Starting phenix.real_space_refine
on Mon Aug 25 02:42:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tz2_41731/08_2025/8tz2_41731_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tz2_41731/08_2025/8tz2_41731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tz2_41731/08_2025/8tz2_41731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tz2_41731/08_2025/8tz2_41731.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tz2_41731/08_2025/8tz2_41731_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tz2_41731/08_2025/8tz2_41731_trim.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.002 sd=   0.089
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: 7
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      87      5.16       5
     Na      6      4.78       5
     C    8256      2.51       5
     N    1926      2.21       5
     O    2145      1.98       5
     H   12165      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 24591
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 8129
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 8129
          Classifications: {'peptide': 533}
          Link IDs: {'PTRANS': 18, 'TRANS': 514}
          Unresolved non-hydrogen bonds: 102
          Unresolved non-hydrogen angles: 122
          Unresolved non-hydrogen dihedrals: 89
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'ASP:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 69
    Chain: "A"
      Number of atoms: 66
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 66
          Unusual residues: {' NA': 2, 'LBN': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 40
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 8.63, per 1000 atoms: 0.35
  Number of scatterers: 24591
  At special positions: 0
  Unit cell: (130.68, 127.44, 75.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      87     16.00
     P       6     15.00
     Na      6     11.00
     O    2145      8.00
     N    1926      7.00
     C    8256      6.00
     H   12165      1.00
    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: 2.11
  Conformation dependent library (CDL) restraints added in 716.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2946

  Finding SS restraints...
    Secondary structure from input PDB file:
      90 helices and 3 sheets defined
      89.6% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 90 through 103
    Processing helix  chain 'A' and resid 103 through 130
    Processing helix  chain 'A' and resid 134 through 157
    Processing helix  chain 'A' and resid 157 through 198
      Proline residue:  A 167  - end of helix
      removed outlier: 4.698A  pdb=" N   PHE A 177 " --> pdb=" O   ASP A 173 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   TRP A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   TRP A 181 " --> pdb=" O   PHE A 177 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL A 182 " --> pdb=" O   TRP A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 203
    Processing helix  chain 'A' and resid 203 through 223
      removed outlier: 3.716A  pdb=" N   LEU A 207 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 230
      removed outlier: 4.126A  pdb=" N   VAL A 230 " --> pdb=" O   PRO A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 251
      removed outlier: 4.610A  pdb=" N   VAL A 235 " --> pdb=" O   TYR A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 270
    Processing helix  chain 'A' and resid 272 through 282
      removed outlier: 4.392A  pdb=" N   GLY A 276 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 287
    Processing helix  chain 'A' and resid 288 through 294
    Processing helix  chain 'A' and resid 294 through 312
    Processing helix  chain 'A' and resid 312 through 330
      removed outlier: 3.527A  pdb=" N   TRP A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 342
    Processing helix  chain 'A' and resid 349 through 361
      Proline residue:  A 356  - end of helix
      Proline residue:  A 359  - end of helix
    Processing helix  chain 'A' and resid 362 through 375
    Processing helix  chain 'A' and resid 381 through 389
      removed outlier: 3.502A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 414
      removed outlier: 4.258A  pdb=" N   ALA A 403 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 423 through 429
    Processing helix  chain 'A' and resid 437 through 479
      removed outlier: 3.503A  pdb=" N   SER A 449 " --> pdb=" O   GLY A 445 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   SER A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LEU A 452 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 487 through 496
      removed outlier: 3.607A  pdb=" N   TYR A 494 " --> pdb=" O   VAL A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 496 through 503
    Processing helix  chain 'A' and resid 506 through 523
      removed outlier: 4.116A  pdb=" N   PHE A 511 " --> pdb=" O   TRP A 507 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   MET A 512 " --> pdb=" O   GLN A 508 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 515 " --> pdb=" O   PHE A 511 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU A 516 " --> pdb=" O   MET A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 542
      removed outlier: 3.709A  pdb=" N   ALA A 528 " --> pdb=" O   ASN A 524 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY A 542 " --> pdb=" O   LEU A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 566
    Processing helix  chain 'A' and resid 571 through 573
      No H-bonds generated for 'chain 'A' and resid 571 through 573'
    Processing helix  chain 'A' and resid 574 through 586
    Processing helix  chain 'A' and resid 589 through 619
      removed outlier: 3.558A  pdb=" N   ALA A 595 " --> pdb=" O   ARG A 591 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   MET A 598 " --> pdb=" O   THR A 594 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   ARG A 599 " --> pdb=" O   ALA A 595 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 103
    Processing helix  chain 'C' and resid 103 through 130
    Processing helix  chain 'C' and resid 134 through 157
    Processing helix  chain 'C' and resid 157 through 198
      Proline residue:  C 167  - end of helix
      removed outlier: 4.698A  pdb=" N   PHE C 177 " --> pdb=" O   ASP C 173 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   TRP C 178 " --> pdb=" O   SER C 174 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   TRP C 181 " --> pdb=" O   PHE C 177 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL C 182 " --> pdb=" O   TRP C 178 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 198 through 203
    Processing helix  chain 'C' and resid 203 through 223
      removed outlier: 3.717A  pdb=" N   LEU C 207 " --> pdb=" O   GLY C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 226 through 230
      removed outlier: 4.126A  pdb=" N   VAL C 230 " --> pdb=" O   PRO C 227 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 231 through 251
      removed outlier: 4.610A  pdb=" N   VAL C 235 " --> pdb=" O   TYR C 231 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 270
    Processing helix  chain 'C' and resid 272 through 282
      removed outlier: 4.392A  pdb=" N   GLY C 276 " --> pdb=" O   TYR C 272 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE C 279 " --> pdb=" O   ALA C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 284 through 287
    Processing helix  chain 'C' and resid 288 through 294
    Processing helix  chain 'C' and resid 294 through 312
    Processing helix  chain 'C' and resid 312 through 330
      removed outlier: 3.527A  pdb=" N   TRP C 316 " --> pdb=" O   GLY C 312 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 332 through 342
    Processing helix  chain 'C' and resid 349 through 361
      Proline residue:  C 356  - end of helix
      Proline residue:  C 359  - end of helix
    Processing helix  chain 'C' and resid 362 through 375
    Processing helix  chain 'C' and resid 381 through 389
      removed outlier: 3.502A  pdb=" N   TYR C 385 " --> pdb=" O   VAL C 381 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 391 through 414
      removed outlier: 4.259A  pdb=" N   ALA C 403 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      Proline residue:  C 404  - end of helix
    Processing helix  chain 'C' and resid 423 through 429
    Processing helix  chain 'C' and resid 437 through 479
      removed outlier: 3.504A  pdb=" N   SER C 449 " --> pdb=" O   GLY C 445 " (cutoff:3.500A)
      removed outlier: 3.893A  pdb=" N   ILE C 450 " --> pdb=" O   ALA C 446 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   SER C 451 " --> pdb=" O   SER C 447 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   LEU C 452 " --> pdb=" O   SER C 448 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 482
      No H-bonds generated for 'chain 'C' and resid 480 through 482'
    Processing helix  chain 'C' and resid 487 through 496
      removed outlier: 3.607A  pdb=" N   TYR C 494 " --> pdb=" O   VAL C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 496 through 503
    Processing helix  chain 'C' and resid 506 through 523
      removed outlier: 4.116A  pdb=" N   PHE C 511 " --> pdb=" O   TRP C 507 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   MET C 512 " --> pdb=" O   GLN C 508 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS C 515 " --> pdb=" O   PHE C 511 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU C 516 " --> pdb=" O   MET C 512 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 524 through 542
      removed outlier: 3.708A  pdb=" N   ALA C 528 " --> pdb=" O   ASN C 524 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY C 542 " --> pdb=" O   LEU C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 555 through 566
    Processing helix  chain 'C' and resid 571 through 573
      No H-bonds generated for 'chain 'C' and resid 571 through 573'
    Processing helix  chain 'C' and resid 574 through 586
    Processing helix  chain 'C' and resid 589 through 619
      removed outlier: 3.558A  pdb=" N   ALA C 595 " --> pdb=" O   ARG C 591 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   MET C 598 " --> pdb=" O   THR C 594 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   ARG C 599 " --> pdb=" O   ALA C 595 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 103
    Processing helix  chain 'B' and resid 103 through 130
    Processing helix  chain 'B' and resid 134 through 157
    Processing helix  chain 'B' and resid 157 through 198
      Proline residue:  B 167  - end of helix
      removed outlier: 4.698A  pdb=" N   PHE B 177 " --> pdb=" O   ASP B 173 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   TRP B 178 " --> pdb=" O   SER B 174 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   TRP B 181 " --> pdb=" O   PHE B 177 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   VAL B 182 " --> pdb=" O   TRP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 203
    Processing helix  chain 'B' and resid 203 through 223
      removed outlier: 3.717A  pdb=" N   LEU B 207 " --> pdb=" O   GLY B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 226 through 230
      removed outlier: 4.127A  pdb=" N   VAL B 230 " --> pdb=" O   PRO B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 251
      removed outlier: 4.610A  pdb=" N   VAL B 235 " --> pdb=" O   TYR B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 270
    Processing helix  chain 'B' and resid 272 through 282
      removed outlier: 4.391A  pdb=" N   GLY B 276 " --> pdb=" O   TYR B 272 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   PHE B 279 " --> pdb=" O   ALA B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 287
    Processing helix  chain 'B' and resid 288 through 294
    Processing helix  chain 'B' and resid 294 through 312
    Processing helix  chain 'B' and resid 312 through 330
      removed outlier: 3.526A  pdb=" N   TRP B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 342
    Processing helix  chain 'B' and resid 349 through 361
      Proline residue:  B 356  - end of helix
      Proline residue:  B 359  - end of helix
    Processing helix  chain 'B' and resid 362 through 375
    Processing helix  chain 'B' and resid 381 through 389
      removed outlier: 3.502A  pdb=" N   TYR B 385 " --> pdb=" O   VAL B 381 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 391 through 414
      removed outlier: 4.258A  pdb=" N   ALA B 403 " --> pdb=" O   SER B 399 " (cutoff:3.500A)
      Proline residue:  B 404  - end of helix
    Processing helix  chain 'B' and resid 423 through 429
    Processing helix  chain 'B' and resid 437 through 479
      removed outlier: 3.503A  pdb=" N   SER B 449 " --> pdb=" O   GLY B 445 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE B 450 " --> pdb=" O   ALA B 446 " (cutoff:3.500A)
      removed outlier: 4.768A  pdb=" N   SER B 451 " --> pdb=" O   SER B 447 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   LEU B 452 " --> pdb=" O   SER B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 482
      No H-bonds generated for 'chain 'B' and resid 480 through 482'
    Processing helix  chain 'B' and resid 487 through 496
      removed outlier: 3.607A  pdb=" N   TYR B 494 " --> pdb=" O   VAL B 490 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 496 through 503
    Processing helix  chain 'B' and resid 506 through 523
      removed outlier: 4.116A  pdb=" N   PHE B 511 " --> pdb=" O   TRP B 507 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   MET B 512 " --> pdb=" O   GLN B 508 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS B 515 " --> pdb=" O   PHE B 511 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LEU B 516 " --> pdb=" O   MET B 512 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 524 through 542
      removed outlier: 3.709A  pdb=" N   ALA B 528 " --> pdb=" O   ASN B 524 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLY B 542 " --> pdb=" O   LEU B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 566
    Processing helix  chain 'B' and resid 571 through 573
      No H-bonds generated for 'chain 'B' and resid 571 through 573'
    Processing helix  chain 'B' and resid 574 through 586
    Processing helix  chain 'B' and resid 589 through 619
      removed outlier: 3.558A  pdb=" N   ALA B 595 " --> pdb=" O   ARG B 591 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   MET B 598 " --> pdb=" O   THR B 594 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   ARG B 599 " --> pdb=" O   ALA B 595 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 546 through 547
    Processing sheet with id=AA2, first strand: chain 'C' and resid 546 through 547
    Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 547

    979 hydrogen bonds defined for protein.
    2874 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: 5.60

  Time building geometry restraints manager: 2.84 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 12147
        1.03 -     1.22: 30
        1.22 -     1.42: 5373
        1.42 -     1.61: 7191
        1.61 -     1.81: 168
  Bond restraints: 24909
  Sorted by residual:
  bond pdb=" O4  LBN A 804 "
       pdb=" P1  LBN A 804 "
    ideal  model  delta    sigma   weight residual
    1.497  1.646 -0.149 2.00e-02 2.50e+03 5.53e+01
  bond pdb=" O4  LBN B 804 "
       pdb=" P1  LBN B 804 "
    ideal  model  delta    sigma   weight residual
    1.497  1.646 -0.149 2.00e-02 2.50e+03 5.52e+01
  bond pdb=" O4  LBN A 803 "
       pdb=" P1  LBN A 803 "
    ideal  model  delta    sigma   weight residual
    1.497  1.645 -0.148 2.00e-02 2.50e+03 5.47e+01
  bond pdb=" O4  LBN B 803 "
       pdb=" P1  LBN B 803 "
    ideal  model  delta    sigma   weight residual
    1.497  1.645 -0.148 2.00e-02 2.50e+03 5.47e+01
  bond pdb=" O4  LBN C 804 "
       pdb=" P1  LBN C 804 "
    ideal  model  delta    sigma   weight residual
    1.497  1.645 -0.148 2.00e-02 2.50e+03 5.46e+01
  ... (remaining 24904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.21: 44676
        3.21 -     6.42: 132
        6.42 -     9.64: 15
        9.64 -    12.85: 6
       12.85 -    16.06: 6
  Bond angle restraints: 44835
  Sorted by residual:
  angle pdb=" O1  LBN C 803 "
        pdb=" P1  LBN C 803 "
        pdb=" O2  LBN C 803 "
      ideal   model   delta    sigma   weight residual
      93.45  109.51  -16.06 3.00e+00 1.11e-01 2.87e+01
  angle pdb=" O1  LBN A 803 "
        pdb=" P1  LBN A 803 "
        pdb=" O2  LBN A 803 "
      ideal   model   delta    sigma   weight residual
      93.45  109.49  -16.04 3.00e+00 1.11e-01 2.86e+01
  angle pdb=" O1  LBN A 804 "
        pdb=" P1  LBN A 804 "
        pdb=" O2  LBN A 804 "
      ideal   model   delta    sigma   weight residual
      93.45  109.45  -16.00 3.00e+00 1.11e-01 2.85e+01
  angle pdb=" O1  LBN B 803 "
        pdb=" P1  LBN B 803 "
        pdb=" O2  LBN B 803 "
      ideal   model   delta    sigma   weight residual
      93.45  109.45  -16.00 3.00e+00 1.11e-01 2.84e+01
  angle pdb=" O1  LBN B 804 "
        pdb=" P1  LBN B 804 "
        pdb=" O2  LBN B 804 "
      ideal   model   delta    sigma   weight residual
      93.45  109.45  -16.00 3.00e+00 1.11e-01 2.84e+01
  ... (remaining 44830 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.57: 11442
       32.57 -    65.14: 411
       65.14 -    97.71: 9
       97.71 -   130.28: 6
      130.28 -   162.85: 6
  Dihedral angle restraints: 11874
    sinusoidal: 6144
      harmonic: 5730
  Sorted by residual:
  dihedral pdb=" O5  LBN C 804 "
           pdb=" C2  LBN C 804 "
           pdb=" C3  LBN C 804 "
           pdb=" O7  LBN C 804 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -100.18  162.85     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" O5  LBN A 804 "
           pdb=" C2  LBN A 804 "
           pdb=" C3  LBN A 804 "
           pdb=" O7  LBN A 804 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -100.13  162.80     1      3.00e+01 1.11e-03 2.09e+01
  dihedral pdb=" O5  LBN B 804 "
           pdb=" C2  LBN B 804 "
           pdb=" C3  LBN B 804 "
           pdb=" O7  LBN B 804 "
      ideal   model   delta sinusoidal    sigma   weight residual
      62.67 -100.10  162.77     1      3.00e+01 1.11e-03 2.09e+01
  ... (remaining 11871 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 1390
       0.038 -    0.075: 437
       0.075 -    0.113: 153
       0.113 -    0.150: 3
       0.150 -    0.188: 6
  Chirality restraints: 1989
  Sorted by residual:
  chirality pdb=" C2  LBN C 804 "
            pdb=" C1  LBN C 804 "
            pdb=" C3  LBN C 804 "
            pdb=" O7  LBN C 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.55    0.19 2.00e-01 2.50e+01 8.82e-01
  chirality pdb=" C2  LBN A 804 "
            pdb=" C1  LBN A 804 "
            pdb=" C3  LBN A 804 "
            pdb=" O7  LBN A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.55    0.19 2.00e-01 2.50e+01 8.73e-01
  chirality pdb=" C2  LBN B 804 "
            pdb=" C1  LBN B 804 "
            pdb=" C3  LBN B 804 "
            pdb=" O7  LBN B 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.55    0.18 2.00e-01 2.50e+01 8.53e-01
  ... (remaining 1986 not shown)

  Planarity restraints: 3639
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 195 "    0.012 2.00e-02 2.50e+03   2.44e-02 5.95e+00
        pdb=" C   LEU B 195 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   LEU B 195 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 196 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 195 "   -0.012 2.00e-02 2.50e+03   2.43e-02 5.91e+00
        pdb=" C   LEU A 195 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LEU A 195 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL A 196 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 195 "   -0.012 2.00e-02 2.50e+03   2.42e-02 5.86e+00
        pdb=" C   LEU C 195 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LEU C 195 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL C 196 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 3636 not shown)

  Histogram of nonbonded interaction distances:
        1.58 -     2.18: 956
        2.18 -     2.79: 47350
        2.79 -     3.39: 68133
        3.39 -     4.00: 88119
        4.00 -     4.60: 139696
  Nonbonded interactions: 344254
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 206 "
            pdb=" H   GLN C 206 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" OE1 GLN A 206 "
            pdb=" H   GLN A 206 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" OE1 GLN B 206 "
            pdb=" H   GLN B 206 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" OE1 GLU B 525 "
            pdb=" H   GLU B 525 "
     model   vdw
     1.642 2.450
  nonbonded pdb=" OE1 GLU C 525 "
            pdb=" H   GLU C 525 "
     model   vdw
     1.642 2.450
  ... (remaining 344249 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.170
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     28.120
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:6.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
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      :  0.007   0.149  12744  Z= 0.341
  Angle     :  0.753  16.062  17313  Z= 0.343
  Chirality :  0.041   0.188   1989
  Planarity :  0.004   0.036   2097
  Dihedral  : 15.024 162.847   4380
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.08 (0.21), residues: 1593
  helix:  2.46 (0.14), residues: 1326
  sheet:  None (None), residues: 0
  loop : -0.12 (0.39), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 355 
 TYR   0.009   0.001   TYR B 231 
 PHE   0.015   0.001   PHE B 413 
 TRP   0.015   0.001   TRP C 316 
 HIS   0.003   0.001   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00719 (12744)
  covalent geometry    : angle       0.75274 (17313)
  hydrogen bonds       : bond        0.13920 (  979)
  hydrogen bonds       : angle       5.35344 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  242 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  436 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7618 (mmt180)
REVERT: C  222 LEU cc_start: 0.7957 (tp) cc_final: 0.7687 (mt)
REVERT: B  222 LEU cc_start: 0.8096 (tp) cc_final: 0.7841 (mt)
REVERT: B  430 MET cc_start: 0.7923 (mtt) cc_final: 0.7649 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.8909
  time to fit residues: 239.4949
Evaluate side-chains
  156 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.8980
   chunk 149 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.144812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.100626 restraints weight = 36830.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 1.39
r_work: 0.2977 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12744  Z= 0.138
  Angle     :  0.492   6.147  17313  Z= 0.263
  Chirality :  0.036   0.121   1989
  Planarity :  0.004   0.043   2097
  Dihedral  : 12.536 127.192   1830
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.18 %
    Favored  : 89.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.57 (0.21), residues: 1593
  helix:  2.81 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop :  0.17 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 589 
 TYR   0.009   0.001   TYR B 231 
 PHE   0.012   0.001   PHE C 279 
 TRP   0.012   0.001   TRP C 316 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12744)
  covalent geometry    : angle       0.49249 (17313)
  hydrogen bonds       : bond        0.05287 (  979)
  hydrogen bonds       : angle       4.12979 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  169 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  436 ARG cc_start: 0.8258 (mtm-85) cc_final: 0.7702 (mmt180)
REVERT: C  201 LYS cc_start: 0.6777 (mptt) cc_final: 0.5948 (tttt)
REVERT: C  222 LEU cc_start: 0.7952 (tp) cc_final: 0.7293 (mt)
REVERT: C  305 MET cc_start: 0.8402 (mmm) cc_final: 0.8155 (mmp)
REVERT: C  370 MET cc_start: 0.8641 (mtm) cc_final: 0.8355 (mtp)
REVERT: C  430 MET cc_start: 0.8141 (mtt) cc_final: 0.7666 (mtt)
REVERT: B  222 LEU cc_start: 0.7740 (tp) cc_final: 0.7385 (mt)
  outliers start: 14
  outliers final: 5
  residues processed: 163
  average time/residue: 0.7968
  time to fit residues: 146.5167
Evaluate side-chains
  150 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 145
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  393 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 106 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 132 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0670
   chunk 62 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   overall best weight:    1.2324

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.142891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.099220 restraints weight = 37019.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.37
r_work: 0.2970 rms_B_bonded: 1.90 restraints_weight: 0.5000
r_work: 0.2868 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  12744  Z= 0.133
  Angle     :  0.466   5.289  17313  Z= 0.246
  Chirality :  0.036   0.122   1989
  Planarity :  0.003   0.043   2097
  Dihedral  : 11.511 130.323   1830
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 1.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.82 %
    Favored  : 88.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.69 (0.21), residues: 1593
  helix:  2.92 (0.14), residues: 1311
  sheet:  None (None), residues: 0
  loop :  0.02 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 436 
 TYR   0.007   0.001   TYR B 231 
 PHE   0.012   0.001   PHE A 279 
 TRP   0.010   0.001   TRP A 316 
 HIS   0.002   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12744)
  covalent geometry    : angle       0.46615 (17313)
  hydrogen bonds       : bond        0.05181 (  979)
  hydrogen bonds       : angle       3.95725 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  176 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 158
  time to evaluate  : 0.625 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.6802 (mmtt) cc_final: 0.6148 (ttpt)
REVERT: C  201 LYS cc_start: 0.6900 (mptt) cc_final: 0.6149 (tttt)
REVERT: C  222 LEU cc_start: 0.7905 (tp) cc_final: 0.7221 (mt)
REVERT: C  305 MET cc_start: 0.8410 (mmm) cc_final: 0.8134 (mmp)
REVERT: C  355 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7297 (ttt-90)
REVERT: C  430 MET cc_start: 0.8260 (mtt) cc_final: 0.7753 (mtt)
REVERT: B  222 LEU cc_start: 0.7801 (tp) cc_final: 0.7401 (mt)
REVERT: B  242 GLN cc_start: 0.8487 (mt0) cc_final: 0.8229 (mt0)
REVERT: B  305 MET cc_start: 0.8333 (mmp) cc_final: 0.7924 (mmt)
  outliers start: 18
  outliers final: 9
  residues processed: 169
  average time/residue: 0.8687
  time to fit residues: 164.2406
Evaluate side-chains
  159 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  413 PHE
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  413 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 106 optimal weight:   40.0000
   chunk 158 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   chunk 120 optimal weight:    0.6980
   chunk 155 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    1.9388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.140388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.096402 restraints weight = 37333.338|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 1.38
r_work: 0.2916 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.2815 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12744  Z= 0.177
  Angle     :  0.510   6.117  17313  Z= 0.271
  Chirality :  0.038   0.122   1989
  Planarity :  0.004   0.046   2097
  Dihedral  : 11.131 133.236   1830
  Min Nonbonded Distance : 2.158

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.08 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.36 (0.21), residues: 1593
  helix:  2.72 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.25 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 133 
 TYR   0.007   0.001   TYR A 483 
 PHE   0.015   0.001   PHE A 279 
 TRP   0.010   0.001   TRP A 316 
 HIS   0.003   0.001   HIS B 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (12744)
  covalent geometry    : angle       0.50960 (17313)
  hydrogen bonds       : bond        0.05799 (  979)
  hydrogen bonds       : angle       4.04690 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  185 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 166
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.6978 (mmtt) cc_final: 0.6321 (tttt)
REVERT: C  201 LYS cc_start: 0.6858 (mptt) cc_final: 0.6098 (tttt)
REVERT: C  222 LEU cc_start: 0.7959 (tp) cc_final: 0.7281 (mt)
REVERT: C  305 MET cc_start: 0.8377 (mmm) cc_final: 0.8136 (mmp)
REVERT: C  355 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7712 (ttt-90)
REVERT: C  430 MET cc_start: 0.8340 (mtt) cc_final: 0.7788 (mtt)
REVERT: C  592 ASP cc_start: 0.7513 (m-30) cc_final: 0.7300 (m-30)
REVERT: B  222 LEU cc_start: 0.7814 (tp) cc_final: 0.7350 (mt)
REVERT: B  424 LEU cc_start: 0.8296 (tp) cc_final: 0.8060 (tm)
  outliers start: 19
  outliers final: 11
  residues processed: 180
  average time/residue: 0.8840
  time to fit residues: 178.2409
Evaluate side-chains
  170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 158
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  413 PHE
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 1 optimal weight:    9.9990
   chunk 62 optimal weight:    0.2980
   chunk 94 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 141 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 138 optimal weight:    0.4980
   chunk 12 optimal weight:    2.9990
   chunk 53 optimal weight:    9.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
C 204 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.141639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.098282 restraints weight = 37210.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.3058 rms_B_bonded: 1.36
r_work: 0.2953 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 3.03 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12744  Z= 0.120
  Angle     :  0.450   5.691  17313  Z= 0.238
  Chirality :  0.035   0.120   1989
  Planarity :  0.003   0.040   2097
  Dihedral  : 10.372 127.656   1830
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 1.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.48 %
    Favored  : 86.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.62 (0.21), residues: 1593
  helix:  2.92 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.24 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 251 
 TYR   0.008   0.001   TYR C 231 
 PHE   0.011   0.001   PHE C 279 
 TRP   0.009   0.001   TRP A 316 
 HIS   0.002   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (12744)
  covalent geometry    : angle       0.45016 (17313)
  hydrogen bonds       : bond        0.04703 (  979)
  hydrogen bonds       : angle       3.83873 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6465 (tttt)
REVERT: A  585 MET cc_start: 0.7415 (mtm) cc_final: 0.7189 (mtt)
REVERT: C  201 LYS cc_start: 0.6868 (mptt) cc_final: 0.6098 (tttt)
REVERT: C  222 LEU cc_start: 0.7891 (tp) cc_final: 0.7191 (mt)
REVERT: C  305 MET cc_start: 0.8379 (mmm) cc_final: 0.8155 (mmp)
REVERT: C  355 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7673 (ttt-90)
REVERT: C  430 MET cc_start: 0.8365 (mtt) cc_final: 0.7790 (mtt)
REVERT: C  489 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6505 (mp0)
REVERT: C  592 ASP cc_start: 0.7506 (m-30) cc_final: 0.7244 (m-30)
REVERT: B  222 LEU cc_start: 0.7753 (tp) cc_final: 0.7259 (mt)
REVERT: B  242 GLN cc_start: 0.8384 (mt0) cc_final: 0.8161 (mt0)
REVERT: B  305 MET cc_start: 0.8328 (mmp) cc_final: 0.7949 (mmt)
REVERT: B  424 LEU cc_start: 0.8238 (tp) cc_final: 0.7997 (tm)
  outliers start: 20
  outliers final: 14
  residues processed: 168
  average time/residue: 0.9139
  time to fit residues: 173.0711
Evaluate side-chains
  167 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  413 PHE
Chi-restraints excluded: chain C residue  489 GLU
Chi-restraints excluded: chain C residue  537 SER
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  439 LEU
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 127 optimal weight:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.140811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.097744 restraints weight = 36427.767|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 1.27
r_work: 0.2917 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12744  Z= 0.162
  Angle     :  0.487   5.987  17313  Z= 0.259
  Chirality :  0.037   0.122   1989
  Planarity :  0.004   0.044   2097
  Dihedral  : 10.468 126.583   1830
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 1.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 11.40 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.44 (0.21), residues: 1593
  helix:  2.79 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.32 (0.34), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 436 
 TYR   0.009   0.001   TYR C 231 
 PHE   0.014   0.001   PHE A 279 
 TRP   0.008   0.001   TRP C 316 
 HIS   0.003   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (12744)
  covalent geometry    : angle       0.48662 (17313)
  hydrogen bonds       : bond        0.05500 (  979)
  hydrogen bonds       : angle       3.95248 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  177 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 152
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7249 (mmtt) cc_final: 0.6541 (tttt)
REVERT: A  424 LEU cc_start: 0.8276 (tp) cc_final: 0.7907 (tm)
REVERT: A  585 MET cc_start: 0.7472 (mtt) cc_final: 0.7245 (mtt)
REVERT: C  201 LYS cc_start: 0.6948 (mptt) cc_final: 0.6220 (tmmt)
REVERT: C  222 LEU cc_start: 0.7977 (tp) cc_final: 0.7279 (mt)
REVERT: C  305 MET cc_start: 0.8451 (mmm) cc_final: 0.8237 (mmp)
REVERT: C  355 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7827 (ttt-90)
REVERT: C  430 MET cc_start: 0.8470 (mtt) cc_final: 0.7851 (mtt)
REVERT: C  489 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.6581 (mp0)
REVERT: C  592 ASP cc_start: 0.7689 (m-30) cc_final: 0.7426 (m-30)
REVERT: B  222 LEU cc_start: 0.7877 (tp) cc_final: 0.7350 (mt)
REVERT: B  242 GLN cc_start: 0.8520 (mt0) cc_final: 0.8249 (mt0)
REVERT: B  424 LEU cc_start: 0.8358 (tp) cc_final: 0.8145 (tm)
  outliers start: 25
  outliers final: 17
  residues processed: 172
  average time/residue: 0.7777
  time to fit residues: 150.7408
Evaluate side-chains
  168 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  342 ASN
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  413 PHE
Chi-restraints excluded: chain C residue  489 GLU
Chi-restraints excluded: chain C residue  537 SER
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  342 ASN
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 65 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 126 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 143 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 108 optimal weight:    5.9990
   chunk 135 optimal weight:    0.9990
   chunk 112 optimal weight:    0.2980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
C 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.144809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.100619 restraints weight = 36103.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3071 rms_B_bonded: 1.36
r_work: 0.2954 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 3.12 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7865
moved from start:          0.3527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12744  Z= 0.103
  Angle     :  0.428   5.265  17313  Z= 0.226
  Chirality :  0.035   0.123   1989
  Planarity :  0.003   0.038   2097
  Dihedral  :  9.925 121.429   1830
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 1.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.88 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.85 (0.21), residues: 1593
  helix:  3.14 (0.14), residues: 1290
  sheet:  None (None), residues: 0
  loop : -0.33 (0.35), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 355 
 TYR   0.006   0.001   TYR C 231 
 PHE   0.011   0.001   PHE A 146 
 TRP   0.009   0.001   TRP A 316 
 HIS   0.001   0.000   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 (12744)
  covalent geometry    : angle       0.42764 (17313)
  hydrogen bonds       : bond        0.04205 (  979)
  hydrogen bonds       : angle       3.72543 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  173 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 153
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7099 (mmtt) cc_final: 0.6439 (tttt)
REVERT: A  242 GLN cc_start: 0.8598 (mt0) cc_final: 0.8355 (mt0)
REVERT: A  424 LEU cc_start: 0.8192 (tp) cc_final: 0.7848 (tm)
REVERT: A  537 SER cc_start: 0.8025 (OUTLIER) cc_final: 0.7673 (m)
REVERT: C  201 LYS cc_start: 0.6827 (mptt) cc_final: 0.6111 (tmmt)
REVERT: C  222 LEU cc_start: 0.7910 (tp) cc_final: 0.7142 (mt)
REVERT: C  242 GLN cc_start: 0.8689 (mt0) cc_final: 0.8355 (mt0)
REVERT: C  305 MET cc_start: 0.8421 (mmm) cc_final: 0.8216 (mmp)
REVERT: C  355 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7703 (ttt-90)
REVERT: C  430 MET cc_start: 0.8405 (mtt) cc_final: 0.7843 (mtt)
REVERT: C  489 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.6541 (mp0)
REVERT: B  201 LYS cc_start: 0.6753 (mptt) cc_final: 0.6089 (tttt)
REVERT: B  305 MET cc_start: 0.8392 (mmp) cc_final: 0.8044 (mmt)
REVERT: B  313 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8122 (mt)
REVERT: B  424 LEU cc_start: 0.8243 (tp) cc_final: 0.8001 (tm)
  outliers start: 20
  outliers final: 11
  residues processed: 168
  average time/residue: 0.7702
  time to fit residues: 145.8085
Evaluate side-chains
  165 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 150
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  489 GLU
Chi-restraints excluded: chain C residue  537 SER
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain C residue  585 MET
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  313 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 143 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.140866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.097835 restraints weight = 36314.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.27
r_work: 0.2913 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2806 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.2806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12744  Z= 0.177
  Angle     :  0.501   6.156  17313  Z= 0.266
  Chirality :  0.037   0.122   1989
  Planarity :  0.004   0.044   2097
  Dihedral  : 10.290 118.555   1830
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 1.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.72 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.47 (0.21), residues: 1593
  helix:  2.81 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.28 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 436 
 TYR   0.007   0.001   TYR B 553 
 PHE   0.014   0.001   PHE C 146 
 TRP   0.006   0.001   TRP A 316 
 HIS   0.004   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (12744)
  covalent geometry    : angle       0.50086 (17313)
  hydrogen bonds       : bond        0.05646 (  979)
  hydrogen bonds       : angle       3.95878 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  182 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 155
  time to evaluate  : 0.532 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7226 (mmtt) cc_final: 0.6533 (tttt)
REVERT: A  424 LEU cc_start: 0.8303 (tp) cc_final: 0.7957 (tm)
REVERT: C  201 LYS cc_start: 0.6961 (mptt) cc_final: 0.6239 (tmmt)
REVERT: C  222 LEU cc_start: 0.8008 (tp) cc_final: 0.7313 (mt)
REVERT: C  305 MET cc_start: 0.8435 (mmm) cc_final: 0.8227 (mmp)
REVERT: C  355 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7828 (ttt-90)
REVERT: C  430 MET cc_start: 0.8475 (mtt) cc_final: 0.7904 (mtt)
REVERT: C  489 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.6646 (mp0)
REVERT: C  592 ASP cc_start: 0.7668 (m-30) cc_final: 0.7407 (m-30)
REVERT: B  222 LEU cc_start: 0.8087 (tt) cc_final: 0.7647 (mt)
REVERT: B  424 LEU cc_start: 0.8390 (tp) cc_final: 0.8179 (tm)
  outliers start: 27
  outliers final: 17
  residues processed: 175
  average time/residue: 0.8663
  time to fit residues: 169.9201
Evaluate side-chains
  171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  489 GLU
Chi-restraints excluded: chain C residue  503 MET
Chi-restraints excluded: chain C residue  537 SER
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 156 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 138 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 131 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
C 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.142257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.099553 restraints weight = 36618.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 1.27
r_work: 0.2944 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.3643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  12744  Z= 0.124
  Angle     :  0.452   5.418  17313  Z= 0.239
  Chirality :  0.035   0.120   1989
  Planarity :  0.003   0.040   2097
  Dihedral  :  9.869 109.896   1830
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 12.35 %
    Favored  : 85.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.67 (0.21), residues: 1593
  helix:  2.96 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.26 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 251 
 TYR   0.007   0.001   TYR C 231 
 PHE   0.012   0.001   PHE C 279 
 TRP   0.008   0.001   TRP A 316 
 HIS   0.002   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12744)
  covalent geometry    : angle       0.45238 (17313)
  hydrogen bonds       : bond        0.04705 (  979)
  hydrogen bonds       : angle       3.81943 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  181 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 155
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.7140 (mmtt) cc_final: 0.6478 (tttt)
REVERT: A  242 GLN cc_start: 0.8659 (mt0) cc_final: 0.8403 (mt0)
REVERT: A  424 LEU cc_start: 0.8290 (tp) cc_final: 0.7951 (tm)
REVERT: A  537 SER cc_start: 0.8123 (OUTLIER) cc_final: 0.7738 (m)
REVERT: C  201 LYS cc_start: 0.6952 (mptt) cc_final: 0.6245 (tttt)
REVERT: C  222 LEU cc_start: 0.7981 (tp) cc_final: 0.7281 (mt)
REVERT: C  242 GLN cc_start: 0.8751 (mt0) cc_final: 0.8353 (mt0)
REVERT: C  355 ARG cc_start: 0.8070 (OUTLIER) cc_final: 0.7784 (ttt-90)
REVERT: C  430 MET cc_start: 0.8439 (mtt) cc_final: 0.7852 (mtt)
REVERT: C  489 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.6514 (mp0)
REVERT: B  222 LEU cc_start: 0.8088 (tt) cc_final: 0.7597 (mt)
REVERT: B  424 LEU cc_start: 0.8323 (tp) cc_final: 0.8099 (tm)
  outliers start: 26
  outliers final: 16
  residues processed: 173
  average time/residue: 0.8764
  time to fit residues: 170.5494
Evaluate side-chains
  170 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.619 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  489 GLU
Chi-restraints excluded: chain C residue  503 MET
Chi-restraints excluded: chain C residue  537 SER
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 158 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 147 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 146 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.2984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.142994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.099405 restraints weight = 36074.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 1.29
r_work: 0.2934 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12744  Z= 0.133
  Angle     :  0.461   6.057  17313  Z= 0.243
  Chirality :  0.036   0.119   1989
  Planarity :  0.003   0.042   2097
  Dihedral  :  9.712 108.907   1830
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 12.75 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.67 (0.21), residues: 1593
  helix:  2.96 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.24 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 436 
 TYR   0.007   0.001   TYR C 231 
 PHE   0.015   0.001   PHE C 146 
 TRP   0.007   0.001   TRP A 316 
 HIS   0.003   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (12744)
  covalent geometry    : angle       0.46115 (17313)
  hydrogen bonds       : bond        0.04878 (  979)
  hydrogen bonds       : angle       3.82741 ( 2874)

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

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

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3186 Ramachandran restraints generated.
    1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Residue MET   92 is missing expected H atoms. Skipping.
Residue MET   96 is missing expected H atoms. Skipping.
Residue SER   97 is missing expected H atoms. Skipping.
Residue LYS  104 is missing expected H atoms. Skipping.
Residue TYR  109 is missing expected H atoms. Skipping.
Residue LYS  156 is missing expected H atoms. Skipping.
Residue LYS  421 is missing expected H atoms. Skipping.
Residue LYS  425 is missing expected H atoms. Skipping.
Residue LEU  610 is missing expected H atoms. Skipping.
Evaluate side-chains
  172 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 MET cc_start: 0.6215 (mmt) cc_final: 0.5921 (mmm)
REVERT: A  201 LYS cc_start: 0.7194 (mmtt) cc_final: 0.6523 (tttt)
REVERT: A  242 GLN cc_start: 0.8677 (mt0) cc_final: 0.8414 (mt0)
REVERT: A  424 LEU cc_start: 0.8281 (tp) cc_final: 0.7955 (tm)
REVERT: C  201 LYS cc_start: 0.6939 (mptt) cc_final: 0.6227 (tttt)
REVERT: C  222 LEU cc_start: 0.7983 (tp) cc_final: 0.7282 (mt)
REVERT: C  305 MET cc_start: 0.8437 (mmm) cc_final: 0.8226 (mmp)
REVERT: C  355 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7790 (ttt-90)
REVERT: C  430 MET cc_start: 0.8436 (mtt) cc_final: 0.7842 (mtt)
REVERT: C  489 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.6576 (mp0)
REVERT: C  585 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.6355 (mtt)
REVERT: B  201 LYS cc_start: 0.6881 (mptt) cc_final: 0.6197 (tttt)
REVERT: B  222 LEU cc_start: 0.8122 (tt) cc_final: 0.7635 (mt)
REVERT: B  424 LEU cc_start: 0.8245 (tp) cc_final: 0.7998 (tm)
  outliers start: 22
  outliers final: 17
  residues processed: 167
  average time/residue: 0.9460
  time to fit residues: 177.4146
Evaluate side-chains
  171 residues out of total 1335 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  350 SER
Chi-restraints excluded: chain A residue  482 ASP
Chi-restraints excluded: chain A residue  537 SER
Chi-restraints excluded: chain A residue  550 VAL
Chi-restraints excluded: chain C residue  331 THR
Chi-restraints excluded: chain C residue  350 SER
Chi-restraints excluded: chain C residue  355 ARG
Chi-restraints excluded: chain C residue  376 THR
Chi-restraints excluded: chain C residue  489 GLU
Chi-restraints excluded: chain C residue  503 MET
Chi-restraints excluded: chain C residue  537 SER
Chi-restraints excluded: chain C residue  550 VAL
Chi-restraints excluded: chain C residue  585 MET
Chi-restraints excluded: chain B residue  149 VAL
Chi-restraints excluded: chain B residue  350 SER
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  413 PHE
Chi-restraints excluded: chain B residue  550 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 128 optimal weight:    1.9990
   chunk 148 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 145 optimal weight:    0.7980
   chunk 142 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0370
   chunk 18 optimal weight:    2.9990
   overall best weight:    1.3664

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

Flipped N/Q/H residues before XYZ refinement:
C 204 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.141879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.099127 restraints weight = 36367.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 1.26
r_work: 0.2937 rms_B_bonded: 1.86 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 2.97 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12744  Z= 0.136
  Angle     :  0.462   6.246  17313  Z= 0.244
  Chirality :  0.036   0.119   1989
  Planarity :  0.003   0.041   2097
  Dihedral  :  9.589 107.219   1830
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 2.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 12.83 %
    Favored  : 85.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.67 (0.21), residues: 1593
  helix:  2.95 (0.14), residues: 1305
  sheet:  None (None), residues: 0
  loop : -0.22 (0.35), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C 436 
 TYR   0.007   0.001   TYR C 231 
 PHE   0.014   0.001   PHE A 146 
 TRP   0.007   0.001   TRP A 316 
 HIS   0.003   0.001   HIS C 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (12744)
  covalent geometry    : angle       0.46240 (17313)
  hydrogen bonds       : bond        0.04895 (  979)
  hydrogen bonds       : angle       3.83289 ( 2874)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6746.53 seconds
wall clock time: 114 minutes 48.89 seconds (6888.89 seconds total)