Starting phenix.real_space_refine
on Fri Jan 17 09:59:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vt2_43516/01_2025/8vt2_43516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vt2_43516/01_2025/8vt2_43516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.14
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vt2_43516/01_2025/8vt2_43516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vt2_43516/01_2025/8vt2_43516.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vt2_43516/01_2025/8vt2_43516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vt2_43516/01_2025/8vt2_43516.cif"
  }
  resolution = 3.14
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.055
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    6678      2.51       5
     N    1818      2.21       5
     O    2115      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 56 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 10674
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 3477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3477
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 14, 'TRANS': 439}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3477
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 14, 'TRANS': 439}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 3477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3477
          Classifications: {'peptide': 454}
          Link IDs: {'PTRANS': 14, 'TRANS': 439}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "H"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "I"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.61, per 1000 atoms: 0.71
  Number of scatterers: 10674
  At special positions: 0
  Unit cell: (83.424, 87.216, 133.668, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    2115      8.00
     N    1818      7.00
     C    6678      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 350 " - pdb=" SG  CYS B 361 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
      " NAG D   2 " - " BMA D   3 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG F   2 " - " BMA F   3 "
      " NAG G   1 " - " NAG G   2 "
      " NAG H   1 " - " NAG H   2 "
      " NAG H   2 " - " BMA H   3 "
      " NAG I   1 " - " NAG I   2 "
    NAG-ASN
      " NAG A 501 " - " ASN A 353 "
      " NAG B 501 " - " ASN B 353 "
      " NAG D   1 " - " ASN A 172 "
      " NAG E   1 " - " ASN A  57 "
      " NAG F   1 " - " ASN B 172 "
      " NAG G   1 " - " ASN B  57 "
      " NAG H   1 " - " ASN C 172 "
      " NAG I   1 " - " ASN C  57 "
  Time building additional restraints: 3.03
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2550

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 14 sheets defined
      36.7% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 58
    Processing helix  chain 'A' and resid 65 through 81
      removed outlier: 3.653A  pdb=" N   THR A  69 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 84
      No H-bonds generated for 'chain 'A' and resid 82 through 84'
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 3.734A  pdb=" N   ALA A 109 " --> pdb=" O   LEU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 129
      removed outlier: 3.846A  pdb=" N   THR A 127 " --> pdb=" O   ALA A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 141
    Processing helix  chain 'A' and resid 163 through 172
      removed outlier: 3.558A  pdb=" N   ASP A 167 " --> pdb=" O   ARG A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 187 through 197
      removed outlier: 3.521A  pdb=" N   VAL A 191 " --> pdb=" O   LEU A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 210
      removed outlier: 3.638A  pdb=" N   ASN A 210 " --> pdb=" O   GLN A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 232
    Processing helix  chain 'A' and resid 237 through 247
    Processing helix  chain 'A' and resid 248 through 253
    Processing helix  chain 'A' and resid 322 through 326
      removed outlier: 3.720A  pdb=" N   CYS A 326 " --> pdb=" O   GLU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 340
      removed outlier: 3.899A  pdb=" N   GLY A 340 " --> pdb=" O   THR A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 344 through 352
      removed outlier: 3.871A  pdb=" N   LYS A 348 " --> pdb=" O   GLU A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 445
    Processing helix  chain 'A' and resid 460 through 480
    Processing helix  chain 'B' and resid 54 through 58
    Processing helix  chain 'B' and resid 65 through 82
      removed outlier: 3.653A  pdb=" N   THR B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS B  82 " --> pdb=" O   LEU B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 104 through 109
      removed outlier: 3.836A  pdb=" N   ALA B 109 " --> pdb=" O   LEU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 129
      removed outlier: 3.840A  pdb=" N   THR B 127 " --> pdb=" O   ALA B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 141
    Processing helix  chain 'B' and resid 163 through 172
      removed outlier: 3.645A  pdb=" N   ASP B 167 " --> pdb=" O   ARG B 163 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 177
      removed outlier: 3.536A  pdb=" N   ALA B 176 " --> pdb=" O   ASN B 172 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 197
      removed outlier: 3.535A  pdb=" N   VAL B 191 " --> pdb=" O   LEU B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 210
      removed outlier: 3.639A  pdb=" N   ASN B 210 " --> pdb=" O   GLN B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 232
    Processing helix  chain 'B' and resid 237 through 247
    Processing helix  chain 'B' and resid 248 through 253
    Processing helix  chain 'B' and resid 338 through 340
      No H-bonds generated for 'chain 'B' and resid 338 through 340'
    Processing helix  chain 'B' and resid 344 through 350
      removed outlier: 3.885A  pdb=" N   LYS B 348 " --> pdb=" O   GLU B 345 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   CYS B 350 " --> pdb=" O   SER B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 480
    Processing helix  chain 'C' and resid 54 through 58
    Processing helix  chain 'C' and resid 66 through 81
    Processing helix  chain 'C' and resid 82 through 84
      No H-bonds generated for 'chain 'C' and resid 82 through 84'
    Processing helix  chain 'C' and resid 104 through 109
      removed outlier: 3.916A  pdb=" N   ALA C 109 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 129
      removed outlier: 3.663A  pdb=" N   ALA C 115 " --> pdb=" O   GLY C 111 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   THR C 127 " --> pdb=" O   ALA C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 130 through 141
    Processing helix  chain 'C' and resid 163 through 172
    Processing helix  chain 'C' and resid 172 through 177
    Processing helix  chain 'C' and resid 187 through 197
    Processing helix  chain 'C' and resid 197 through 210
      removed outlier: 3.676A  pdb=" N   ASN C 210 " --> pdb=" O   GLN C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 223 through 232
    Processing helix  chain 'C' and resid 237 through 247
    Processing helix  chain 'C' and resid 248 through 253
    Processing helix  chain 'C' and resid 338 through 340
      No H-bonds generated for 'chain 'C' and resid 338 through 340'
    Processing helix  chain 'C' and resid 344 through 350
      removed outlier: 3.898A  pdb=" N   CYS C 350 " --> pdb=" O   SER C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 441 through 446
      removed outlier: 3.766A  pdb=" N   PHE C 446 " --> pdb=" O   SER C 443 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 480
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 24
      removed outlier: 7.138A  pdb=" N   SER A  29 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   ALA A 288 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   ILE A  31 " --> pdb=" O   VAL A 286 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL A 286 " --> pdb=" O   ILE A  31 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   GLU A  33 " --> pdb=" O   TRP A 284 " (cutoff:3.500A)
      removed outlier: 7.176A  pdb=" N   TRP A 284 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   TYR A  35 " --> pdb=" O   PRO A 282 " (cutoff:3.500A)
      removed outlier: 5.689A  pdb=" N   SER A  37 " --> pdb=" O   ASP A 280 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A 278 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 316 through 320
    current: chain 'A' and resid 332 through 334
    Processing sheet with id=AA2, first strand: chain 'A' and resid 146 through 150
      removed outlier: 9.421A  pdb=" N   TRP A  43 " --> pdb=" O   ARG A 156 " (cutoff:3.500A)
      removed outlier: 9.357A  pdb=" N   LEU A 158 " --> pdb=" O   TRP A  43 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   THR A  45 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 7.835A  pdb=" N   THR A 160 " --> pdb=" O   THR A  45 " (cutoff:3.500A)
      removed outlier: 5.934A  pdb=" N   VAL A  47 " --> pdb=" O   THR A 160 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   VAL A 162 " --> pdb=" O   VAL A  47 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   THR A  49 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   SER A 266 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   VAL A 262 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   ILE A 268 " --> pdb=" O   ILE A 260 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY A 257 " --> pdb=" O   THR A 214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295
    Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 376
    Processing sheet with id=AA5, first strand: chain 'A' and resid 399 through 402
    Processing sheet with id=AA6, first strand: chain 'B' and resid 20 through 24
      removed outlier: 7.183A  pdb=" N   SER B  29 " --> pdb=" O   ALA B 288 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ALA B 288 " --> pdb=" O   SER B  29 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   ILE B  31 " --> pdb=" O   VAL B 286 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   VAL B 286 " --> pdb=" O   ILE B  31 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   GLU B  33 " --> pdb=" O   TRP B 284 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   TRP B 284 " --> pdb=" O   GLU B  33 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   TYR B  35 " --> pdb=" O   PRO B 282 " (cutoff:3.500A)
      removed outlier: 5.649A  pdb=" N   SER B  37 " --> pdb=" O   ASP B 280 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL B 278 " --> pdb=" O   LEU B  39 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 316 through 320
    current: chain 'B' and resid 332 through 336
    Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 150
      removed outlier: 8.307A  pdb=" N   ARG B 156 " --> pdb=" O   TRP B  43 " (cutoff:3.500A)
      removed outlier: 5.398A  pdb=" N   THR B  45 " --> pdb=" O   ARG B 156 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   SER B 266 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL B 262 " --> pdb=" O   SER B 266 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE B 268 " --> pdb=" O   ILE B 260 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLY B 257 " --> pdb=" O   THR B 214 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 295
    Processing sheet with id=AA9, first strand: chain 'B' and resid 372 through 376
    Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 402
    Processing sheet with id=AB2, first strand: chain 'C' and resid 20 through 24
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 29 through 51
    current: chain 'C' and resid 156 through 162
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 156 through 162
    current: chain 'C' and resid 256 through 263
      removed outlier: 6.702A  pdb=" N   ILE C 268 " --> pdb=" O   ILE C 260 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   VAL C 262 " --> pdb=" O   SER C 266 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   SER C 266 " --> pdb=" O   VAL C 262 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 316 through 320
    current: chain 'C' and resid 332 through 336
    Processing sheet with id=AB3, first strand: chain 'C' and resid 291 through 295
      removed outlier: 7.522A  pdb=" N   THR C 365 " --> pdb=" O   PHE C 456 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   PHE C 456 " --> pdb=" O   THR C 365 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 372 through 376
    Processing sheet with id=AB5, first strand: chain 'C' and resid 399 through 402

    493 hydrogen bonds defined for protein.
    1290 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.77

  Time building geometry restraints manager: 3.43 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2943
        1.33 -     1.45: 1680
        1.45 -     1.57: 6115
        1.57 -     1.69: 2
        1.69 -     1.81: 84
  Bond restraints: 10824
  Sorted by residual:
  bond pdb=" C1  NAG E   1 "
       pdb=" O5  NAG E   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.465 -0.059 2.00e-02 2.50e+03 8.59e+00
  bond pdb=" C1  BMA D   3 "
       pdb=" C2  BMA D   3 "
    ideal  model  delta    sigma   weight residual
    1.519  1.571 -0.052 2.00e-02 2.50e+03 6.65e+00
  bond pdb=" CB  THR C 160 "
       pdb=" CG2 THR C 160 "
    ideal  model  delta    sigma   weight residual
    1.521  1.438  0.083 3.30e-02 9.18e+02 6.29e+00
  bond pdb=" CB  THR A 160 "
       pdb=" CG2 THR A 160 "
    ideal  model  delta    sigma   weight residual
    1.521  1.440  0.081 3.30e-02 9.18e+02 5.98e+00
  bond pdb=" C1  NAG E   2 "
       pdb=" O5  NAG E   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.97e+00
  ... (remaining 10819 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 13767
        1.77 -     3.54: 736
        3.54 -     5.30: 125
        5.30 -     7.07: 24
        7.07 -     8.84: 9
  Bond angle restraints: 14661
  Sorted by residual:
  angle pdb=" N   ILE A 420 "
        pdb=" CA  ILE A 420 "
        pdb=" C   ILE A 420 "
      ideal   model   delta    sigma   weight residual
     109.46  103.74    5.72 1.38e+00 5.25e-01 1.72e+01
  angle pdb=" N   ILE C 352 "
        pdb=" CA  ILE C 352 "
        pdb=" C   ILE C 352 "
      ideal   model   delta    sigma   weight residual
     112.12  109.00    3.12 8.40e-01 1.42e+00 1.38e+01
  angle pdb=" N   ARG A 248 "
        pdb=" CA  ARG A 248 "
        pdb=" C   ARG A 248 "
      ideal   model   delta    sigma   weight residual
     110.80  118.22   -7.42 2.13e+00 2.20e-01 1.21e+01
  angle pdb=" N   ARG C 248 "
        pdb=" CA  ARG C 248 "
        pdb=" C   ARG C 248 "
      ideal   model   delta    sigma   weight residual
     110.80  118.06   -7.26 2.13e+00 2.20e-01 1.16e+01
  angle pdb=" C   THR C 411 "
        pdb=" N   ASN C 412 "
        pdb=" CA  ASN C 412 "
      ideal   model   delta    sigma   weight residual
     122.56  116.85    5.71 1.72e+00 3.38e-01 1.10e+01
  ... (remaining 14656 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.72: 6360
       21.72 -    43.43: 352
       43.43 -    65.15: 76
       65.15 -    86.86: 29
       86.86 -   108.58: 14
  Dihedral angle restraints: 6831
    sinusoidal: 2886
      harmonic: 3945
  Sorted by residual:
  dihedral pdb=" CA  ILE A 420 "
           pdb=" C   ILE A 420 "
           pdb=" N   ASP A 421 "
           pdb=" CA  ASP A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.48  -24.52     0      5.00e+00 4.00e-02 2.41e+01
  dihedral pdb=" CA  ILE B 420 "
           pdb=" C   ILE B 420 "
           pdb=" N   ASP B 421 "
           pdb=" CA  ASP B 421 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.55  -23.45     0      5.00e+00 4.00e-02 2.20e+01
  dihedral pdb=" CA  ILE C 420 "
           pdb=" C   ILE C 420 "
           pdb=" N   ASP C 421 "
           pdb=" CA  ASP C 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.53  -22.47     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 6828 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.140: 1753
       0.140 -    0.279: 27
       0.279 -    0.419: 3
       0.419 -    0.558: 0
       0.558 -    0.698: 1
  Chirality restraints: 1784
  Sorted by residual:
  chirality pdb=" C1  NAG G   1 "
            pdb=" ND2 ASN B  57 "
            pdb=" C2  NAG G   1 "
            pdb=" O5  NAG G   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.70   -0.70 2.00e-01 2.50e+01 1.22e+01
  chirality pdb=" CB  THR C 357 "
            pdb=" CA  THR C 357 "
            pdb=" OG1 THR C 357 "
            pdb=" CG2 THR C 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.24    0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  THR A 357 "
            pdb=" CA  THR A 357 "
            pdb=" OG1 THR A 357 "
            pdb=" CG2 THR A 357 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.30 2.00e-01 2.50e+01 2.20e+00
  ... (remaining 1781 not shown)

  Planarity restraints: 1865
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 193 "    0.021 2.00e-02 2.50e+03   2.58e-02 1.16e+01
        pdb=" CG  PHE C 193 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 193 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 193 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 193 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 193 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 193 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 193 "    0.021 2.00e-02 2.50e+03   2.57e-02 1.15e+01
        pdb=" CG  PHE A 193 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 193 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 193 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 193 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 193 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 193 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C  63 "    0.033 5.00e-02 4.00e+02   4.95e-02 3.91e+00
        pdb=" N   PRO C  64 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO C  64 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO C  64 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1862 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 439
        2.70 -     3.25: 9958
        3.25 -     3.80: 15146
        3.80 -     4.35: 20625
        4.35 -     4.90: 36543
  Nonbonded interactions: 82711
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C  45 "
            pdb=" OE1 GLN C 272 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   ASP C  62 "
            pdb=" O6  BMA F   3 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" OE2 GLU B 305 "
            pdb=" OG  SER B 364 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OE2 GLU A 305 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.152 3.040
  nonbonded pdb=" OG1 THR B  45 "
            pdb=" OE1 GLN B 272 "
     model   vdw
     2.162 3.040
  ... (remaining 82706 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.990
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
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      :  0.014   0.086  10824  Z= 0.876
  Angle     :  0.957   8.841  14661  Z= 0.511
  Chirality :  0.064   0.698   1784
  Planarity :  0.006   0.049   1857
  Dihedral  : 15.923 108.580   4278
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.22), residues: 1350
  helix:  0.14 (0.25), residues: 408
  sheet: -0.02 (0.28), residues: 345
  loop : -2.13 (0.23), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP B 473 
 HIS   0.005   0.002   HIS C 435 
 PHE   0.059   0.003   PHE C 193 
 TYR   0.022   0.004   TYR C 310 
 ARG   0.008   0.001   ARG B 205 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
REVERT: C   54 ASP cc_start: 0.7987 (p0) cc_final: 0.7681 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.3453
  time to fit residues: 48.6163
Evaluate side-chains
  92 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 69 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 105 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
B 402 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.130951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.099496 restraints weight = 11407.847|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.32
r_work: 0.2944 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7495
moved from start:          0.1015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10824  Z= 0.180
  Angle     :  0.621   7.257  14661  Z= 0.319
  Chirality :  0.048   0.488   1784
  Planarity :  0.005   0.047   1857
  Dihedral  : 12.257  94.206   1836
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  3.70 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.71 (0.22), residues: 1350
  helix:  0.69 (0.25), residues: 429
  sheet:  0.16 (0.27), residues: 342
  loop : -1.78 (0.25), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 284 
 HIS   0.002   0.001   HIS A 332 
 PHE   0.019   0.001   PHE A 193 
 TYR   0.011   0.001   TYR A 385 
 ARG   0.004   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 1.343 
Fit side-chains
REVERT: B  179 LYS cc_start: 0.7896 (mmtm) cc_final: 0.7680 (mmtm)
  outliers start: 6
  outliers final: 5
  residues processed: 104
  average time/residue: 0.3095
  time to fit residues: 43.2480
Evaluate side-chains
  97 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   61 SER
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  293 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9980
   chunk 130 optimal weight:    0.4980
   chunk 125 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 57 optimal weight:    0.0970
   chunk 85 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
A 422 ASN
A 457 ASN
** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 353 ASN
C 422 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.131570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.098852 restraints weight = 11629.673|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.47
r_work: 0.2983 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2821 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10824  Z= 0.156
  Angle     :  0.563   7.186  14661  Z= 0.286
  Chirality :  0.047   0.539   1784
  Planarity :  0.004   0.045   1857
  Dihedral  :  9.795  81.802   1836
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.04 %
    Favored  : 94.96 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  5.94 %
    Favored  : 93.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.23), residues: 1350
  helix:  1.16 (0.25), residues: 435
  sheet:  0.34 (0.28), residues: 345
  loop : -1.54 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.001   0.001   HIS A 332 
 PHE   0.015   0.001   PHE C 193 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.005   0.000   ARG A 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 1.432 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7961 (m-30) cc_final: 0.7691 (m-30)
REVERT: B  179 LYS cc_start: 0.7907 (mmtm) cc_final: 0.7660 (mmtm)
REVERT: B  296 LYS cc_start: 0.8497 (mmmt) cc_final: 0.8214 (mmmm)
REVERT: C   62 ASP cc_start: 0.7780 (m-30) cc_final: 0.7373 (m-30)
REVERT: C  156 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7102 (ttt-90)
  outliers start: 4
  outliers final: 2
  residues processed: 100
  average time/residue: 0.2845
  time to fit residues: 39.2371
Evaluate side-chains
  91 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 1.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  293 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 26 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 86 optimal weight:    0.0000
   chunk 16 optimal weight:    1.9990
   chunk 109 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN
** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 466 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.131464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.098677 restraints weight = 11496.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.46
r_work: 0.2975 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2817 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10824  Z= 0.183
  Angle     :  0.555   7.468  14661  Z= 0.281
  Chirality :  0.047   0.524   1784
  Planarity :  0.004   0.043   1857
  Dihedral  :  8.650  72.385   1836
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  6.72 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.06 (0.23), residues: 1350
  helix:  1.31 (0.25), residues: 435
  sheet:  0.39 (0.28), residues: 345
  loop : -1.40 (0.26), residues: 570

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 284 
 HIS   0.001   0.001   HIS A 332 
 PHE   0.016   0.001   PHE C 193 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.005   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7941 (m-30) cc_final: 0.7738 (m-30)
REVERT: B  197 ASN cc_start: 0.8347 (p0) cc_final: 0.8071 (p0)
REVERT: B  296 LYS cc_start: 0.8526 (mmmt) cc_final: 0.8237 (mmmm)
REVERT: C   62 ASP cc_start: 0.7819 (m-30) cc_final: 0.7394 (m-30)
REVERT: C  197 ASN cc_start: 0.8210 (p0) cc_final: 0.7928 (p0)
  outliers start: 8
  outliers final: 5
  residues processed: 103
  average time/residue: 0.2802
  time to fit residues: 39.7842
Evaluate side-chains
  99 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  293 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   chunk 40 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 106 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 131 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.132454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.099683 restraints weight = 11456.249|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.46
r_work: 0.2988 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10824  Z= 0.156
  Angle     :  0.539   8.035  14661  Z= 0.272
  Chirality :  0.046   0.561   1784
  Planarity :  0.004   0.043   1857
  Dihedral  :  7.990  63.544   1836
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  8.53 %
    Favored  : 90.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.23), residues: 1350
  helix:  1.44 (0.25), residues: 438
  sheet:  0.51 (0.28), residues: 345
  loop : -1.36 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 284 
 HIS   0.001   0.001   HIS C 332 
 PHE   0.012   0.001   PHE C 193 
 TYR   0.011   0.001   TYR A 385 
 ARG   0.006   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 92
  time to evaluate  : 1.252 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7927 (m-30) cc_final: 0.7721 (m-30)
REVERT: B  197 ASN cc_start: 0.8279 (p0) cc_final: 0.7995 (p0)
REVERT: B  296 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8220 (mmmm)
REVERT: C   62 ASP cc_start: 0.7778 (m-30) cc_final: 0.7330 (m-30)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.2682
  time to fit residues: 37.3058
Evaluate side-chains
  98 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  293 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 75 optimal weight:    5.9990
   chunk 95 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 116 optimal weight:    5.9990
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
C 353 ASN
** C 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.132590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.100545 restraints weight = 11461.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.35
r_work: 0.2932 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10824  Z= 0.192
  Angle     :  0.549   8.166  14661  Z= 0.278
  Chirality :  0.047   0.569   1784
  Planarity :  0.004   0.042   1857
  Dihedral  :  7.428  58.296   1836
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  9.04 %
    Favored  : 90.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.23), residues: 1350
  helix:  1.46 (0.25), residues: 438
  sheet:  0.51 (0.28), residues: 345
  loop : -1.33 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 284 
 HIS   0.002   0.001   HIS C 332 
 PHE   0.015   0.001   PHE C 193 
 TYR   0.009   0.001   TYR A 385 
 ARG   0.006   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.199 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7710 (m-30) cc_final: 0.7381 (m-30)
REVERT: B  197 ASN cc_start: 0.7948 (p0) cc_final: 0.7636 (p0)
REVERT: B  296 LYS cc_start: 0.8505 (mmmt) cc_final: 0.8217 (mmmm)
REVERT: C   62 ASP cc_start: 0.7663 (m-30) cc_final: 0.7212 (m-30)
  outliers start: 10
  outliers final: 8
  residues processed: 105
  average time/residue: 0.2692
  time to fit residues: 39.3648
Evaluate side-chains
  102 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  293 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 120 optimal weight:    2.9990
   chunk 62 optimal weight:    2.9990
   chunk 102 optimal weight:    4.9990
   chunk 111 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 115 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 434 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 = 0.3428 r_free = 0.3428 target = 0.129074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.096421 restraints weight = 11729.614|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.48
r_work: 0.2924 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10824  Z= 0.277
  Angle     :  0.589   8.198  14661  Z= 0.299
  Chirality :  0.048   0.559   1784
  Planarity :  0.004   0.043   1857
  Dihedral  :  7.203  59.571   1836
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.82 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.23), residues: 1350
  helix:  1.42 (0.25), residues: 429
  sheet:  0.40 (0.28), residues: 345
  loop : -1.36 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 284 
 HIS   0.002   0.001   HIS C 332 
 PHE   0.019   0.001   PHE C 193 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.006   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 1.221 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7812 (m-30) cc_final: 0.7533 (m-30)
REVERT: B  197 ASN cc_start: 0.8479 (p0) cc_final: 0.8193 (p0)
REVERT: B  296 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8311 (mmmm)
REVERT: C   62 ASP cc_start: 0.7755 (m-30) cc_final: 0.7353 (m-30)
REVERT: C  197 ASN cc_start: 0.8326 (p0) cc_final: 0.8050 (p0)
  outliers start: 8
  outliers final: 8
  residues processed: 102
  average time/residue: 0.2816
  time to fit residues: 39.3440
Evaluate side-chains
  102 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  293 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 44 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 131 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.7384

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 434 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 = 0.3479 r_free = 0.3479 target = 0.132465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.100534 restraints weight = 11413.809|
|-----------------------------------------------------------------------------|
r_work (start): 0.3021 rms_B_bonded: 2.38
r_work: 0.2896 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2739 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.1555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10824  Z= 0.273
  Angle     :  0.587   7.979  14661  Z= 0.299
  Chirality :  0.048   0.539   1784
  Planarity :  0.004   0.043   1857
  Dihedral  :  6.951  59.627   1836
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.25 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.23), residues: 1350
  helix:  1.37 (0.25), residues: 429
  sheet:  0.35 (0.28), residues: 345
  loop : -1.40 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.002   0.001   HIS C 332 
 PHE   0.018   0.001   PHE C 193 
 TYR   0.010   0.002   TYR B 310 
 ARG   0.006   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.241 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7776 (m-30) cc_final: 0.7465 (m-30)
REVERT: B  197 ASN cc_start: 0.8401 (p0) cc_final: 0.8116 (p0)
REVERT: B  296 LYS cc_start: 0.8572 (mmmt) cc_final: 0.8288 (mmmm)
REVERT: C   62 ASP cc_start: 0.7707 (m-30) cc_final: 0.7296 (m-30)
REVERT: C  197 ASN cc_start: 0.8232 (p0) cc_final: 0.7956 (p0)
  outliers start: 11
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2765
  time to fit residues: 40.8124
Evaluate side-chains
  105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  293 SER
Chi-restraints excluded: chain C residue  357 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 108 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 109 optimal weight:    2.9990
   chunk 94 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 434 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 = 0.3481 r_free = 0.3481 target = 0.132719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.100606 restraints weight = 11485.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.39
r_work: 0.2914 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10824  Z= 0.267
  Angle     :  0.587   7.655  14661  Z= 0.299
  Chirality :  0.048   0.533   1784
  Planarity :  0.004   0.044   1857
  Dihedral  :  6.747  59.610   1836
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 10.34 %
    Favored  : 88.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.23), residues: 1350
  helix:  1.37 (0.25), residues: 429
  sheet:  0.31 (0.28), residues: 345
  loop : -1.40 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.002   0.001   HIS C 332 
 PHE   0.017   0.001   PHE C 193 
 TYR   0.010   0.001   TYR A 269 
 ARG   0.006   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 1.488 
Fit side-chains
REVERT: A   62 ASP cc_start: 0.7765 (m-30) cc_final: 0.7453 (m-30)
REVERT: B  197 ASN cc_start: 0.8435 (p0) cc_final: 0.8150 (p0)
REVERT: B  296 LYS cc_start: 0.8573 (mmmt) cc_final: 0.8290 (mmmm)
REVERT: C   62 ASP cc_start: 0.7715 (m-30) cc_final: 0.7266 (m-30)
REVERT: C  197 ASN cc_start: 0.8259 (p0) cc_final: 0.7983 (p0)
  outliers start: 12
  outliers final: 11
  residues processed: 109
  average time/residue: 0.2476
  time to fit residues: 37.4475
Evaluate side-chains
  107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  293 SER
Chi-restraints excluded: chain C residue  357 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 118 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 119 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 125 optimal weight:    3.9990
   chunk 97 optimal weight:    4.9990
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 434 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 = 0.3458 r_free = 0.3458 target = 0.130820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.098773 restraints weight = 11575.116|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 2.40
r_work: 0.2874 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10824  Z= 0.352
  Angle     :  0.627   7.407  14661  Z= 0.319
  Chirality :  0.049   0.526   1784
  Planarity :  0.004   0.044   1857
  Dihedral  :  6.732  59.427   1836
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.51 %
    Favored  : 88.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.23), residues: 1350
  helix:  1.20 (0.25), residues: 429
  sheet:  0.19 (0.28), residues: 345
  loop : -1.47 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.002   0.001   HIS A 332 
 PHE   0.021   0.002   PHE C 193 
 TYR   0.011   0.002   TYR B 310 
 ARG   0.006   0.000   ARG C 175 

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

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

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2700 Ramachandran restraints generated.
    1350 Oldfield, 0 Emsley, 1350 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 1.261 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASP cc_start: 0.7754 (m-30) cc_final: 0.7428 (m-30)
REVERT: B  197 ASN cc_start: 0.8496 (p0) cc_final: 0.8201 (p0)
REVERT: B  296 LYS cc_start: 0.8543 (mmmt) cc_final: 0.8261 (mmmm)
REVERT: C   62 ASP cc_start: 0.7716 (m-30) cc_final: 0.7246 (m-30)
REVERT: C  197 ASN cc_start: 0.8338 (p0) cc_final: 0.8047 (p0)
  outliers start: 11
  outliers final: 11
  residues processed: 106
  average time/residue: 0.2737
  time to fit residues: 40.3520
Evaluate side-chains
  105 residues out of total 1161 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 THR
Chi-restraints excluded: chain A residue  281 THR
Chi-restraints excluded: chain B residue   27 SER
Chi-restraints excluded: chain B residue  281 THR
Chi-restraints excluded: chain B residue  357 THR
Chi-restraints excluded: chain B residue  399 ILE
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain C residue  162 VAL
Chi-restraints excluded: chain C residue  281 THR
Chi-restraints excluded: chain C residue  293 SER
Chi-restraints excluded: chain C residue  357 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 117 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 121 optimal weight:    4.9990
   chunk 60 optimal weight:    7.9990
   chunk 51 optimal weight:    4.9990
   chunk 81 optimal weight:    0.5980
   overall best weight:    1.8386

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

Flipped N/Q/H residues before XYZ refinement:
B 206 GLN
** B 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 434 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 = 0.3437 r_free = 0.3437 target = 0.129392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.097563 restraints weight = 11533.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3015 rms_B_bonded: 2.35
r_work: 0.2893 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10824  Z= 0.288
  Angle     :  0.599   7.318  14661  Z= 0.306
  Chirality :  0.048   0.522   1784
  Planarity :  0.004   0.044   1857
  Dihedral  :  6.563  59.836   1836
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  : 10.59 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.23), residues: 1350
  helix:  1.24 (0.25), residues: 429
  sheet:  0.21 (0.28), residues: 345
  loop : -1.46 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 284 
 HIS   0.002   0.001   HIS C 332 
 PHE   0.018   0.001   PHE C 193 
 TYR   0.011   0.002   TYR A 269 
 ARG   0.006   0.000   ARG C 175 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5024.35 seconds
wall clock time: 90 minutes 28.21 seconds (5428.21 seconds total)