Starting phenix.real_space_refine
on Thu Feb 13 22:14:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j0j_35904/02_2025/8j0j_35904_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j0j_35904/02_2025/8j0j_35904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2025/8j0j_35904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2025/8j0j_35904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2025/8j0j_35904_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j0j_35904/02_2025/8j0j_35904_trim.cif"
  }
  resolution = 2.7
  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=   0.003 sd=   0.059
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
     S      48      5.16       5
     Cl      3      4.86       5
     C    6174      2.51       5
     N    1419      2.21       5
     O    1494      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9138
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 377, 3010
          Classifications: {'peptide': 377}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 22, 'TRANS': 354}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {' CL': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {' CL': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 36
          Unusual residues: {' CL': 1, 'Y01': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 6.16, per 1000 atoms: 0.67
  Number of scatterers: 9138
  At special positions: 0
  Unit cell: (104.676, 100.386, 77.22, 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)
     Cl      3     17.00
     S      48     16.00
     O    1494      8.00
     N    1419      7.00
     C    6174      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Time building additional restraints: 2.25
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 3 sheets defined
      76.1% alpha, 0.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 152 through 159
      removed outlier: 3.577A  pdb=" N   TYR A 156 " --> pdb=" O   ASP A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 187
    Processing helix  chain 'A' and resid 189 through 192
      removed outlier: 3.601A  pdb=" N   CYS A 192 " --> pdb=" O   PRO A 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 189 through 192'
    Processing helix  chain 'A' and resid 193 through 210
      removed outlier: 3.934A  pdb=" N   GLN A 202 " --> pdb=" O   GLY A 198 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA A 210 " --> pdb=" O   TRP A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
      removed outlier: 3.555A  pdb=" N   ASN A 216 " --> pdb=" O   PRO A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 250
      removed outlier: 3.679A  pdb=" N   LEU A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 259
      removed outlier: 3.824A  pdb=" N   VAL A 254 " --> pdb=" O   TYR A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 267
      removed outlier: 3.540A  pdb=" N   ASN A 265 " --> pdb=" O   VAL A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 279
      removed outlier: 3.662A  pdb=" N   VAL A 272 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   CYS A 274 " --> pdb=" O   PRO A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 293 through 316
      removed outlier: 4.378A  pdb=" N   TRP A 297 " --> pdb=" O   HIS A 293 " (cutoff:3.500A)
      Proline residue:  A 303  - end of helix
      removed outlier: 3.621A  pdb=" N   LYS A 310 " --> pdb=" O   PHE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 327
    Processing helix  chain 'A' and resid 328 through 334
      removed outlier: 3.773A  pdb=" N   HIS A 332 " --> pdb=" O   PRO A 329 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER A 334 " --> pdb=" O   SER A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 348
      removed outlier: 4.254A  pdb=" N   PHE A 339 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE A 343 " --> pdb=" O   PHE A 339 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A 344 " --> pdb=" O   VAL A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 372
      removed outlier: 3.682A  pdb=" N   LEU A 366 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL A 367 " --> pdb=" O   ALA A 363 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 372 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 393
    Processing helix  chain 'A' and resid 394 through 409
    Processing helix  chain 'A' and resid 412 through 431
      removed outlier: 3.622A  pdb=" N   THR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE A 424 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 438
    Processing helix  chain 'A' and resid 442 through 448
    Processing helix  chain 'A' and resid 449 through 466
      removed outlier: 3.530A  pdb=" N   ALA A 455 " --> pdb=" O   PRO A 451 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A 457 " --> pdb=" O   THR A 453 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 465 " --> pdb=" O   LYS A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 499
      removed outlier: 3.627A  pdb=" N   LEU A 474 " --> pdb=" O   PRO A 470 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU A 489 " --> pdb=" O   MET A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 511
      removed outlier: 3.791A  pdb=" N   ILE A 510 " --> pdb=" O   ASP A 507 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 159
      removed outlier: 3.577A  pdb=" N   TYR B 156 " --> pdb=" O   ASP B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 187
    Processing helix  chain 'B' and resid 189 through 192
      removed outlier: 3.602A  pdb=" N   CYS B 192 " --> pdb=" O   PRO B 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 189 through 192'
    Processing helix  chain 'B' and resid 193 through 210
      removed outlier: 3.935A  pdb=" N   GLN B 202 " --> pdb=" O   GLY B 198 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA B 203 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   VAL B 204 " --> pdb=" O   SER B 200 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LEU B 205 " --> pdb=" O   SER B 201 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA B 210 " --> pdb=" O   TRP B 206 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 216
      removed outlier: 3.554A  pdb=" N   ASN B 216 " --> pdb=" O   PRO B 213 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 250
      removed outlier: 3.680A  pdb=" N   LEU B 226 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 250 through 259
      removed outlier: 3.824A  pdb=" N   VAL B 254 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 267
      removed outlier: 3.540A  pdb=" N   ASN B 265 " --> pdb=" O   VAL B 262 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 279
      removed outlier: 3.662A  pdb=" N   VAL B 272 " --> pdb=" O   PHE B 268 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   CYS B 274 " --> pdb=" O   PRO B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 286
    Processing helix  chain 'B' and resid 293 through 316
      removed outlier: 4.378A  pdb=" N   TRP B 297 " --> pdb=" O   HIS B 293 " (cutoff:3.500A)
      Proline residue:  B 303  - end of helix
      removed outlier: 3.622A  pdb=" N   LYS B 310 " --> pdb=" O   PHE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 327
    Processing helix  chain 'B' and resid 328 through 334
      removed outlier: 3.774A  pdb=" N   HIS B 332 " --> pdb=" O   PRO B 329 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   SER B 334 " --> pdb=" O   SER B 331 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 335 through 348
      removed outlier: 4.253A  pdb=" N   PHE B 339 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE B 343 " --> pdb=" O   PHE B 339 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU B 344 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 372
      removed outlier: 3.682A  pdb=" N   LEU B 366 " --> pdb=" O   PHE B 362 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL B 367 " --> pdb=" O   ALA B 363 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU B 372 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 393
    Processing helix  chain 'B' and resid 394 through 409
    Processing helix  chain 'B' and resid 412 through 431
      removed outlier: 3.622A  pdb=" N   THR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE B 424 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
    Processing helix  chain 'B' and resid 442 through 448
    Processing helix  chain 'B' and resid 449 through 466
      removed outlier: 3.530A  pdb=" N   ALA B 455 " --> pdb=" O   PRO B 451 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL B 457 " --> pdb=" O   THR B 453 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA B 465 " --> pdb=" O   LYS B 461 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 499
      removed outlier: 3.626A  pdb=" N   LEU B 474 " --> pdb=" O   PRO B 470 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU B 489 " --> pdb=" O   MET B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 511
      removed outlier: 3.790A  pdb=" N   ILE B 510 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 159
      removed outlier: 3.577A  pdb=" N   TYR C 156 " --> pdb=" O   ASP C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 183 through 187
    Processing helix  chain 'C' and resid 189 through 192
      removed outlier: 3.601A  pdb=" N   CYS C 192 " --> pdb=" O   PRO C 189 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 189 through 192'
    Processing helix  chain 'C' and resid 193 through 210
      removed outlier: 3.935A  pdb=" N   GLN C 202 " --> pdb=" O   GLY C 198 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ALA C 203 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   VAL C 204 " --> pdb=" O   SER C 200 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LEU C 205 " --> pdb=" O   SER C 201 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA C 210 " --> pdb=" O   TRP C 206 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 212 through 216
      removed outlier: 3.555A  pdb=" N   ASN C 216 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 250
      removed outlier: 3.680A  pdb=" N   LEU C 226 " --> pdb=" O   PRO C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 259
      removed outlier: 3.824A  pdb=" N   VAL C 254 " --> pdb=" O   TYR C 250 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 262 through 267
      removed outlier: 3.540A  pdb=" N   ASN C 265 " --> pdb=" O   VAL C 262 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 268 through 279
      removed outlier: 3.663A  pdb=" N   VAL C 272 " --> pdb=" O   PHE C 268 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   CYS C 274 " --> pdb=" O   PRO C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 286
    Processing helix  chain 'C' and resid 293 through 316
      removed outlier: 4.378A  pdb=" N   TRP C 297 " --> pdb=" O   HIS C 293 " (cutoff:3.500A)
      Proline residue:  C 303  - end of helix
      removed outlier: 3.622A  pdb=" N   LYS C 310 " --> pdb=" O   PHE C 306 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 322 through 327
    Processing helix  chain 'C' and resid 328 through 334
      removed outlier: 3.774A  pdb=" N   HIS C 332 " --> pdb=" O   PRO C 329 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   SER C 334 " --> pdb=" O   SER C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 335 through 348
      removed outlier: 4.254A  pdb=" N   PHE C 339 " --> pdb=" O   VAL C 335 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE C 343 " --> pdb=" O   PHE C 339 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU C 344 " --> pdb=" O   VAL C 340 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 372
      removed outlier: 3.682A  pdb=" N   LEU C 366 " --> pdb=" O   PHE C 362 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   VAL C 367 " --> pdb=" O   ALA C 363 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU C 372 " --> pdb=" O   VAL C 368 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 387 through 393
    Processing helix  chain 'C' and resid 394 through 409
    Processing helix  chain 'C' and resid 412 through 431
      removed outlier: 3.623A  pdb=" N   THR C 417 " --> pdb=" O   GLY C 413 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE C 424 " --> pdb=" O   PHE C 420 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 438
    Processing helix  chain 'C' and resid 442 through 448
    Processing helix  chain 'C' and resid 449 through 466
      removed outlier: 3.530A  pdb=" N   ALA C 455 " --> pdb=" O   PRO C 451 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL C 457 " --> pdb=" O   THR C 453 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA C 465 " --> pdb=" O   LYS C 461 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 468 through 499
      removed outlier: 3.627A  pdb=" N   LEU C 474 " --> pdb=" O   PRO C 470 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   LEU C 489 " --> pdb=" O   MET C 485 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 511
      removed outlier: 3.791A  pdb=" N   ILE C 510 " --> pdb=" O   ASP C 507 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161
      removed outlier: 3.583A  pdb=" N   GLU A 167 " --> pdb=" O   ARG A 161 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161
      removed outlier: 3.584A  pdb=" N   GLU B 167 " --> pdb=" O   ARG B 161 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 161
      removed outlier: 3.583A  pdb=" N   GLU C 167 " --> pdb=" O   ARG C 161 " (cutoff:3.500A)

    513 hydrogen bonds defined for protein.
    1377 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: 2.52

  Time building geometry restraints manager: 2.63 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: 1601
        1.33 -     1.45: 2648
        1.45 -     1.57: 5138
        1.57 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 9456
  Sorted by residual:
  bond pdb=" CBD Y01 A 902 "
       pdb=" CBF Y01 A 902 "
    ideal  model  delta    sigma   weight residual
    1.536  1.404  0.132 2.00e-02 2.50e+03 4.37e+01
  bond pdb=" CBD Y01 B 901 "
       pdb=" CBF Y01 B 901 "
    ideal  model  delta    sigma   weight residual
    1.536  1.404  0.132 2.00e-02 2.50e+03 4.36e+01
  bond pdb=" CBD Y01 C 901 "
       pdb=" CBF Y01 C 901 "
    ideal  model  delta    sigma   weight residual
    1.536  1.404  0.132 2.00e-02 2.50e+03 4.35e+01
  bond pdb=" CAV Y01 B 901 "
       pdb=" CBC Y01 B 901 "
    ideal  model  delta    sigma   weight residual
    1.523  1.434  0.089 2.00e-02 2.50e+03 1.99e+01
  bond pdb=" CAV Y01 C 901 "
       pdb=" CBC Y01 C 901 "
    ideal  model  delta    sigma   weight residual
    1.523  1.434  0.089 2.00e-02 2.50e+03 1.99e+01
  ... (remaining 9451 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.94: 12816
        2.94 -     5.89: 74
        5.89 -     8.83: 25
        8.83 -    11.77: 12
       11.77 -    14.71: 3
  Bond angle restraints: 12930
  Sorted by residual:
  angle pdb=" CAR Y01 B 901 "
        pdb=" CBC Y01 B 901 "
        pdb=" OAW Y01 B 901 "
      ideal   model   delta    sigma   weight residual
     107.47  122.18  -14.71 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" CAR Y01 A 902 "
        pdb=" CBC Y01 A 902 "
        pdb=" OAW Y01 A 902 "
      ideal   model   delta    sigma   weight residual
     107.47  122.18  -14.71 3.00e+00 1.11e-01 2.41e+01
  angle pdb=" CAR Y01 C 901 "
        pdb=" CBC Y01 C 901 "
        pdb=" OAW Y01 C 901 "
      ideal   model   delta    sigma   weight residual
     107.47  122.15  -14.68 3.00e+00 1.11e-01 2.40e+01
  angle pdb=" CAR Y01 A 902 "
        pdb=" CBC Y01 A 902 "
        pdb=" CAV Y01 A 902 "
      ideal   model   delta    sigma   weight residual
     110.42   99.65   10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" CAK Y01 C 901 "
        pdb=" CAI Y01 C 901 "
        pdb=" CAZ Y01 C 901 "
      ideal   model   delta    sigma   weight residual
     124.96  114.21   10.75 3.00e+00 1.11e-01 1.28e+01
  ... (remaining 12925 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 4830
       17.59 -    35.19: 516
       35.19 -    52.78: 168
       52.78 -    70.38: 18
       70.38 -    87.97: 6
  Dihedral angle restraints: 5538
    sinusoidal: 2208
      harmonic: 3330
  Sorted by residual:
  dihedral pdb=" CB  GLU C 257 "
           pdb=" CG  GLU C 257 "
           pdb=" CD  GLU C 257 "
           pdb=" OE1 GLU C 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.97  -87.97     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU A 257 "
           pdb=" CG  GLU A 257 "
           pdb=" CD  GLU A 257 "
           pdb=" OE1 GLU A 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.95  -87.95     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CB  GLU B 257 "
           pdb=" CG  GLU B 257 "
           pdb=" CD  GLU B 257 "
           pdb=" OE1 GLU B 257 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.95  -87.95     1      3.00e+01 1.11e-03 1.03e+01
  ... (remaining 5535 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1440
       0.127 -    0.253: 0
       0.253 -    0.380: 6
       0.380 -    0.506: 3
       0.506 -    0.633: 6
  Chirality restraints: 1455
  Sorted by residual:
  chirality pdb=" CBF Y01 A 902 "
            pdb=" CAS Y01 A 902 "
            pdb=" CBD Y01 A 902 "
            pdb=" CBH Y01 A 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -1.81   -0.63 2.00e-01 2.50e+01 1.00e+01
  chirality pdb=" CBF Y01 C 901 "
            pdb=" CAS Y01 C 901 "
            pdb=" CBD Y01 C 901 "
            pdb=" CBH Y01 C 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -1.81   -0.63 2.00e-01 2.50e+01 1.00e+01
  chirality pdb=" CBF Y01 B 901 "
            pdb=" CAS Y01 B 901 "
            pdb=" CBD Y01 B 901 "
            pdb=" CBH Y01 B 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -1.82   -0.63 2.00e-01 2.50e+01 9.91e+00
  ... (remaining 1452 not shown)

  Planarity restraints: 1563
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR C 469 "    0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO C 470 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO C 470 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 470 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR B 469 "    0.037 5.00e-02 4.00e+02   5.60e-02 5.02e+00
        pdb=" N   PRO B 470 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 470 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 470 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 469 "   -0.037 5.00e-02 4.00e+02   5.60e-02 5.02e+00
        pdb=" N   PRO A 470 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 470 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 470 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1560 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1897
        2.77 -     3.30: 8034
        3.30 -     3.84: 14001
        3.84 -     4.37: 17824
        4.37 -     4.90: 29815
  Nonbonded interactions: 71571
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 164 "
            pdb=" OH  TYR C 448 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OE2 GLU B 164 "
            pdb=" OH  TYR B 448 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OE2 GLU A 164 "
            pdb=" OH  TYR A 448 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" OD1 ASP A 166 "
            pdb=" NH2 ARG A 263 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OD1 ASP C 166 "
            pdb=" NH2 ARG C 263 "
     model   vdw
     2.264 3.120
  ... (remaining 71566 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: 0.03
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 105 through 516)
  selection = (chain 'B' and resid 105 through 516)
  selection = (chain 'C' and resid 105 through 516)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.670
  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:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.060
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
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      :  0.005   0.132   9456  Z= 0.334
  Angle     :  0.700  14.713  12930  Z= 0.281
  Chirality :  0.059   0.633   1455
  Planarity :  0.005   0.056   1563
  Dihedral  : 16.091  87.973   3378
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 21.94 %
    Favored  : 76.80 %
  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: -2.18 (0.23), residues: 1119
  helix: -1.73 (0.17), residues: 705
  sheet:  None (None), residues: 0
  loop : -0.53 (0.29), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 404 
 HIS   0.009   0.001   HIS C 387 
 PHE   0.010   0.001   PHE B 217 
 TYR   0.012   0.001   TYR A 365 
 ARG   0.002   0.000   ARG B 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 92
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  366 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8173 (mt)
REVERT: B  168 VAL cc_start: 0.8493 (t) cc_final: 0.8282 (m)
REVERT: B  450 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7467 (t80)
REVERT: C  216 ASN cc_start: 0.7809 (t0) cc_final: 0.7501 (t0)
REVERT: C  366 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8142 (mt)
REVERT: C  405 ASN cc_start: 0.8770 (t0) cc_final: 0.8474 (t160)
  outliers start: 12
  outliers final: 5
  residues processed: 101
  average time/residue: 0.8682
  time to fit residues: 96.9594
Evaluate side-chains
  95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  450 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0060
   chunk 87 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.9602

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS
C 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.140458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.118032 restraints weight = 8635.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 0.86
r_work: 0.2933 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9456  Z= 0.197
  Angle     :  0.655   7.627  12930  Z= 0.331
  Chirality :  0.043   0.180   1455
  Planarity :  0.006   0.047   1563
  Dihedral  :  8.019  59.965   1435
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.72 %
    Favored  : 79.83 %
  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: -0.00 (0.25), residues: 1119
  helix:  0.26 (0.20), residues: 711
  sheet:  None (None), residues: 0
  loop : -0.24 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 229 
 HIS   0.007   0.001   HIS C 387 
 PHE   0.020   0.002   PHE C 450 
 TYR   0.013   0.002   TYR B 408 
 ARG   0.005   0.001   ARG C 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 91
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.7756 (OUTLIER) cc_final: 0.7491 (t70)
REVERT: A  180 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6789 (pt0)
REVERT: A  322 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7706 (ptp-170)
REVERT: A  333 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8365 (tt)
REVERT: A  450 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.6594 (t80)
REVERT: B  322 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7597 (ptp-170)
REVERT: B  382 LEU cc_start: 0.7219 (tp) cc_final: 0.6921 (mt)
REVERT: B  410 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7909 (pm20)
REVERT: C  161 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7905 (ptt-90)
REVERT: C  166 ASP cc_start: 0.7488 (OUTLIER) cc_final: 0.7208 (t70)
REVERT: C  216 ASN cc_start: 0.8060 (t0) cc_final: 0.7629 (t0)
REVERT: C  322 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7809 (ptm160)
REVERT: C  450 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6647 (t80)
REVERT: C  452 MET cc_start: 0.8094 (mtp) cc_final: 0.7873 (mtt)
REVERT: C  514 LYS cc_start: 0.8216 (ttpt) cc_final: 0.7657 (tttm)
  outliers start: 33
  outliers final: 8
  residues processed: 116
  average time/residue: 1.1432
  time to fit residues: 142.7718
Evaluate side-chains
  92 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  410 GLN
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain C residue  166 ASP
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  322 ARG
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  450 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 72 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 18 optimal weight:    0.6980
   chunk 106 optimal weight:    1.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS
C 314 GLN
C 387 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.137040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.114568 restraints weight = 8651.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 0.90
r_work: 0.2881 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8658
moved from start:          0.2215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9456  Z= 0.216
  Angle     :  0.665   7.096  12930  Z= 0.337
  Chirality :  0.044   0.183   1455
  Planarity :  0.006   0.051   1563
  Dihedral  :  7.181  55.362   1431
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 16.41 %
    Favored  : 80.25 %
  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:  0.81 (0.25), residues: 1119
  helix:  1.02 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.11 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 229 
 HIS   0.009   0.002   HIS C 387 
 PHE   0.021   0.002   PHE B 450 
 TYR   0.012   0.002   TYR B 408 
 ARG   0.004   0.001   ARG A 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 75
  time to evaluate  : 0.979 
Fit side-chains
REVERT: A  322 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7721 (ptp-170)
REVERT: B  180 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6494 (pt0)
REVERT: B  190 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8140 (tp)
REVERT: B  322 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7531 (ptp-170)
REVERT: B  450 PHE cc_start: 0.8438 (OUTLIER) cc_final: 0.7100 (t80)
REVERT: C  161 ARG cc_start: 0.8310 (ptt90) cc_final: 0.8040 (ptt-90)
REVERT: C  216 ASN cc_start: 0.8077 (t0) cc_final: 0.7617 (t0)
REVERT: C  322 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7773 (ptm160)
REVERT: C  452 MET cc_start: 0.8372 (mtp) cc_final: 0.8084 (mtt)
REVERT: C  514 LYS cc_start: 0.8376 (ttpt) cc_final: 0.7715 (tttm)
  outliers start: 32
  outliers final: 17
  residues processed: 100
  average time/residue: 1.0709
  time to fit residues: 116.1029
Evaluate side-chains
  99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain C residue  218 LEU
Chi-restraints excluded: chain C residue  322 ARG
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  450 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 71 optimal weight:    4.9990
   chunk 16 optimal weight:    0.5980
   chunk 101 optimal weight:    5.9990
   chunk 43 optimal weight:    4.9990
   chunk 9 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 78 optimal weight:    6.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS
C 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.137210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.112734 restraints weight = 8638.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 0.97
r_work: 0.2861 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9456  Z= 0.211
  Angle     :  0.643   6.795  12930  Z= 0.328
  Chirality :  0.044   0.176   1455
  Planarity :  0.006   0.053   1563
  Dihedral  :  6.594  51.740   1429
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.41 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.25), residues: 1119
  helix:  1.26 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.12 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 229 
 HIS   0.008   0.002   HIS C 387 
 PHE   0.021   0.002   PHE B 450 
 TYR   0.013   0.002   TYR B 408 
 ARG   0.004   0.001   ARG A 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 83
  time to evaluate  : 1.087 
Fit side-chains
REVERT: A  322 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7550 (ptp-170)
REVERT: B  190 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8074 (tp)
REVERT: B  322 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7454 (ptp-170)
REVERT: C  161 ARG cc_start: 0.8256 (ptt90) cc_final: 0.7996 (ptt-90)
REVERT: C  216 ASN cc_start: 0.8074 (t0) cc_final: 0.7603 (t0)
REVERT: C  322 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7679 (ptm160)
REVERT: C  325 LYS cc_start: 0.8361 (OUTLIER) cc_final: 0.7948 (mtpp)
REVERT: C  452 MET cc_start: 0.8299 (mtp) cc_final: 0.8026 (mtt)
  outliers start: 26
  outliers final: 16
  residues processed: 103
  average time/residue: 1.1296
  time to fit residues: 125.5213
Evaluate side-chains
  95 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain C residue  322 ARG
Chi-restraints excluded: chain C residue  325 LYS
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  429 LEU
Chi-restraints excluded: chain C residue  450 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 67 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   chunk 92 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS
C 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.140636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.118999 restraints weight = 8691.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 0.77
r_work: 0.2976 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.2568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   9456  Z= 0.166
  Angle     :  0.576   6.374  12930  Z= 0.292
  Chirality :  0.042   0.178   1455
  Planarity :  0.006   0.052   1563
  Dihedral  :  6.270  50.225   1425
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 16.09 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.26), residues: 1119
  helix:  1.38 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.02 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 229 
 HIS   0.006   0.001   HIS B 387 
 PHE   0.021   0.001   PHE B 450 
 TYR   0.011   0.001   TYR B 408 
 ARG   0.003   0.001   ARG A 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 1.077 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6727 (pt0)
REVERT: A  322 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7599 (ptp-170)
REVERT: B  180 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6624 (pt0)
REVERT: B  190 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8061 (tp)
REVERT: B  322 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7531 (ptp-170)
REVERT: B  416 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8760 (mtt180)
REVERT: B  452 MET cc_start: 0.8262 (mtp) cc_final: 0.8056 (mtt)
REVERT: C  161 ARG cc_start: 0.8294 (ptt90) cc_final: 0.8045 (ptt-90)
REVERT: C  216 ASN cc_start: 0.8082 (t0) cc_final: 0.7608 (t0)
REVERT: C  392 MET cc_start: 0.8679 (mmm) cc_final: 0.8459 (mmt)
REVERT: C  452 MET cc_start: 0.8187 (mtp) cc_final: 0.7909 (mtt)
  outliers start: 29
  outliers final: 14
  residues processed: 103
  average time/residue: 1.2409
  time to fit residues: 137.8047
Evaluate side-chains
  96 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  429 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 40 optimal weight:    0.0270
   chunk 9 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   overall best weight:    1.5442

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS
C 387 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.134479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.105630 restraints weight = 8640.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3065 rms_B_bonded: 1.19
r_work: 0.2847 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   9456  Z= 0.232
  Angle     :  0.658   6.715  12930  Z= 0.336
  Chirality :  0.045   0.182   1455
  Planarity :  0.006   0.052   1563
  Dihedral  :  6.278  51.087   1423
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.46 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.25), residues: 1119
  helix:  1.42 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.10 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 206 
 HIS   0.008   0.002   HIS B 387 
 PHE   0.020   0.002   PHE B 450 
 TYR   0.013   0.002   TYR B 408 
 ARG   0.002   0.000   ARG A 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6873 (pt0)
REVERT: A  322 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7569 (ptp-170)
REVERT: A  325 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.7935 (mtpp)
REVERT: A  333 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8321 (tt)
REVERT: B  180 GLU cc_start: 0.7263 (OUTLIER) cc_final: 0.6748 (pt0)
REVERT: B  190 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8135 (tp)
REVERT: B  322 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7506 (ptp-170)
REVERT: B  416 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8834 (mtt180)
REVERT: C  161 ARG cc_start: 0.8354 (ptt90) cc_final: 0.8096 (ptt-90)
REVERT: C  180 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7188 (pt0)
REVERT: C  216 ASN cc_start: 0.8180 (t0) cc_final: 0.7717 (t0)
REVERT: C  452 MET cc_start: 0.8379 (mtp) cc_final: 0.8069 (mtt)
  outliers start: 29
  outliers final: 16
  residues processed: 102
  average time/residue: 1.1278
  time to fit residues: 124.1938
Evaluate side-chains
  102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 1.016 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  325 LYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  416 ARG
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain C residue  180 GLU
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  513 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0570
   chunk 96 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    1.1902

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.136269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.105210 restraints weight = 8827.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.58
r_work: 0.2873 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8595
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9456  Z= 0.198
  Angle     :  0.616   6.549  12930  Z= 0.314
  Chirality :  0.043   0.183   1455
  Planarity :  0.006   0.052   1563
  Dihedral  :  6.139  50.541   1423
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 15.46 %
    Favored  : 81.61 %
  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:  1.17 (0.25), residues: 1119
  helix:  1.33 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.08 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 206 
 HIS   0.008   0.001   HIS B 387 
 PHE   0.021   0.002   PHE B 450 
 TYR   0.012   0.002   TYR B 408 
 ARG   0.003   0.000   ARG A 472 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 77
  time to evaluate  : 1.055 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6845 (pt0)
REVERT: A  322 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7479 (ptp-170)
REVERT: B  180 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6640 (pt0)
REVERT: B  190 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8050 (tp)
REVERT: B  322 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7427 (ptp-170)
REVERT: C  161 ARG cc_start: 0.8295 (ptt90) cc_final: 0.8031 (ptt-90)
REVERT: C  180 GLU cc_start: 0.7333 (OUTLIER) cc_final: 0.7071 (pt0)
REVERT: C  216 ASN cc_start: 0.8076 (t0) cc_final: 0.7600 (t0)
REVERT: C  392 MET cc_start: 0.8647 (mmm) cc_final: 0.8420 (mmt)
REVERT: C  452 MET cc_start: 0.8260 (mtp) cc_final: 0.7937 (mtt)
  outliers start: 28
  outliers final: 19
  residues processed: 99
  average time/residue: 1.0967
  time to fit residues: 117.2625
Evaluate side-chains
  99 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain C residue  180 GLU
Chi-restraints excluded: chain C residue  201 SER
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  513 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 107 optimal weight:    0.6980
   chunk 90 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 35 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0170
   chunk 85 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.4622

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.134834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.105789 restraints weight = 8875.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3068 rms_B_bonded: 1.17
r_work: 0.2860 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2751 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8655
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   9456  Z= 0.224
  Angle     :  0.648   6.596  12930  Z= 0.332
  Chirality :  0.044   0.187   1455
  Planarity :  0.006   0.051   1563
  Dihedral  :  6.217  51.105   1423
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.26 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.25), residues: 1119
  helix:  1.44 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.10 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 206 
 HIS   0.010   0.002   HIS B 387 
 PHE   0.020   0.002   PHE B 450 
 TYR   0.013   0.002   TYR B 408 
 ARG   0.003   0.000   ARG A 110 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 74
  time to evaluate  : 1.103 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.8134 (t70) cc_final: 0.7761 (m-30)
REVERT: A  180 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6903 (pt0)
REVERT: A  322 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7557 (ptp-170)
REVERT: A  325 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7933 (mtpp)
REVERT: A  333 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8313 (tt)
REVERT: B  180 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6718 (pt0)
REVERT: B  190 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8140 (tp)
REVERT: B  322 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7505 (ptp-170)
REVERT: C  161 ARG cc_start: 0.8356 (ptt90) cc_final: 0.8096 (ptt-90)
REVERT: C  180 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7133 (pt0)
REVERT: C  216 ASN cc_start: 0.8154 (t0) cc_final: 0.7687 (t0)
REVERT: C  392 MET cc_start: 0.8724 (mmm) cc_final: 0.8497 (mmt)
REVERT: C  452 MET cc_start: 0.8336 (mtp) cc_final: 0.8044 (mtt)
  outliers start: 31
  outliers final: 18
  residues processed: 99
  average time/residue: 1.0888
  time to fit residues: 116.7227
Evaluate side-chains
  101 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  325 LYS
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain C residue  180 GLU
Chi-restraints excluded: chain C residue  201 SER
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  410 GLN
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  513 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.137125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.109800 restraints weight = 8706.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3118 rms_B_bonded: 1.12
r_work: 0.2896 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2784 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8619
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   0.023   9456  Z= 0.184
  Angle     :  0.598   6.488  12930  Z= 0.306
  Chirality :  0.042   0.184   1455
  Planarity :  0.006   0.052   1563
  Dihedral  :  6.059  50.336   1423
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.78 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.26), residues: 1119
  helix:  1.40 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.01 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 206 
 HIS   0.011   0.001   HIS B 387 
 PHE   0.021   0.001   PHE B 450 
 TYR   0.011   0.002   TYR B 408 
 ARG   0.004   0.000   ARG A 110 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  180 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.6930 (pt0)
REVERT: A  322 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7632 (ptp-170)
REVERT: B  112 LYS cc_start: 0.7736 (mttp) cc_final: 0.6613 (mmtt)
REVERT: B  161 ARG cc_start: 0.8442 (ptt90) cc_final: 0.8229 (ptt90)
REVERT: B  180 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6699 (pt0)
REVERT: B  190 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8095 (tp)
REVERT: B  322 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7538 (ptp-170)
REVERT: B  452 MET cc_start: 0.8314 (mtp) cc_final: 0.8102 (mtt)
REVERT: C  161 ARG cc_start: 0.8370 (ptt90) cc_final: 0.8117 (ptt-90)
REVERT: C  180 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7080 (pt0)
REVERT: C  216 ASN cc_start: 0.8163 (t0) cc_final: 0.7699 (t0)
REVERT: C  392 MET cc_start: 0.8677 (mmm) cc_final: 0.8427 (mmt)
REVERT: C  452 MET cc_start: 0.8259 (mtp) cc_final: 0.7961 (mtt)
REVERT: C  514 LYS cc_start: 0.8283 (ttpt) cc_final: 0.7631 (tttm)
  outliers start: 26
  outliers final: 18
  residues processed: 99
  average time/residue: 1.0496
  time to fit residues: 112.9095
Evaluate side-chains
  102 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 78
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain C residue  180 GLU
Chi-restraints excluded: chain C residue  201 SER
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  513 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 96 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 97 optimal weight:    0.3980
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.134071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.106873 restraints weight = 8786.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3080 rms_B_bonded: 1.09
r_work: 0.2844 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   9456  Z= 0.243
  Angle     :  0.669   6.637  12930  Z= 0.343
  Chirality :  0.045   0.188   1455
  Planarity :  0.006   0.051   1563
  Dihedral  :  6.284  51.483   1423
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.88 %
    Favored  : 81.30 %
  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:  1.19 (0.25), residues: 1119
  helix:  1.40 (0.20), residues: 687
  sheet:  None (None), residues: 0
  loop : -0.11 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP C 206 
 HIS   0.011   0.002   HIS B 387 
 PHE   0.020   0.002   PHE B 450 
 TYR   0.013   0.002   TYR B 408 
 ARG   0.003   0.000   ARG A 110 

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 79
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  166 ASP cc_start: 0.8134 (t70) cc_final: 0.7801 (m-30)
REVERT: A  180 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6891 (pt0)
REVERT: A  322 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7581 (ptp-170)
REVERT: A  333 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8349 (tt)
REVERT: B  112 LYS cc_start: 0.7738 (mttp) cc_final: 0.6604 (mmtt)
REVERT: B  180 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6755 (pt0)
REVERT: B  190 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8181 (tp)
REVERT: B  322 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7512 (ptp-170)
REVERT: C  161 ARG cc_start: 0.8367 (ptt90) cc_final: 0.8105 (ptt-90)
REVERT: C  180 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.7128 (pt0)
REVERT: C  216 ASN cc_start: 0.8175 (t0) cc_final: 0.7718 (t0)
REVERT: C  452 MET cc_start: 0.8362 (mtp) cc_final: 0.8058 (mtt)
  outliers start: 27
  outliers final: 18
  residues processed: 100
  average time/residue: 1.1012
  time to fit residues: 119.4057
Evaluate side-chains
  103 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 GLU
Chi-restraints excluded: chain A residue  201 SER
Chi-restraints excluded: chain A residue  322 ARG
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  410 GLN
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  485 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  166 ASP
Chi-restraints excluded: chain B residue  180 GLU
Chi-restraints excluded: chain B residue  190 ILE
Chi-restraints excluded: chain B residue  201 SER
Chi-restraints excluded: chain B residue  322 ARG
Chi-restraints excluded: chain B residue  333 LEU
Chi-restraints excluded: chain B residue  428 SER
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  513 THR
Chi-restraints excluded: chain C residue  180 GLU
Chi-restraints excluded: chain C residue  201 SER
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain C residue  366 LEU
Chi-restraints excluded: chain C residue  428 SER
Chi-restraints excluded: chain C residue  450 PHE
Chi-restraints excluded: chain C residue  513 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 66 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    7.9990
   chunk 88 optimal weight:    0.9980
   chunk 100 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 387 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.135823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.107170 restraints weight = 8775.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3083 rms_B_bonded: 1.21
r_work: 0.2866 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9456  Z= 0.204
  Angle     :  0.623   6.554  12930  Z= 0.319
  Chirality :  0.043   0.186   1455
  Planarity :  0.006   0.052   1563
  Dihedral  :  6.153  50.864   1423
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 16.20 %
    Favored  : 81.09 %
  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:  1.16 (0.25), residues: 1119
  helix:  1.31 (0.20), residues: 708
  sheet:  None (None), residues: 0
  loop : -0.06 (0.30), residues: 411

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 206 
 HIS   0.011   0.002   HIS B 387 
 PHE   0.021   0.002   PHE B 450 
 TYR   0.012   0.002   TYR B 408 
 ARG   0.004   0.000   ARG A 110 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5431.40 seconds
wall clock time: 96 minutes 37.81 seconds (5797.81 seconds total)