Starting phenix.real_space_refine
on Fri Oct 10 19:31:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w69_37318/10_2025/8w69_37318.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w69_37318/10_2025/8w69_37318.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w69_37318/10_2025/8w69_37318.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w69_37318/10_2025/8w69_37318.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w69_37318/10_2025/8w69_37318.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w69_37318/10_2025/8w69_37318.map"
  }
  resolution = 3.6
  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=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    5412      2.51       5
     N    1529      2.21       5
     O    1691      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8650
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 2178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2178
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2178
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2178
          Classifications: {'peptide': 300}
          Link IDs: {'PTRANS': 12, 'TRANS': 287}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 667
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "F"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 667
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 667
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 3, 'TRANS': 87}
    Chain: "G"
      Number of atoms: 45
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 45
          Classifications: {'peptide': 9}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 18
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 9
          Planarities with less than four sites: {'UNK:plan-1': 9}
          Unresolved non-hydrogen planarities: 9
    Chain: "H"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 35
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
    Chain: "I"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 35
          Classifications: {'peptide': 7}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'TRANS': 6}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'UNK:plan-1': 7}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 2.19, per 1000 atoms: 0.25
  Number of scatterers: 8650
  At special positions: 0
  Unit cell: (113.118, 114.428, 111.808, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O    1691      8.00
     N    1529      7.00
     C    5412      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 440.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 19 sheets defined
      21.8% alpha, 39.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 42 through 48
      removed outlier: 4.434A  pdb=" N   LYS A  48 " --> pdb=" O   PRO A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 112
      removed outlier: 3.972A  pdb=" N   ILE A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 177
      removed outlier: 3.721A  pdb=" N   GLY A 176 " --> pdb=" O   ASN A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 262
    Processing helix  chain 'A' and resid 278 through 284
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 324 through 335
      removed outlier: 3.586A  pdb=" N   LEU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 42 through 47
    Processing helix  chain 'C' and resid 107 through 112
      removed outlier: 3.534A  pdb=" N   ILE C 111 " --> pdb=" O   ASN C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 162
    Processing helix  chain 'C' and resid 173 through 177
      removed outlier: 4.094A  pdb=" N   GLY C 176 " --> pdb=" O   ASN C 173 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 248 through 262
    Processing helix  chain 'C' and resid 277 through 285
      removed outlier: 3.628A  pdb=" N   ALA C 281 " --> pdb=" O   SER C 277 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 307
    Processing helix  chain 'C' and resid 324 through 335
      removed outlier: 3.966A  pdb=" N   LEU C 328 " --> pdb=" O   SER C 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 48
      removed outlier: 3.549A  pdb=" N   LEU B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   LYS B  48 " --> pdb=" O   PRO B  44 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 107 through 111
    Processing helix  chain 'B' and resid 158 through 162
    Processing helix  chain 'B' and resid 173 through 177
      removed outlier: 3.950A  pdb=" N   GLY B 176 " --> pdb=" O   ASN B 173 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 247 through 261
    Processing helix  chain 'B' and resid 277 through 285
      removed outlier: 3.597A  pdb=" N   ALA B 281 " --> pdb=" O   SER B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 307
    Processing helix  chain 'B' and resid 324 through 335
    Processing helix  chain 'D' and resid 372 through 376
    Processing helix  chain 'D' and resid 401 through 406
    Processing helix  chain 'D' and resid 424 through 433
      removed outlier: 3.841A  pdb=" N   MET D 428 " --> pdb=" O   SER D 424 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 372 through 376
    Processing helix  chain 'F' and resid 401 through 406
    Processing helix  chain 'F' and resid 424 through 434
      removed outlier: 3.657A  pdb=" N   MET F 428 " --> pdb=" O   SER F 424 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   ALA F 434 " --> pdb=" O   LYS F 430 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 372 through 376
    Processing helix  chain 'E' and resid 401 through 406
    Processing helix  chain 'E' and resid 424 through 433
      removed outlier: 3.815A  pdb=" N   MET E 428 " --> pdb=" O   SER E 424 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 60
      removed outlier: 6.909A  pdb=" N   TYR A 103 " --> pdb=" O   ILE A  97 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ILE A 140 " --> pdb=" O   SER A 134 " (cutoff:3.500A)
      removed outlier: 4.780A  pdb=" N   SER A 134 " --> pdb=" O   ILE A 140 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   LEU A 142 " --> pdb=" O   ILE A 132 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE A 119 " --> pdb=" O   PHE A 127 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ILE A 117 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
      removed outlier: 7.629A  pdb=" N   LEU A 131 " --> pdb=" O   GLN A 115 " (cutoff:3.500A)
      removed outlier: 11.051A  pdb=" N   GLN A 115 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLN A 120 " --> pdb=" O   SER A  55 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 167 through 172
      removed outlier: 5.572A  pdb=" N   PHE A 202 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   PHE A 244 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 226 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 268
    Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 275
      removed outlier: 6.919A  pdb=" N   LYS A 272 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 271 through 275
      removed outlier: 6.919A  pdb=" N   LYS A 272 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   GLY A 344 " --> pdb=" O   THR A 315 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   LEU A 317 " --> pdb=" O   LYS A 342 " (cutoff:3.500A)
      removed outlier: 7.337A  pdb=" N   LYS A 342 " --> pdb=" O   LEU A 317 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 60
      removed outlier: 3.505A  pdb=" N   VAL C  95 " --> pdb=" O   LEU C 105 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   TYR C 103 " --> pdb=" O   ILE C  97 " (cutoff:3.500A)
      removed outlier: 7.593A  pdb=" N   ILE C 140 " --> pdb=" O   SER C 134 " (cutoff:3.500A)
      removed outlier: 5.086A  pdb=" N   SER C 134 " --> pdb=" O   ILE C 140 " (cutoff:3.500A)
      removed outlier: 7.106A  pdb=" N   LEU C 142 " --> pdb=" O   ILE C 132 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN C 144 " --> pdb=" O   LYS C 130 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LYS C 130 " --> pdb=" O   GLN C 144 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE C 119 " --> pdb=" O   PHE C 127 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA C 129 " --> pdb=" O   ILE C 117 " (cutoff:3.500A)
      removed outlier: 4.788A  pdb=" N   ILE C 117 " --> pdb=" O   ALA C 129 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 167 through 172
      removed outlier: 5.599A  pdb=" N   PHE C 202 " --> pdb=" O   GLY C 190 " (cutoff:3.500A)
      removed outlier: 7.021A  pdb=" N   PHE C 244 " --> pdb=" O   THR C 230 " (cutoff:3.500A)
      removed outlier: 6.559A  pdb=" N   LEU C 218 " --> pdb=" O   ILE C 226 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 267 through 268
    Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 275
      removed outlier: 6.849A  pdb=" N   LYS C 272 " --> pdb=" O   SER C 295 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 271 through 275
      removed outlier: 6.849A  pdb=" N   LYS C 272 " --> pdb=" O   SER C 295 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE C 313 " --> pdb=" O   LEU C 346 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   GLY C 344 " --> pdb=" O   THR C 315 " (cutoff:3.500A)
      removed outlier: 4.861A  pdb=" N   LEU C 317 " --> pdb=" O   LYS C 342 " (cutoff:3.500A)
      removed outlier: 7.153A  pdb=" N   LYS C 342 " --> pdb=" O   LEU C 317 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 53 through 60
      removed outlier: 6.574A  pdb=" N   TYR B 103 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   GLY B 133 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   GLN B 144 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
      removed outlier: 5.947A  pdb=" N   LEU B 131 " --> pdb=" O   GLN B 144 " (cutoff:3.500A)
      removed outlier: 4.626A  pdb=" N   ILE B 117 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLN B 120 " --> pdb=" O   SER B  55 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'I' and resid 30 through 31
      removed outlier: 6.984A  pdb=" N   PHE B 244 " --> pdb=" O   THR B 230 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   PHE B 202 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU B 218 " --> pdb=" O   ILE B 226 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 267 through 268
    Processing sheet with id=AB5, first strand: chain 'B' and resid 271 through 275
      removed outlier: 6.739A  pdb=" N   LYS B 272 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASP B 312 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 271 through 275
      removed outlier: 6.739A  pdb=" N   LYS B 272 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ASP B 312 " --> pdb=" O   VAL B 294 " (cutoff:3.500A)
      removed outlier: 5.222A  pdb=" N   ILE B 314 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   LEU B 346 " --> pdb=" O   ILE B 314 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   VAL B 354 " --> pdb=" O   LEU B 343 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 378 through 381
      removed outlier: 6.504A  pdb=" N   THR D 379 " --> pdb=" O   ASP D 395 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 378 through 381
      removed outlier: 6.504A  pdb=" N   THR D 379 " --> pdb=" O   ASP D 395 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   VAL D 413 " --> pdb=" O   VAL D 444 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   GLN D 442 " --> pdb=" O   ILE D 415 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE D 443 " --> pdb=" O   ILE D 450 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'F' and resid 378 through 382
      removed outlier: 6.642A  pdb=" N   THR F 379 " --> pdb=" O   ASP F 395 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   VAL F 413 " --> pdb=" O   VAL F 444 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   GLN F 442 " --> pdb=" O   ILE F 415 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   VAL F 417 " --> pdb=" O   ALA F 440 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   ALA F 440 " --> pdb=" O   VAL F 417 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'E' and resid 378 through 384
      removed outlier: 6.852A  pdb=" N   THR E 379 " --> pdb=" O   ASP E 395 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLY E 391 " --> pdb=" O   GLY E 383 " (cutoff:3.500A)
      removed outlier: 12.040A  pdb=" N   LYS E 390 " --> pdb=" O   GLY E 416 " (cutoff:3.500A)
      removed outlier: 7.090A  pdb=" N   GLY E 416 " --> pdb=" O   LYS E 390 " (cutoff:3.500A)
      removed outlier: 6.048A  pdb=" N   ILE E 414 " --> pdb=" O   VAL E 444 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   VAL E 444 " --> pdb=" O   ILE E 414 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    966 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: 1.40

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2994
        1.34 -     1.46: 1141
        1.46 -     1.58: 4553
        1.58 -     1.69: 1
        1.69 -     1.81: 36
  Bond restraints: 8725
  Sorted by residual:
  bond pdb=" CG  PRO A 321 "
       pdb=" CD  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.503  1.341  0.162 3.40e-02 8.65e+02 2.26e+01
  bond pdb=" N   PRO A 321 "
       pdb=" CD  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.473  1.526 -0.053 1.40e-02 5.10e+03 1.41e+01
  bond pdb=" CB  PRO A 321 "
       pdb=" CG  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.492  1.667 -0.175 5.00e-02 4.00e+02 1.22e+01
  bond pdb=" N   PRO A 321 "
       pdb=" CA  PRO A 321 "
    ideal  model  delta    sigma   weight residual
    1.465  1.439  0.026 1.10e-02 8.26e+03 5.55e+00
  bond pdb=" CA  ASN A 147 "
       pdb=" CB  ASN A 147 "
    ideal  model  delta    sigma   weight residual
    1.525  1.538 -0.013 8.30e-03 1.45e+04 2.45e+00
  ... (remaining 8720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.45: 11721
        3.45 -     6.90: 50
        6.90 -    10.35: 7
       10.35 -    13.80: 1
       13.80 -    17.25: 1
  Bond angle restraints: 11780
  Sorted by residual:
  angle pdb=" CA  PRO A 321 "
        pdb=" N   PRO A 321 "
        pdb=" CD  PRO A 321 "
      ideal   model   delta    sigma   weight residual
     112.00   94.75   17.25 1.40e+00 5.10e-01 1.52e+02
  angle pdb=" N   PRO A 321 "
        pdb=" CD  PRO A 321 "
        pdb=" CG  PRO A 321 "
      ideal   model   delta    sigma   weight residual
     103.20   92.47   10.73 1.50e+00 4.44e-01 5.12e+01
  angle pdb=" CA  PRO A 321 "
        pdb=" CB  PRO A 321 "
        pdb=" CG  PRO A 321 "
      ideal   model   delta    sigma   weight residual
     104.50   96.33    8.17 1.90e+00 2.77e-01 1.85e+01
  angle pdb=" C   GLN A 146 "
        pdb=" N   ASN A 147 "
        pdb=" CA  ASN A 147 "
      ideal   model   delta    sigma   weight residual
     124.21  128.55   -4.34 1.21e+00 6.83e-01 1.28e+01
  angle pdb=" CB  MET D 428 "
        pdb=" CG  MET D 428 "
        pdb=" SD  MET D 428 "
      ideal   model   delta    sigma   weight residual
     112.70  122.78  -10.08 3.00e+00 1.11e-01 1.13e+01
  ... (remaining 11775 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.66: 4572
       16.66 -    33.32: 591
       33.32 -    49.98: 141
       49.98 -    66.64: 32
       66.64 -    83.30: 13
  Dihedral angle restraints: 5349
    sinusoidal: 2049
      harmonic: 3300
  Sorted by residual:
  dihedral pdb=" CA  ASN B 107 "
           pdb=" CB  ASN B 107 "
           pdb=" CG  ASN B 107 "
           pdb=" OD1 ASN B 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -172.42  -67.58     2      2.00e+01 2.50e-03 1.03e+01
  dihedral pdb=" CG  ARG E 445 "
           pdb=" CD  ARG E 445 "
           pdb=" NE  ARG E 445 "
           pdb=" CZ  ARG E 445 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  133.43  -43.43     2      1.50e+01 4.44e-03 1.01e+01
  dihedral pdb=" CG  ARG B 191 "
           pdb=" CD  ARG B 191 "
           pdb=" NE  ARG B 191 "
           pdb=" CZ  ARG B 191 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -136.62  -43.38     2      1.50e+01 4.44e-03 1.01e+01
  ... (remaining 5346 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1045
       0.040 -    0.081: 218
       0.081 -    0.121: 142
       0.121 -    0.162: 17
       0.162 -    0.202: 2
  Chirality restraints: 1424
  Sorted by residual:
  chirality pdb=" CA  PRO A 321 "
            pdb=" N   PRO A 321 "
            pdb=" C   PRO A 321 "
            pdb=" CB  PRO A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CA  ILE E 443 "
            pdb=" N   ILE E 443 "
            pdb=" C   ILE E 443 "
            pdb=" CB  ILE E 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.61e-01
  chirality pdb=" CA  ILE B 228 "
            pdb=" N   ILE B 228 "
            pdb=" C   ILE B 228 "
            pdb=" CB  ILE B 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.84e-01
  ... (remaining 1421 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 320 "    0.089 5.00e-02 4.00e+02   1.21e-01 2.33e+01
        pdb=" N   PRO A 321 "   -0.208 5.00e-02 4.00e+02
        pdb=" CA  PRO A 321 "    0.054 5.00e-02 4.00e+02
        pdb=" CD  PRO A 321 "    0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C  43 "   -0.034 5.00e-02 4.00e+02   5.16e-02 4.26e+00
        pdb=" N   PRO C  44 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO C  44 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C  44 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 298 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO B 299 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 299 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 299 "    0.026 5.00e-02 4.00e+02
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.67: 146
        2.67 -     3.23: 7704
        3.23 -     3.79: 12542
        3.79 -     4.34: 16418
        4.34 -     4.90: 27966
  Nonbonded interactions: 64776
  Sorted by model distance:
  nonbonded pdb=" O   ARG E 419 "
            pdb=" NH1 ARG E 419 "
     model   vdw
     2.114 3.120
  nonbonded pdb=" OE1 GLN B 146 "
            pdb=" ND2 ASN B 147 "
     model   vdw
     2.153 3.120
  nonbonded pdb=" OG  SER F 381 "
            pdb=" O   LYS F 393 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   ARG C 347 "
            pdb=" NZ  LYS C 350 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" OE1 GLU B 275 "
            pdb=" OG  SER B 324 "
     model   vdw
     2.331 3.040
  ... (remaining 64771 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'H'
  selection = chain 'I'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             31.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.920
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.175   8725  Z= 0.146
  Angle     :  0.672  17.253  11780  Z= 0.354
  Chirality :  0.045   0.202   1424
  Planarity :  0.005   0.121   1550
  Dihedral  : 16.271  83.300   3239
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 27.61 %
    Favored  : 72.17 %
  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: -0.17 (0.25), residues: 1155
  helix:  0.10 (0.39), residues: 186
  sheet: -0.12 (0.28), residues: 348
  loop : -0.03 (0.26), residues: 621

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 290 
 TYR   0.013   0.002   TYR C 103 
 PHE   0.021   0.001   PHE C  88 
 HIS   0.002   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 8725)
  covalent geometry    : angle       0.67225 (11780)
  hydrogen bonds       : bond        0.23792 (  359)
  hydrogen bonds       : angle      10.35758 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 142
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.7765 (mm) cc_final: 0.7520 (mp)
REVERT: A  224 GLU cc_start: 0.7518 (mt-10) cc_final: 0.6927 (mt-10)
REVERT: C  194 LEU cc_start: 0.8605 (mt) cc_final: 0.8266 (tp)
REVERT: B  194 LEU cc_start: 0.8889 (mt) cc_final: 0.8583 (mm)
REVERT: B  268 LEU cc_start: 0.8486 (tt) cc_final: 0.8164 (tt)
REVERT: B  327 GLU cc_start: 0.7672 (tt0) cc_final: 0.7341 (tm-30)
REVERT: E  454 MET cc_start: 0.5847 (pmm) cc_final: 0.5523 (pmm)
  outliers start: 2
  outliers final: 1
  residues processed: 142
  average time/residue: 0.0966
  time to fit residues: 18.2945
Evaluate side-chains
  139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  113 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.0030
   chunk 49 optimal weight:    0.3980
   chunk 97 optimal weight:    0.3980
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0970
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    9.9990
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
C 120 GLN
B 107 ASN
B 109 HIS
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 257 GLN
F 447 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.119907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.083715 restraints weight = 17907.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.086564 restraints weight = 9920.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.088483 restraints weight = 6849.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.089627 restraints weight = 5418.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.090326 restraints weight = 4658.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   8725  Z= 0.118
  Angle     :  0.589   9.268  11780  Z= 0.303
  Chirality :  0.046   0.193   1424
  Planarity :  0.004   0.047   1550
  Dihedral  :  4.278  37.494   1241
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 26.62 %
    Favored  : 70.74 %
  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:  0.12 (0.25), residues: 1155
  helix:  0.54 (0.38), residues: 186
  sheet:  0.01 (0.27), residues: 339
  loop :  0.12 (0.27), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 290 
 TYR   0.011   0.002   TYR C 103 
 PHE   0.013   0.001   PHE A 244 
 HIS   0.001   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8725)
  covalent geometry    : angle       0.58937 (11780)
  hydrogen bonds       : bond        0.04100 (  359)
  hydrogen bonds       : angle       6.85160 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 135
  time to evaluate  : 0.394 
Fit side-chains
REVERT: A  224 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7169 (mt-10)
REVERT: C   57 ARG cc_start: 0.7170 (mtp-110) cc_final: 0.6753 (ttm110)
REVERT: C  345 LEU cc_start: 0.8849 (mt) cc_final: 0.8584 (mm)
REVERT: B  194 LEU cc_start: 0.8828 (mt) cc_final: 0.8384 (mm)
REVERT: B  327 GLU cc_start: 0.7445 (tt0) cc_final: 0.7143 (tm-30)
  outliers start: 24
  outliers final: 11
  residues processed: 152
  average time/residue: 0.0991
  time to fit residues: 20.1006
Evaluate side-chains
  137 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  158 ASP
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 106 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0970
   chunk 46 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 100 optimal weight:    9.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
C 210 ASN
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.118952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083832 restraints weight = 18008.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.086506 restraints weight = 10094.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.088315 restraints weight = 7022.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.089568 restraints weight = 5567.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.090183 restraints weight = 4750.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.1715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8725  Z= 0.168
  Angle     :  0.618   9.690  11780  Z= 0.310
  Chirality :  0.046   0.195   1424
  Planarity :  0.004   0.046   1550
  Dihedral  :  4.092  17.805   1238
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 25.96 %
    Favored  : 69.75 %
  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:  0.20 (0.25), residues: 1155
  helix:  0.82 (0.40), residues: 177
  sheet:  0.01 (0.28), residues: 339
  loop :  0.14 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  57 
 TYR   0.007   0.002   TYR C 103 
 PHE   0.012   0.002   PHE C 325 
 HIS   0.002   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8725)
  covalent geometry    : angle       0.61814 (11780)
  hydrogen bonds       : bond        0.03753 (  359)
  hydrogen bonds       : angle       6.27139 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 137
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: A  218 LEU cc_start: 0.8459 (tp) cc_final: 0.8204 (tt)
REVERT: A  224 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7125 (mt-10)
REVERT: C  275 GLU cc_start: 0.8613 (pm20) cc_final: 0.8406 (pm20)
REVERT: C  336 GLU cc_start: 0.8364 (pm20) cc_final: 0.8112 (pm20)
REVERT: B  132 ILE cc_start: 0.8551 (mm) cc_final: 0.8082 (tt)
REVERT: B  194 LEU cc_start: 0.8840 (mt) cc_final: 0.8569 (mm)
REVERT: B  327 GLU cc_start: 0.7532 (tt0) cc_final: 0.7241 (tm-30)
  outliers start: 39
  outliers final: 23
  residues processed: 165
  average time/residue: 0.0819
  time to fit residues: 18.9762
Evaluate side-chains
  146 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue   95 VAL
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  210 ASN
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  298 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain F residue  443 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0040
   chunk 72 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 2 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0670
   overall best weight:    0.5730

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 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 = 0.3896 r_free = 0.3896 target = 0.119922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.084302 restraints weight = 18301.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.087072 restraints weight = 10213.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.089000 restraints weight = 7064.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.089983 restraints weight = 5532.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.090979 restraints weight = 4780.979|
|-----------------------------------------------------------------------------|
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8725  Z= 0.114
  Angle     :  0.611  11.627  11780  Z= 0.299
  Chirality :  0.045   0.188   1424
  Planarity :  0.004   0.047   1550
  Dihedral  :  3.982  18.174   1238
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 28.16 %
    Favored  : 67.77 %
  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:  0.34 (0.26), residues: 1155
  helix:  0.91 (0.40), residues: 177
  sheet:  0.14 (0.28), residues: 339
  loop :  0.21 (0.27), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F 419 
 TYR   0.008   0.001   TYR A 103 
 PHE   0.008   0.001   PHE C 325 
 HIS   0.001   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8725)
  covalent geometry    : angle       0.61131 (11780)
  hydrogen bonds       : bond        0.03226 (  359)
  hydrogen bonds       : angle       5.83564 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8175 (mm) cc_final: 0.7909 (mm)
REVERT: A  218 LEU cc_start: 0.8407 (tp) cc_final: 0.8109 (mt)
REVERT: A  224 GLU cc_start: 0.7522 (mt-10) cc_final: 0.7099 (mt-10)
REVERT: C  336 GLU cc_start: 0.8341 (pm20) cc_final: 0.8119 (pm20)
REVERT: C  345 LEU cc_start: 0.8916 (mt) cc_final: 0.8652 (mm)
REVERT: B   93 SER cc_start: 0.8813 (m) cc_final: 0.8495 (t)
REVERT: B  132 ILE cc_start: 0.8535 (mm) cc_final: 0.8085 (tt)
REVERT: B  194 LEU cc_start: 0.8819 (mt) cc_final: 0.8554 (mm)
REVERT: B  312 ASP cc_start: 0.6317 (t0) cc_final: 0.6028 (t0)
  outliers start: 37
  outliers final: 25
  residues processed: 154
  average time/residue: 0.0885
  time to fit residues: 19.1019
Evaluate side-chains
  149 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  343 LEU
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  312 ASP
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  380 LEU
Chi-restraints excluded: chain E residue  415 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0770
   chunk 103 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 73 optimal weight:    0.7980
   chunk 30 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    1.1744

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
C 107 ASN
C 210 ASN
B 120 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.118621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.083196 restraints weight = 18172.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.086082 restraints weight = 9872.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.088069 restraints weight = 6742.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.089345 restraints weight = 5251.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.090123 restraints weight = 4472.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8725  Z= 0.163
  Angle     :  0.628  11.712  11780  Z= 0.312
  Chirality :  0.046   0.189   1424
  Planarity :  0.004   0.044   1550
  Dihedral  :  4.149  18.982   1238
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  5.50 %
    Allowed  : 26.29 %
    Favored  : 68.21 %
  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:  0.24 (0.26), residues: 1155
  helix:  0.88 (0.40), residues: 177
  sheet:  0.01 (0.28), residues: 342
  loop :  0.17 (0.27), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F 419 
 TYR   0.006   0.001   TYR E 451 
 PHE   0.012   0.002   PHE C 325 
 HIS   0.002   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 8725)
  covalent geometry    : angle       0.62814 (11780)
  hydrogen bonds       : bond        0.03342 (  359)
  hydrogen bonds       : angle       5.74099 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 128
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7096 (mt-10)
REVERT: C  336 GLU cc_start: 0.8392 (pm20) cc_final: 0.8132 (pm20)
REVERT: B  120 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7380 (pm20)
REVERT: B  132 ILE cc_start: 0.8552 (mm) cc_final: 0.8136 (tt)
REVERT: B  194 LEU cc_start: 0.8873 (mt) cc_final: 0.8606 (mm)
REVERT: B  327 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7434 (tm-30)
REVERT: F  419 ARG cc_start: 0.7580 (tpp80) cc_final: 0.7029 (mtt90)
  outliers start: 50
  outliers final: 30
  residues processed: 166
  average time/residue: 0.0851
  time to fit residues: 19.6158
Evaluate side-chains
  150 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  415 ILE
Chi-restraints excluded: chain E residue  443 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 195 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.117233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.082385 restraints weight = 18108.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.085253 restraints weight = 9979.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.087009 restraints weight = 6854.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.088319 restraints weight = 5434.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.089012 restraints weight = 4650.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8725  Z= 0.179
  Angle     :  0.640  12.286  11780  Z= 0.316
  Chirality :  0.046   0.187   1424
  Planarity :  0.004   0.043   1550
  Dihedral  :  4.208  19.385   1238
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.06 %
    Favored  : 67.99 %
  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:  0.13 (0.25), residues: 1155
  helix:  0.82 (0.40), residues: 177
  sheet:  0.01 (0.28), residues: 336
  loop :  0.04 (0.26), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F 445 
 TYR   0.006   0.001   TYR B 103 
 PHE   0.012   0.002   PHE C 325 
 HIS   0.002   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 ( 8725)
  covalent geometry    : angle       0.63980 (11780)
  hydrogen bonds       : bond        0.03350 (  359)
  hydrogen bonds       : angle       5.72281 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 125
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7613 (mm-30)
REVERT: A  224 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7077 (mt-10)
REVERT: A  358 LEU cc_start: 0.9170 (mt) cc_final: 0.8920 (mp)
REVERT: C  336 GLU cc_start: 0.8375 (pm20) cc_final: 0.8110 (pm20)
REVERT: B   57 ARG cc_start: 0.7463 (mtm110) cc_final: 0.6985 (mtm110)
REVERT: B  132 ILE cc_start: 0.8584 (mm) cc_final: 0.8193 (tt)
REVERT: B  194 LEU cc_start: 0.8856 (mt) cc_final: 0.8601 (mm)
REVERT: B  218 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8014 (mp)
  outliers start: 45
  outliers final: 35
  residues processed: 161
  average time/residue: 0.0823
  time to fit residues: 18.7762
Evaluate side-chains
  155 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 119
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  171 VAL
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  380 LEU
Chi-restraints excluded: chain E residue  415 ILE
Chi-restraints excluded: chain E residue  443 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 101 optimal weight:    5.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 100 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 108 optimal weight:    0.0060
   chunk 94 optimal weight:   10.0000
   chunk 85 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
C 107 ASN
C 120 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.118155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.083191 restraints weight = 18185.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.085921 restraints weight = 10210.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.087772 restraints weight = 7088.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.089049 restraints weight = 5602.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.089682 restraints weight = 4781.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8725  Z= 0.125
  Angle     :  0.625  13.450  11780  Z= 0.304
  Chirality :  0.045   0.184   1424
  Planarity :  0.004   0.041   1550
  Dihedral  :  4.082  19.306   1238
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 27.94 %
    Favored  : 67.33 %
  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:  0.20 (0.26), residues: 1155
  helix:  0.87 (0.40), residues: 177
  sheet:  0.17 (0.28), residues: 339
  loop :  0.02 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 290 
 TYR   0.012   0.002   TYR E 451 
 PHE   0.008   0.001   PHE C 325 
 HIS   0.002   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 8725)
  covalent geometry    : angle       0.62489 (11780)
  hydrogen bonds       : bond        0.03001 (  359)
  hydrogen bonds       : angle       5.51124 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8172 (mm) cc_final: 0.7711 (mp)
REVERT: A  200 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7537 (mm-30)
REVERT: A  224 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7069 (mt-10)
REVERT: A  358 LEU cc_start: 0.9180 (mt) cc_final: 0.8929 (mp)
REVERT: C   49 VAL cc_start: 0.8963 (t) cc_final: 0.8750 (m)
REVERT: C   57 ARG cc_start: 0.7200 (mtp-110) cc_final: 0.6865 (ttm110)
REVERT: C  336 GLU cc_start: 0.8392 (pm20) cc_final: 0.8115 (pm20)
REVERT: B   93 SER cc_start: 0.8801 (m) cc_final: 0.8507 (t)
REVERT: B  132 ILE cc_start: 0.8573 (mm) cc_final: 0.8177 (tt)
REVERT: B  194 LEU cc_start: 0.8852 (mt) cc_final: 0.8595 (mm)
REVERT: B  218 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7921 (mp)
REVERT: B  327 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7344 (tm-30)
REVERT: D  419 ARG cc_start: 0.8039 (ttm-80) cc_final: 0.7755 (ttm-80)
  outliers start: 43
  outliers final: 35
  residues processed: 166
  average time/residue: 0.0846
  time to fit residues: 19.6707
Evaluate side-chains
  158 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 122
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  380 LEU
Chi-restraints excluded: chain E residue  415 ILE
Chi-restraints excluded: chain E residue  443 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 109 optimal weight:   10.0000
   chunk 104 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 69 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 115 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
A 195 ASN
** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 120 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.116929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.082257 restraints weight = 18090.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.085087 restraints weight = 9945.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.086987 restraints weight = 6853.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.088317 restraints weight = 5381.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.088873 restraints weight = 4580.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8725  Z= 0.151
  Angle     :  0.637  13.293  11780  Z= 0.310
  Chirality :  0.046   0.183   1424
  Planarity :  0.004   0.042   1550
  Dihedral  :  4.143  19.261   1238
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 27.94 %
    Favored  : 67.44 %
  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:  0.15 (0.26), residues: 1155
  helix:  0.82 (0.40), residues: 177
  sheet:  0.14 (0.28), residues: 339
  loop : -0.02 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 290 
 TYR   0.012   0.002   TYR E 451 
 PHE   0.021   0.001   PHE C  88 
 HIS   0.002   0.001   HIS C 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 8725)
  covalent geometry    : angle       0.63738 (11780)
  hydrogen bonds       : bond        0.03119 (  359)
  hydrogen bonds       : angle       5.52200 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 129
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8196 (mm) cc_final: 0.7837 (mp)
REVERT: A  200 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7529 (mm-30)
REVERT: A  224 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7062 (mt-10)
REVERT: A  358 LEU cc_start: 0.9200 (mt) cc_final: 0.8945 (mp)
REVERT: C  336 GLU cc_start: 0.8401 (pm20) cc_final: 0.8097 (pm20)
REVERT: B   93 SER cc_start: 0.8777 (m) cc_final: 0.8510 (t)
REVERT: B  132 ILE cc_start: 0.8570 (mm) cc_final: 0.8187 (tt)
REVERT: B  194 LEU cc_start: 0.8884 (mt) cc_final: 0.8627 (mm)
REVERT: B  218 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7969 (mp)
REVERT: B  345 LEU cc_start: 0.7731 (tp) cc_final: 0.7418 (pp)
  outliers start: 42
  outliers final: 39
  residues processed: 162
  average time/residue: 0.0801
  time to fit residues: 18.3434
Evaluate side-chains
  161 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 121
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  385 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  415 ILE
Chi-restraints excluded: chain E residue  443 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 70 optimal weight:    0.2980
   chunk 16 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 112 optimal weight:    6.9990
   chunk 81 optimal weight:    0.8980
   chunk 91 optimal weight:    9.9990
   chunk 45 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0980
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
C 107 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.115902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.083347 restraints weight = 18292.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.084664 restraints weight = 9918.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.086763 restraints weight = 7244.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.086898 restraints weight = 5767.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.087027 restraints weight = 5218.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8725  Z= 0.122
  Angle     :  0.641  13.803  11780  Z= 0.312
  Chirality :  0.046   0.181   1424
  Planarity :  0.004   0.046   1550
  Dihedral  :  4.062  19.215   1238
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 28.16 %
    Favored  : 67.22 %
  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:  0.19 (0.26), residues: 1155
  helix:  0.87 (0.41), residues: 177
  sheet:  0.16 (0.28), residues: 339
  loop :  0.01 (0.27), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 290 
 TYR   0.024   0.002   TYR A 103 
 PHE   0.021   0.001   PHE C  88 
 HIS   0.002   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 8725)
  covalent geometry    : angle       0.64110 (11780)
  hydrogen bonds       : bond        0.02953 (  359)
  hydrogen bonds       : angle       5.43522 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 129
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLU cc_start: 0.6470 (pm20) cc_final: 0.5761 (pp20)
REVERT: A  199 LEU cc_start: 0.8188 (mm) cc_final: 0.7693 (mp)
REVERT: A  200 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7491 (mm-30)
REVERT: A  224 GLU cc_start: 0.7507 (mt-10) cc_final: 0.7079 (mt-10)
REVERT: C  140 ILE cc_start: 0.7663 (OUTLIER) cc_final: 0.7353 (mt)
REVERT: C  336 GLU cc_start: 0.8402 (pm20) cc_final: 0.8095 (pm20)
REVERT: B   93 SER cc_start: 0.8793 (m) cc_final: 0.8519 (t)
REVERT: B  132 ILE cc_start: 0.8578 (mm) cc_final: 0.8201 (tt)
REVERT: B  194 LEU cc_start: 0.8861 (mt) cc_final: 0.8605 (mm)
REVERT: B  218 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7978 (mp)
REVERT: B  345 LEU cc_start: 0.7758 (tp) cc_final: 0.7393 (pp)
  outliers start: 42
  outliers final: 36
  residues processed: 162
  average time/residue: 0.0885
  time to fit residues: 19.9853
Evaluate side-chains
  156 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   54 VAL
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  182 THR
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  385 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  415 ILE
Chi-restraints excluded: chain E residue  443 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 83 optimal weight:    0.0010
   chunk 92 optimal weight:    0.0980
   chunk 80 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
C 107 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 447 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.118042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.084669 restraints weight = 18133.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.087326 restraints weight = 9638.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.087681 restraints weight = 6844.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.088293 restraints weight = 6110.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.088338 restraints weight = 5500.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8725  Z= 0.116
  Angle     :  0.651  14.360  11780  Z= 0.313
  Chirality :  0.046   0.178   1424
  Planarity :  0.004   0.039   1550
  Dihedral  :  4.034  18.799   1238
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 28.49 %
    Favored  : 67.33 %
  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:  0.27 (0.26), residues: 1155
  helix:  0.97 (0.41), residues: 177
  sheet:  0.19 (0.28), residues: 339
  loop :  0.05 (0.27), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 290 
 TYR   0.021   0.002   TYR A 103 
 PHE   0.021   0.001   PHE C  88 
 HIS   0.001   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8725)
  covalent geometry    : angle       0.65109 (11780)
  hydrogen bonds       : bond        0.02851 (  359)
  hydrogen bonds       : angle       5.35411 (  966)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 127
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.6500 (pm20) cc_final: 0.5847 (pp20)
REVERT: A  199 LEU cc_start: 0.8180 (mm) cc_final: 0.7652 (mp)
REVERT: A  200 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7524 (mm-30)
REVERT: A  224 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7061 (mt-10)
REVERT: C  140 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7366 (mt)
REVERT: C  336 GLU cc_start: 0.8412 (pm20) cc_final: 0.8069 (pm20)
REVERT: B   57 ARG cc_start: 0.7421 (mtm110) cc_final: 0.6909 (mtm110)
REVERT: B   93 SER cc_start: 0.8777 (m) cc_final: 0.8533 (t)
REVERT: B  132 ILE cc_start: 0.8565 (mm) cc_final: 0.8200 (tt)
REVERT: B  194 LEU cc_start: 0.8872 (mt) cc_final: 0.8605 (mm)
REVERT: B  218 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7915 (mp)
  outliers start: 38
  outliers final: 33
  residues processed: 156
  average time/residue: 0.0860
  time to fit residues: 18.4830
Evaluate side-chains
  162 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  140 ILE
Chi-restraints excluded: chain C residue  142 LEU
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  218 LEU
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  385 LEU
Chi-restraints excluded: chain E residue  392 ILE
Chi-restraints excluded: chain E residue  415 ILE
Chi-restraints excluded: chain E residue  443 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    0.0570
   chunk 83 optimal weight:    0.0070
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    4.9990
   chunk 99 optimal weight:    0.1980
   chunk 88 optimal weight:    4.9990
   chunk 27 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 105 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   overall best weight:    0.3716

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.118194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.084585 restraints weight = 18284.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.086897 restraints weight = 9671.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.087242 restraints weight = 7080.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.087944 restraints weight = 6421.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.088004 restraints weight = 5823.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8725  Z= 0.106
  Angle     :  0.643  14.581  11780  Z= 0.311
  Chirality :  0.046   0.183   1424
  Planarity :  0.004   0.039   1550
  Dihedral  :  3.927  18.375   1238
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 29.37 %
    Favored  : 66.89 %
  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:  0.36 (0.26), residues: 1155
  helix:  1.07 (0.41), residues: 177
  sheet:  0.27 (0.28), residues: 339
  loop :  0.10 (0.27), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 290 
 TYR   0.020   0.002   TYR A 103 
 PHE   0.022   0.001   PHE C  88 
 HIS   0.001   0.001   HIS B 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8725)
  covalent geometry    : angle       0.64335 (11780)
  hydrogen bonds       : bond        0.02706 (  359)
  hydrogen bonds       : angle       5.23185 (  966)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2650.88 seconds
wall clock time: 46 minutes 12.60 seconds (2772.60 seconds total)