunk 159 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 97 optimal weight:    1.9990
   chunk 119 optimal weight:    0.9980
   chunk 185 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 601 GLN
B 601 GLN
C 601 GLN
D 601 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.119906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.091831 restraints weight = 17726.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2897 rms_B_bonded: 1.91
r_work: 0.2789 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  15696  Z= 0.155
  Angle     :  0.548   4.465  21404  Z= 0.302
  Chirality :  0.046   0.146   2484
  Planarity :  0.004   0.039   2712
  Dihedral  :  4.789  21.380   2280
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  3.63 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.95 (0.18), residues: 2028
  helix:  2.92 (0.27), residues: 316
  sheet:  0.83 (0.18), residues: 772
  loop : -0.32 (0.20), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 274 
 HIS   0.004   0.001   HIS B 194 
 PHE   0.019   0.002   PHE B 523 
 TYR   0.016   0.002   TYR D 446 
 ARG   0.002   0.000   ARG D 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00232 (    4)
  link_NAG-ASN         : angle       1.05573 (   12)
  hydrogen bonds       : bond        0.05329 (  553)
  hydrogen bonds       : angle       5.29818 ( 1503)
  metal coordination   : bond        0.00893 (    8)
  SS BOND              : bond        0.00261 (   28)
  SS BOND              : angle       0.94725 (   56)
  covalent geometry    : bond        0.00381 (15656)
  covalent geometry    : angle       0.54591 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 156
  time to evaluate  : 1.699 
Fit side-chains
REVERT: A  247 GLU cc_start: 0.8151 (tt0) cc_final: 0.7868 (tt0)
REVERT: A  488 MET cc_start: 0.8748 (ttm) cc_final: 0.8484 (ttm)
REVERT: A  520 ASP cc_start: 0.8099 (t0) cc_final: 0.7787 (t0)
REVERT: B  247 GLU cc_start: 0.8144 (tt0) cc_final: 0.7861 (tt0)
REVERT: B  488 MET cc_start: 0.8749 (ttm) cc_final: 0.8483 (ttm)
REVERT: B  520 ASP cc_start: 0.8096 (t0) cc_final: 0.7790 (t0)
REVERT: C  247 GLU cc_start: 0.8153 (tt0) cc_final: 0.7871 (tt0)
REVERT: C  488 MET cc_start: 0.8742 (ttm) cc_final: 0.8477 (ttm)
REVERT: C  520 ASP cc_start: 0.8118 (t0) cc_final: 0.7808 (t0)
REVERT: D  247 GLU cc_start: 0.8159 (tt0) cc_final: 0.7878 (tt0)
REVERT: D  488 MET cc_start: 0.8754 (ttm) cc_final: 0.8488 (ttm)
REVERT: D  520 ASP cc_start: 0.8109 (t0) cc_final: 0.7797 (t0)
  outliers start: 20
  outliers final: 16
  residues processed: 168
  average time/residue: 0.2637
  time to fit residues: 66.0627
Evaluate side-chains
  160 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 144
  time to evaluate  : 1.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 121 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 151 optimal weight:    2.9990
   chunk 150 optimal weight:    0.9980
   chunk 78 optimal weight:    2.9990
   chunk 201 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 157 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   overall best weight:    0.8782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.118090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.090219 restraints weight = 17822.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 1.88
r_work: 0.2754 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2619 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8605
moved from start:          0.1902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024  15696  Z= 0.150
  Angle     :  0.505   4.497  21404  Z= 0.277
  Chirality :  0.046   0.146   2484
  Planarity :  0.004   0.040   2712
  Dihedral  :  4.498  17.329   2280
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 1.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  :  3.63 %
    Favored  : 94.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.83 (0.19), residues: 2028
  helix:  3.43 (0.26), residues: 316
  sheet:  0.66 (0.19), residues: 772
  loop : -0.54 (0.20), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 274 
 HIS   0.004   0.001   HIS B 194 
 PHE   0.017   0.002   PHE B 523 
 TYR   0.017   0.002   TYR A 446 
 ARG   0.001   0.000   ARG B 398 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00173 (    4)
  link_NAG-ASN         : angle       0.85367 (   12)
  hydrogen bonds       : bond        0.04527 (  553)
  hydrogen bonds       : angle       5.00136 ( 1503)
  metal coordination   : bond        0.00439 (    8)
  SS BOND              : bond        0.00275 (   28)
  SS BOND              : angle       0.95219 (   56)
  covalent geometry    : bond        0.00369 (15656)
  covalent geometry    : angle       0.50276 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 148
  time to evaluate  : 1.711 
Fit side-chains
REVERT: A  474 SER cc_start: 0.8795 (p) cc_final: 0.8339 (m)
REVERT: A  520 ASP cc_start: 0.8177 (t0) cc_final: 0.7776 (t0)
REVERT: B  474 SER cc_start: 0.8795 (p) cc_final: 0.8339 (m)
REVERT: B  520 ASP cc_start: 0.8158 (t0) cc_final: 0.7754 (t0)
REVERT: C  474 SER cc_start: 0.8792 (p) cc_final: 0.8337 (m)
REVERT: C  520 ASP cc_start: 0.8164 (t0) cc_final: 0.7766 (t0)
REVERT: D  474 SER cc_start: 0.8797 (p) cc_final: 0.8344 (m)
REVERT: D  520 ASP cc_start: 0.8174 (t0) cc_final: 0.7774 (t0)
  outliers start: 28
  outliers final: 20
  residues processed: 168
  average time/residue: 0.2372
  time to fit residues: 61.9376
Evaluate side-chains
  152 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 132
  time to evaluate  : 1.695 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue   90 VAL
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue   90 VAL
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue   90 VAL
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 182 optimal weight:    3.9990
   chunk 143 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 159 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 28 optimal weight:    0.2980
   chunk 17 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 601 GLN
** C 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.118777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2893 r_free = 0.2893 target = 0.090970 restraints weight = 17816.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 1.87
r_work: 0.2769 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  15696  Z= 0.115
  Angle     :  0.470   4.572  21404  Z= 0.255
  Chirality :  0.045   0.145   2484
  Planarity :  0.004   0.037   2712
  Dihedral  :  4.285  17.510   2280
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 1.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  5.63 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.81 (0.19), residues: 2028
  helix:  3.54 (0.26), residues: 320
  sheet:  0.66 (0.19), residues: 772
  loop : -0.64 (0.20), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 274 
 HIS   0.003   0.001   HIS B 194 
 PHE   0.015   0.002   PHE B 523 
 TYR   0.014   0.001   TYR B 446 
 ARG   0.001   0.000   ARG B 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00123 (    4)
  link_NAG-ASN         : angle       0.81276 (   12)
  hydrogen bonds       : bond        0.03862 (  553)
  hydrogen bonds       : angle       4.82185 ( 1503)
  metal coordination   : bond        0.00200 (    8)
  SS BOND              : bond        0.00172 (   28)
  SS BOND              : angle       0.71258 (   56)
  covalent geometry    : bond        0.00275 (15656)
  covalent geometry    : angle       0.46940 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 1.870 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8498 (mt)
REVERT: A  474 SER cc_start: 0.8860 (p) cc_final: 0.8415 (m)
REVERT: A  520 ASP cc_start: 0.8236 (t0) cc_final: 0.7825 (t0)
REVERT: B  410 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: B  474 SER cc_start: 0.8858 (p) cc_final: 0.8413 (m)
REVERT: B  520 ASP cc_start: 0.8235 (t0) cc_final: 0.7826 (t0)
REVERT: C  410 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: C  474 SER cc_start: 0.8859 (p) cc_final: 0.8418 (m)
REVERT: C  520 ASP cc_start: 0.8241 (t0) cc_final: 0.7834 (t0)
REVERT: D  410 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8494 (mt)
REVERT: D  474 SER cc_start: 0.8860 (p) cc_final: 0.8421 (m)
REVERT: D  520 ASP cc_start: 0.8240 (t0) cc_final: 0.7828 (t0)
  outliers start: 21
  outliers final: 13
  residues processed: 156
  average time/residue: 0.2471
  time to fit residues: 59.8396
Evaluate side-chains
  149 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  245 THR
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  245 THR
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  245 THR
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  245 THR
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 165 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 30 optimal weight:    5.9990
   chunk 135 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 124 optimal weight:    0.8980
   chunk 156 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 601 GLN
C 601 GLN
D 601 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.116206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.088414 restraints weight = 18230.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2842 rms_B_bonded: 1.85
r_work: 0.2736 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2602 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8641
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  15696  Z= 0.174
  Angle     :  0.516   4.506  21404  Z= 0.278
  Chirality :  0.046   0.149   2484
  Planarity :  0.004   0.038   2712
  Dihedral  :  4.407  17.195   2280
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 1.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  5.70 %
    Favored  : 93.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.57 (0.19), residues: 2028
  helix:  3.48 (0.27), residues: 320
  sheet:  0.50 (0.19), residues: 764
  loop : -0.83 (0.20), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 274 
 HIS   0.004   0.001   HIS D 194 
 PHE   0.016   0.003   PHE D 523 
 TYR   0.017   0.002   TYR C 446 
 ARG   0.002   0.000   ARG D 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00121 (    4)
  link_NAG-ASN         : angle       0.86356 (   12)
  hydrogen bonds       : bond        0.04407 (  553)
  hydrogen bonds       : angle       4.84850 ( 1503)
  metal coordination   : bond        0.00229 (    8)
  SS BOND              : bond        0.00267 (   28)
  SS BOND              : angle       0.89580 (   56)
  covalent geometry    : bond        0.00438 (15656)
  covalent geometry    : angle       0.51461 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 1.753 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8549 (mt)
REVERT: A  474 SER cc_start: 0.8909 (p) cc_final: 0.8496 (m)
REVERT: A  501 MET cc_start: 0.8930 (mmt) cc_final: 0.8047 (mmt)
REVERT: A  520 ASP cc_start: 0.8252 (t0) cc_final: 0.7826 (t0)
REVERT: B  410 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8550 (mt)
REVERT: B  474 SER cc_start: 0.8910 (p) cc_final: 0.8497 (m)
REVERT: B  501 MET cc_start: 0.8933 (mmt) cc_final: 0.8043 (mmt)
REVERT: B  520 ASP cc_start: 0.8248 (t0) cc_final: 0.7822 (t0)
REVERT: C  410 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8552 (mt)
REVERT: C  474 SER cc_start: 0.8909 (p) cc_final: 0.8497 (m)
REVERT: C  501 MET cc_start: 0.8933 (mmt) cc_final: 0.8047 (mmt)
REVERT: C  520 ASP cc_start: 0.8254 (t0) cc_final: 0.7829 (t0)
REVERT: D  410 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8553 (mt)
REVERT: D  474 SER cc_start: 0.8909 (p) cc_final: 0.8499 (m)
REVERT: D  501 MET cc_start: 0.8934 (mmt) cc_final: 0.8035 (mmt)
REVERT: D  520 ASP cc_start: 0.8253 (t0) cc_final: 0.7828 (t0)
  outliers start: 20
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2567
  time to fit residues: 58.9643
Evaluate side-chains
  148 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 133 optimal weight:    1.9990
   chunk 172 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9980
   chunk 160 optimal weight:    0.0370
   chunk 189 optimal weight:    0.9980
   chunk 93 optimal weight:    0.2980
   chunk 193 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9990
   chunk 185 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   overall best weight:    0.6658

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.117398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.089716 restraints weight = 18106.852|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 1.85
r_work: 0.2756 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2622 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8620
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  15696  Z= 0.117
  Angle     :  0.473   4.829  21404  Z= 0.253
  Chirality :  0.045   0.142   2484
  Planarity :  0.004   0.035   2712
  Dihedral  :  4.217  16.655   2280
  Min Nonbonded Distance : 2.078

Molprobity Statistics.
  All-atom Clashscore : 1.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  6.54 %
    Favored  : 92.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.61 (0.19), residues: 2028
  helix:  3.62 (0.26), residues: 320
  sheet:  0.50 (0.19), residues: 748
  loop : -0.80 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 274 
 HIS   0.003   0.001   HIS D 312 
 PHE   0.013   0.002   PHE B 523 
 TYR   0.013   0.001   TYR A 446 
 ARG   0.001   0.000   ARG B 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    4)
  link_NAG-ASN         : angle       0.78825 (   12)
  hydrogen bonds       : bond        0.03762 (  553)
  hydrogen bonds       : angle       4.71742 ( 1503)
  metal coordination   : bond        0.00134 (    8)
  SS BOND              : bond        0.00186 (   28)
  SS BOND              : angle       0.66790 (   56)
  covalent geometry    : bond        0.00284 (15656)
  covalent geometry    : angle       0.47243 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 1.956 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8481 (mt)
REVERT: A  474 SER cc_start: 0.8887 (p) cc_final: 0.8459 (m)
REVERT: A  520 ASP cc_start: 0.8219 (t0) cc_final: 0.7799 (t0)
REVERT: B  410 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8502 (mt)
REVERT: B  474 SER cc_start: 0.8885 (p) cc_final: 0.8458 (m)
REVERT: B  520 ASP cc_start: 0.8223 (t0) cc_final: 0.7804 (t0)
REVERT: B  603 MET cc_start: 0.8116 (mmt) cc_final: 0.7833 (mmt)
REVERT: C  410 ILE cc_start: 0.8761 (OUTLIER) cc_final: 0.8484 (mt)
REVERT: C  474 SER cc_start: 0.8884 (p) cc_final: 0.8461 (m)
REVERT: C  520 ASP cc_start: 0.8220 (t0) cc_final: 0.7802 (t0)
REVERT: D  410 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8486 (mt)
REVERT: D  474 SER cc_start: 0.8884 (p) cc_final: 0.8462 (m)
REVERT: D  520 ASP cc_start: 0.8222 (t0) cc_final: 0.7801 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 163
  average time/residue: 0.2458
  time to fit residues: 61.7672
Evaluate side-chains
  163 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 144
  time to evaluate  : 1.622 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 133 optimal weight:    0.6980
   chunk 12 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 127 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   chunk 106 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
D 430 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.118079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2884 r_free = 0.2884 target = 0.090316 restraints weight = 17962.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 1.88
r_work: 0.2765 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2629 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8589
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  15696  Z= 0.105
  Angle     :  0.463   4.577  21404  Z= 0.248
  Chirality :  0.044   0.142   2484
  Planarity :  0.003   0.035   2712
  Dihedral  :  4.119  15.881   2280
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 1.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  :  6.09 %
    Favored  : 92.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.66 (0.19), residues: 2028
  helix:  3.70 (0.26), residues: 320
  sheet:  0.54 (0.19), residues: 748
  loop : -0.80 (0.20), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 274 
 HIS   0.002   0.001   HIS B 194 
 PHE   0.013   0.002   PHE B 523 
 TYR   0.012   0.001   TYR B 446 
 ARG   0.001   0.000   ARG D 584 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00142 (    4)
  link_NAG-ASN         : angle       0.77164 (   12)
  hydrogen bonds       : bond        0.03565 (  553)
  hydrogen bonds       : angle       4.66907 ( 1503)
  metal coordination   : bond        0.00124 (    8)
  SS BOND              : bond        0.00165 (   28)
  SS BOND              : angle       0.59843 (   56)
  covalent geometry    : bond        0.00250 (15656)
  covalent geometry    : angle       0.46269 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.670 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8434 (mt)
REVERT: A  474 SER cc_start: 0.8871 (p) cc_final: 0.8443 (m)
REVERT: A  520 ASP cc_start: 0.8254 (t0) cc_final: 0.7815 (t0)
REVERT: A  603 MET cc_start: 0.8098 (mmt) cc_final: 0.7800 (mmt)
REVERT: B  410 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8448 (mt)
REVERT: B  474 SER cc_start: 0.8871 (p) cc_final: 0.8443 (m)
REVERT: B  520 ASP cc_start: 0.8260 (t0) cc_final: 0.7818 (t0)
REVERT: B  603 MET cc_start: 0.8107 (mmt) cc_final: 0.7831 (mmt)
REVERT: C  410 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8440 (mt)
REVERT: C  474 SER cc_start: 0.8870 (p) cc_final: 0.8448 (m)
REVERT: C  520 ASP cc_start: 0.8255 (t0) cc_final: 0.7813 (t0)
REVERT: C  603 MET cc_start: 0.8101 (mmt) cc_final: 0.7804 (mmt)
REVERT: D  410 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8439 (mt)
REVERT: D  474 SER cc_start: 0.8864 (p) cc_final: 0.8447 (m)
REVERT: D  520 ASP cc_start: 0.8274 (t0) cc_final: 0.7833 (t0)
REVERT: D  603 MET cc_start: 0.8092 (mmt) cc_final: 0.7795 (mmt)
  outliers start: 18
  outliers final: 14
  residues processed: 152
  average time/residue: 0.2514
  time to fit residues: 58.7653
Evaluate side-chains
  158 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.657 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 124 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 146 optimal weight:    0.6980
   chunk 148 optimal weight:    2.9990
   chunk 90 optimal weight:    0.0770
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6740

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

Flipped N/Q/H residues before XYZ refinement:
A 430 GLN
B 430 GLN
C 430 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.117383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.089738 restraints weight = 17979.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.2867 rms_B_bonded: 1.85
r_work: 0.2762 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2628 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  15696  Z= 0.117
  Angle     :  0.466   4.573  21404  Z= 0.250
  Chirality :  0.045   0.145   2484
  Planarity :  0.004   0.034   2712
  Dihedral  :  4.100  15.025   2280
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  6.48 %
    Favored  : 92.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.64 (0.19), residues: 2028
  helix:  3.72 (0.26), residues: 320
  sheet:  0.51 (0.20), residues: 748
  loop : -0.81 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 274 
 HIS   0.003   0.001   HIS C 194 
 PHE   0.013   0.002   PHE B 523 
 TYR   0.014   0.001   TYR B 446 
 ARG   0.001   0.000   ARG A 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    4)
  link_NAG-ASN         : angle       0.77831 (   12)
  hydrogen bonds       : bond        0.03654 (  553)
  hydrogen bonds       : angle       4.63704 ( 1503)
  metal coordination   : bond        0.00164 (    8)
  SS BOND              : bond        0.00159 (   28)
  SS BOND              : angle       0.65309 (   56)
  covalent geometry    : bond        0.00286 (15656)
  covalent geometry    : angle       0.46519 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 148
  time to evaluate  : 1.898 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8451 (mt)
REVERT: A  474 SER cc_start: 0.8883 (p) cc_final: 0.8487 (m)
REVERT: A  501 MET cc_start: 0.8903 (mmt) cc_final: 0.7872 (mmt)
REVERT: A  520 ASP cc_start: 0.8229 (t0) cc_final: 0.7815 (t0)
REVERT: A  603 MET cc_start: 0.8105 (mmt) cc_final: 0.7833 (mmt)
REVERT: B  410 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8457 (mt)
REVERT: B  474 SER cc_start: 0.8884 (p) cc_final: 0.8489 (m)
REVERT: B  501 MET cc_start: 0.8907 (mmt) cc_final: 0.7876 (mmt)
REVERT: B  520 ASP cc_start: 0.8239 (t0) cc_final: 0.7821 (t0)
REVERT: B  603 MET cc_start: 0.8089 (mmt) cc_final: 0.7831 (mmt)
REVERT: C  410 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8457 (mt)
REVERT: C  474 SER cc_start: 0.8885 (p) cc_final: 0.8496 (m)
REVERT: C  501 MET cc_start: 0.8906 (mmt) cc_final: 0.7878 (mmt)
REVERT: C  520 ASP cc_start: 0.8238 (t0) cc_final: 0.7820 (t0)
REVERT: C  603 MET cc_start: 0.8106 (mmt) cc_final: 0.7833 (mmt)
REVERT: D  410 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8453 (mt)
REVERT: D  474 SER cc_start: 0.8885 (p) cc_final: 0.8493 (m)
REVERT: D  501 MET cc_start: 0.8909 (mmt) cc_final: 0.7872 (mmt)
REVERT: D  520 ASP cc_start: 0.8245 (t0) cc_final: 0.7829 (t0)
REVERT: D  603 MET cc_start: 0.8100 (mmt) cc_final: 0.7829 (mmt)
  outliers start: 20
  outliers final: 16
  residues processed: 160
  average time/residue: 0.2677
  time to fit residues: 66.1509
Evaluate side-chains
  164 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 144
  time to evaluate  : 1.911 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 LEU
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  135 GLU
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  135 GLU
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue   86 LEU
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  135 GLU
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue   86 LEU
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  135 GLU
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 77 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 171 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 184 optimal weight:    2.9990
   chunk 143 optimal weight:    0.9990
   chunk 102 optimal weight:    9.9990
   chunk 124 optimal weight:    2.9990
   overall best weight:    1.1990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.115183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.087505 restraints weight = 18144.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.2850 rms_B_bonded: 1.85
r_work: 0.2744 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  15696  Z= 0.188
  Angle     :  0.525   4.554  21404  Z= 0.281
  Chirality :  0.046   0.152   2484
  Planarity :  0.004   0.037   2712
  Dihedral  :  4.357  15.044   2280
  Min Nonbonded Distance : 2.037

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  :  6.35 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.48 (0.19), residues: 2028
  helix:  3.59 (0.27), residues: 320
  sheet:  0.41 (0.20), residues: 752
  loop : -0.92 (0.20), residues: 956

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 274 
 HIS   0.004   0.001   HIS B 194 
 PHE   0.016   0.003   PHE B 523 
 TYR   0.018   0.002   TYR D 446 
 ARG   0.001   0.000   ARG D 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00072 (    4)
  link_NAG-ASN         : angle       0.91453 (   12)
  hydrogen bonds       : bond        0.04400 (  553)
  hydrogen bonds       : angle       4.77822 ( 1503)
  metal coordination   : bond        0.00300 (    8)
  SS BOND              : bond        0.00270 (   28)
  SS BOND              : angle       0.91944 (   56)
  covalent geometry    : bond        0.00478 (15656)
  covalent geometry    : angle       0.52370 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 140
  time to evaluate  : 1.749 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8533 (mt)
REVERT: A  474 SER cc_start: 0.8917 (p) cc_final: 0.8539 (m)
REVERT: A  501 MET cc_start: 0.8933 (mmt) cc_final: 0.8104 (mmt)
REVERT: A  520 ASP cc_start: 0.8253 (t0) cc_final: 0.7810 (t0)
REVERT: A  603 MET cc_start: 0.8123 (mmt) cc_final: 0.7820 (mmt)
REVERT: B  410 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8550 (mt)
REVERT: B  474 SER cc_start: 0.8917 (p) cc_final: 0.8539 (m)
REVERT: B  501 MET cc_start: 0.8934 (mmt) cc_final: 0.8108 (mmt)
REVERT: B  520 ASP cc_start: 0.8265 (t0) cc_final: 0.7820 (t0)
REVERT: B  603 MET cc_start: 0.8116 (mmt) cc_final: 0.7825 (mmt)
REVERT: C  410 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (mt)
REVERT: C  474 SER cc_start: 0.8915 (p) cc_final: 0.8541 (m)
REVERT: C  501 MET cc_start: 0.8933 (mmt) cc_final: 0.8108 (mmt)
REVERT: C  520 ASP cc_start: 0.8269 (t0) cc_final: 0.7825 (t0)
REVERT: C  603 MET cc_start: 0.8125 (mmt) cc_final: 0.7826 (mmt)
REVERT: D  410 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8538 (mt)
REVERT: D  474 SER cc_start: 0.8916 (p) cc_final: 0.8543 (m)
REVERT: D  501 MET cc_start: 0.8934 (mmt) cc_final: 0.8106 (mmt)
REVERT: D  520 ASP cc_start: 0.8272 (t0) cc_final: 0.7828 (t0)
REVERT: D  603 MET cc_start: 0.8122 (mmt) cc_final: 0.7820 (mmt)
  outliers start: 21
  outliers final: 9
  residues processed: 156
  average time/residue: 0.2533
  time to fit residues: 60.8644
Evaluate side-chains
  153 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 1.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 146 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 114 optimal weight:    8.9990
   chunk 78 optimal weight:    0.7980
   chunk 137 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 139 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 193 optimal weight:    6.9990
   chunk 3 optimal weight:    0.5980
   overall best weight:    0.8182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.088658 restraints weight = 18233.192|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 1.87
r_work: 0.2745 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2610 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  15696  Z= 0.137
  Angle     :  0.487   5.043  21404  Z= 0.260
  Chirality :  0.045   0.145   2484
  Planarity :  0.004   0.036   2712
  Dihedral  :  4.252  15.740   2280
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.99 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.46 (0.19), residues: 2028
  helix:  3.63 (0.26), residues: 320
  sheet:  0.38 (0.20), residues: 748
  loop : -0.92 (0.20), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 274 
 HIS   0.003   0.001   HIS D 194 
 PHE   0.014   0.002   PHE D 523 
 TYR   0.015   0.001   TYR D 446 
 ARG   0.001   0.000   ARG B 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00119 (    4)
  link_NAG-ASN         : angle       0.80834 (   12)
  hydrogen bonds       : bond        0.03983 (  553)
  hydrogen bonds       : angle       4.71323 ( 1503)
  metal coordination   : bond        0.00184 (    8)
  SS BOND              : bond        0.00201 (   28)
  SS BOND              : angle       0.71807 (   56)
  covalent geometry    : bond        0.00339 (15656)
  covalent geometry    : angle       0.48555 (21336)

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

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

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4056 Ramachandran restraints generated.
    2028 Oldfield, 0 Emsley, 2028 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 1.839 
Fit side-chains
REVERT: A  410 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8486 (mt)
REVERT: A  474 SER cc_start: 0.8914 (p) cc_final: 0.8533 (m)
REVERT: A  501 MET cc_start: 0.8924 (mmt) cc_final: 0.8107 (mmt)
REVERT: A  520 ASP cc_start: 0.8267 (t0) cc_final: 0.7833 (t0)
REVERT: A  603 MET cc_start: 0.8105 (mmt) cc_final: 0.7821 (mmt)
REVERT: B  410 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (mt)
REVERT: B  474 SER cc_start: 0.8912 (p) cc_final: 0.8533 (m)
REVERT: B  501 MET cc_start: 0.8928 (mmt) cc_final: 0.8113 (mmt)
REVERT: B  520 ASP cc_start: 0.8274 (t0) cc_final: 0.7840 (t0)
REVERT: B  603 MET cc_start: 0.8088 (mmt) cc_final: 0.7812 (mmt)
REVERT: C  410 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: C  474 SER cc_start: 0.8912 (p) cc_final: 0.8535 (m)
REVERT: C  501 MET cc_start: 0.8927 (mmt) cc_final: 0.8114 (mmt)
REVERT: C  520 ASP cc_start: 0.8281 (t0) cc_final: 0.7843 (t0)
REVERT: C  603 MET cc_start: 0.8099 (mmt) cc_final: 0.7820 (mmt)
REVERT: D  410 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8493 (mt)
REVERT: D  474 SER cc_start: 0.8912 (p) cc_final: 0.8535 (m)
REVERT: D  501 MET cc_start: 0.8930 (mmt) cc_final: 0.8111 (mmt)
REVERT: D  520 ASP cc_start: 0.8285 (t0) cc_final: 0.7851 (t0)
REVERT: D  603 MET cc_start: 0.8096 (mmt) cc_final: 0.7813 (mmt)
  outliers start: 17
  outliers final: 9
  residues processed: 156
  average time/residue: 0.2578
  time to fit residues: 62.3950
Evaluate side-chains
  149 residues out of total 1820 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 136
  time to evaluate  : 1.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  128 GLN
Chi-restraints excluded: chain A residue  201 VAL
Chi-restraints excluded: chain A residue  410 ILE
Chi-restraints excluded: chain B residue   86 LEU
Chi-restraints excluded: chain B residue  128 GLN
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  410 ILE
Chi-restraints excluded: chain C residue  128 GLN
Chi-restraints excluded: chain C residue  201 VAL
Chi-restraints excluded: chain C residue  410 ILE
Chi-restraints excluded: chain D residue  128 GLN
Chi-restraints excluded: chain D residue  201 VAL
Chi-restraints excluded: chain D residue  410 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 204
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 161 optimal weight:    2.9990
   chunk 62 optimal weight:    0.5980
   chunk 143 optimal weight:    0.8980
   chunk 102 optimal weight:    7.9990
   chunk 137 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 181 optimal weight:    3.9990
   chunk 149 optimal weight:    0.6980
   chunk 145 optimal weight:    0.7980
   chunk 127 optimal weight:    0.7980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.116655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.088975 restraints weight = 18066.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2871 rms_B_bonded: 1.86
r_work: 0.2766 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2634 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8629
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  15696  Z= 0.125
  Angle     :  0.477   4.720  21404  Z= 0.256
  Chirality :  0.045   0.144   2484
  Planarity :  0.004   0.035   2712
  Dihedral  :  4.164  15.555   2280
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  7.84 %
    Favored  : 91.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.51 (0.19), residues: 2028
  helix:  3.72 (0.26), residues: 320
  sheet:  0.43 (0.20), residues: 748
  loop : -0.94 (0.19), residues: 960

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 274 
 HIS   0.003   0.001   HIS D 194 
 PHE   0.013   0.002   PHE D 523 
 TYR   0.013   0.001   TYR D 446 
 ARG   0.001   0.000   ARG C 463 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00111 (    4)
  link_NAG-ASN         : angle       0.79196 (   12)
  hydrogen bonds       : bond        0.03776 (  553)
  hydrogen bonds       : angle       4.66190 ( 1503)
  metal coordination   : bond        0.00176 (    8)
  SS BOND              : bond        0.00178 (   28)
  SS BOND              : angle       0.66858 (   56)
  covalent geometry    : bond        0.00306 (15656)
  covalent geometry    : angle       0.47649 (21336)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7869.17 seconds
wall clock time: 136 minutes 51.64 seconds (8211.64 seconds total)