Starting phenix.real_space_refine
on Mon May 12 04:22:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w69_37318/05_2025/8w69_37318.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w69_37318/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8w69_37318/05_2025/8w69_37318.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w69_37318/05_2025/8w69_37318.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w69_37318/05_2025/8w69_37318.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w69_37318/05_2025/8w69_37318.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.003
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 10.47, per 1000 atoms: 1.21
  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: 1.94
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 1.25
  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: 2.63

  Time building geometry restraints manager: 2.28 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:             29.350
  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:          0.760
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.020
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.380
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (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
 HIS   0.002   0.001   HIS B 109 
 PHE   0.021   0.001   PHE C  88 
 TYR   0.013   0.002   TYR C 103 
 ARG   0.007   0.001   ARG A 290 

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

*********************** 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  : 0.859 
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: 0.2307
  time to fit residues: 43.5693
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  : 0.863 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9990
   chunk 88 optimal weight:    6.9990
   chunk 49 optimal weight:    0.3980
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 47 optimal weight:    0.3980
   chunk 91 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 68 optimal weight:    0.4980
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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**
A 195 ASN
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 = 0.3887 r_free = 0.3887 target = 0.120266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.084529 restraints weight = 17992.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.087226 restraints weight = 10086.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.089074 restraints weight = 7001.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   8725  Z= 0.160
  Angle     :  0.616   8.778  11780  Z= 0.316
  Chirality :  0.047   0.200   1424
  Planarity :  0.004   0.047   1550
  Dihedral  :  4.463  37.816   1241
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 26.07 %
    Favored  : 70.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.01 (0.25), residues: 1155
  helix:  0.46 (0.38), residues: 186
  sheet: -0.07 (0.27), residues: 339
  loop :  0.05 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B 109 
 PHE   0.013   0.002   PHE C 325 
 TYR   0.011   0.002   TYR C 103 
 ARG   0.004   0.001   ARG A 191 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04319 (  359)
  hydrogen bonds       : angle       6.90007 (  966)
  covalent geometry    : bond        0.00378 ( 8725)
  covalent geometry    : angle       0.61614 (11780)

*********************** 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
  166 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 1.015 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.7695 (mp0) cc_final: 0.7474 (pm20)
REVERT: A  224 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7146 (mt-10)
REVERT: C  194 LEU cc_start: 0.8611 (mt) cc_final: 0.8387 (tp)
REVERT: B  194 LEU cc_start: 0.8864 (mt) cc_final: 0.8558 (mm)
REVERT: B  327 GLU cc_start: 0.7526 (tt0) cc_final: 0.7217 (tm-30)
  outliers start: 33
  outliers final: 19
  residues processed: 157
  average time/residue: 0.2329
  time to fit residues: 49.4565
Evaluate side-chains
  145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 126
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  142 LEU
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  158 ASP
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 B residue  210 ASN
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  258 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 F residue  443 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 48 optimal weight:    0.4980
   chunk 62 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
B 120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.116851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.082134 restraints weight = 18454.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.084852 restraints weight = 10240.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.086577 restraints weight = 7077.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1784

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= 0.146
  Angle     :  0.597   9.387  11780  Z= 0.302
  Chirality :  0.046   0.191   1424
  Planarity :  0.004   0.047   1550
  Dihedral  :  4.068  18.069   1238
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 26.51 %
    Favored  : 68.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.25), residues: 1155
  helix:  0.83 (0.40), residues: 177
  sheet: -0.07 (0.28), residues: 339
  loop :  0.09 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 109 
 PHE   0.011   0.001   PHE C 325 
 TYR   0.007   0.002   TYR A 103 
 ARG   0.006   0.001   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03697 (  359)
  hydrogen bonds       : angle       6.27679 (  966)
  covalent geometry    : bond        0.00348 ( 8725)
  covalent geometry    : angle       0.59678 (11780)

*********************** 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
  173 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 131
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7139 (mt-10)
REVERT: C   89 GLU cc_start: 0.2845 (pp20) cc_final: 0.2573 (pp20)
REVERT: C  194 LEU cc_start: 0.8665 (mt) cc_final: 0.8378 (tp)
REVERT: C  336 GLU cc_start: 0.8370 (pm20) cc_final: 0.8119 (pm20)
REVERT: C  345 LEU cc_start: 0.8905 (mt) cc_final: 0.8644 (mm)
REVERT: B  132 ILE cc_start: 0.8561 (mm) cc_final: 0.8094 (tt)
REVERT: B  194 LEU cc_start: 0.8851 (mt) cc_final: 0.8569 (mm)
REVERT: B  327 GLU cc_start: 0.7536 (tt0) cc_final: 0.7267 (tm-30)
  outliers start: 42
  outliers final: 25
  residues processed: 163
  average time/residue: 0.1951
  time to fit residues: 43.9061
Evaluate side-chains
  148 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
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  104 VAL
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  221 LEU
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  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  149 SER
Chi-restraints excluded: chain B residue  210 ASN
Chi-restraints excluded: chain B residue  221 LEU
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 106 optimal weight:    4.9990
   chunk 29 optimal weight:    9.9990
   chunk 22 optimal weight:    0.7980
   chunk 10 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9990
   chunk 94 optimal weight:    7.9990
   chunk 79 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 105 optimal weight:    0.4980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 120 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 = 0.3880 r_free = 0.3880 target = 0.118621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.085015 restraints weight = 18205.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.087033 restraints weight = 9980.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.088540 restraints weight = 6978.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2073

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= 0.112
  Angle     :  0.594  11.390  11780  Z= 0.294
  Chirality :  0.045   0.186   1424
  Planarity :  0.004   0.043   1550
  Dihedral  :  3.948  18.529   1238
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.96 %
    Allowed  : 27.94 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1155
  helix:  0.91 (0.40), residues: 177
  sheet:  0.01 (0.28), residues: 339
  loop :  0.15 (0.27), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 109 
 PHE   0.008   0.001   PHE C 325 
 TYR   0.008   0.001   TYR A 103 
 ARG   0.007   0.000   ARG D 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  359)
  hydrogen bonds       : angle       5.82756 (  966)
  covalent geometry    : bond        0.00261 ( 8725)
  covalent geometry    : angle       0.59447 (11780)

*********************** 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
  171 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 135
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLU cc_start: 0.7772 (mp0) cc_final: 0.7493 (pm20)
REVERT: A  224 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7073 (mt-10)
REVERT: C   57 ARG cc_start: 0.7239 (mtp-110) cc_final: 0.6869 (ttm110)
REVERT: C  194 LEU cc_start: 0.8635 (mt) cc_final: 0.8408 (tp)
REVERT: C  287 ASP cc_start: 0.8160 (t0) cc_final: 0.7950 (t0)
REVERT: C  336 GLU cc_start: 0.8374 (pm20) cc_final: 0.8085 (pm20)
REVERT: C  345 LEU cc_start: 0.8942 (mt) cc_final: 0.8649 (mm)
REVERT: B   93 SER cc_start: 0.8798 (m) cc_final: 0.8508 (t)
REVERT: B  132 ILE cc_start: 0.8549 (mm) cc_final: 0.8108 (tt)
REVERT: B  194 LEU cc_start: 0.8841 (mt) cc_final: 0.8565 (mm)
  outliers start: 36
  outliers final: 26
  residues processed: 161
  average time/residue: 0.1902
  time to fit residues: 42.4799
Evaluate side-chains
  145 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
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  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  111 ILE
Chi-restraints excluded: chain C residue  113 GLN
Chi-restraints excluded: chain C residue  120 GLN
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  210 ASN
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  210 ASN
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  242 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 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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 101 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    0.8586

-------------------------------------------------------------------------------
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
** B 120 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 = 0.3875 r_free = 0.3875 target = 0.118387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.082859 restraints weight = 18098.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.085618 restraints weight = 10200.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.087351 restraints weight = 7103.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.2285

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= 0.131
  Angle     :  0.604  12.269  11780  Z= 0.299
  Chirality :  0.045   0.179   1424
  Planarity :  0.004   0.042   1550
  Dihedral  :  3.983  18.619   1238
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  5.72 %
    Allowed  : 26.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.26), residues: 1155
  helix:  0.96 (0.41), residues: 177
  sheet:  0.00 (0.28), residues: 339
  loop :  0.14 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 109 
 PHE   0.009   0.001   PHE C 325 
 TYR   0.006   0.001   TYR A 103 
 ARG   0.006   0.000   ARG D 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 (  359)
  hydrogen bonds       : angle       5.70758 (  966)
  covalent geometry    : bond        0.00314 ( 8725)
  covalent geometry    : angle       0.60420 (11780)

*********************** 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
  182 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 130
  time to evaluate  : 0.867 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7563 (mm-30)
REVERT: A  224 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7128 (mt-10)
REVERT: C  112 ASN cc_start: 0.8344 (t0) cc_final: 0.8119 (p0)
REVERT: C  287 ASP cc_start: 0.8149 (t0) cc_final: 0.7907 (t0)
REVERT: C  336 GLU cc_start: 0.8365 (pm20) cc_final: 0.8094 (pm20)
REVERT: B   93 SER cc_start: 0.8822 (m) cc_final: 0.8518 (t)
REVERT: B  132 ILE cc_start: 0.8568 (mm) cc_final: 0.8144 (tt)
REVERT: B  194 LEU cc_start: 0.8855 (mt) cc_final: 0.8579 (mm)
REVERT: B  218 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7804 (mp)
  outliers start: 52
  outliers final: 35
  residues processed: 171
  average time/residue: 0.1906
  time to fit residues: 45.3398
Evaluate side-chains
  160 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
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  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  295 SER
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  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  210 ASN
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  327 GLU
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  221 LEU
Chi-restraints excluded: chain B residue  240 VAL
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 103 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 100 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
C 195 ASN
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 249 ASN
** F 442 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 = 0.3801 r_free = 0.3801 target = 0.113802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.079569 restraints weight = 18316.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.082283 restraints weight = 10143.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.084181 restraints weight = 7025.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7725
moved from start:          0.2999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   8725  Z= 0.270
  Angle     :  0.745  11.948  11780  Z= 0.368
  Chirality :  0.049   0.219   1424
  Planarity :  0.005   0.049   1550
  Dihedral  :  4.735  19.696   1238
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 27.61 %
    Favored  : 66.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1155
  helix:  0.54 (0.40), residues: 177
  sheet: -0.17 (0.28), residues: 336
  loop : -0.15 (0.26), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 109 
 PHE   0.018   0.003   PHE B 325 
 TYR   0.005   0.002   TYR D 451 
 ARG   0.013   0.001   ARG F 445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  359)
  hydrogen bonds       : angle       6.14720 (  966)
  covalent geometry    : bond        0.00641 ( 8725)
  covalent geometry    : angle       0.74469 (11780)

*********************** 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
  185 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 132
  time to evaluate  : 0.891 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ASP cc_start: 0.7726 (t0) cc_final: 0.7489 (t0)
REVERT: A  200 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7619 (mm-30)
REVERT: A  358 LEU cc_start: 0.9225 (mt) cc_final: 0.8981 (mp)
REVERT: C  287 ASP cc_start: 0.8252 (t0) cc_final: 0.8024 (t0)
REVERT: C  336 GLU cc_start: 0.8458 (pm20) cc_final: 0.8075 (pm20)
REVERT: B  132 ILE cc_start: 0.8613 (mm) cc_final: 0.8228 (tt)
REVERT: B  194 LEU cc_start: 0.8948 (mt) cc_final: 0.8698 (mm)
REVERT: B  327 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7438 (tm-30)
REVERT: E  454 MET cc_start: 0.6250 (pmm) cc_final: 0.5991 (pmm)
  outliers start: 53
  outliers final: 42
  residues processed: 173
  average time/residue: 0.1948
  time to fit residues: 46.8428
Evaluate side-chains
  160 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 118
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
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  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  221 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  142 LEU
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  279 ASP
Chi-restraints excluded: chain B residue   54 VAL
Chi-restraints excluded: chain B residue   88 PHE
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  219 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  239 SER
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  288 VAL
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 49 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 94 optimal weight:    8.9990
   chunk 8 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    0.3980
   chunk 19 optimal weight:    0.9980
   chunk 107 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 109 HIS
A 204 GLN
C 107 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: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.115245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.080538 restraints weight = 18173.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.083417 restraints weight = 9856.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.085395 restraints weight = 6757.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3116

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= 0.121
  Angle     :  0.639  13.744  11780  Z= 0.311
  Chirality :  0.046   0.183   1424
  Planarity :  0.004   0.043   1550
  Dihedral  :  4.276  19.768   1238
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.82 %
    Favored  : 66.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1155
  helix:  0.76 (0.41), residues: 177
  sheet:  0.05 (0.28), residues: 321
  loop : -0.12 (0.26), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 109 
 PHE   0.009   0.001   PHE C 244 
 TYR   0.013   0.002   TYR E 451 
 ARG   0.007   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03056 (  359)
  hydrogen bonds       : angle       5.66917 (  966)
  covalent geometry    : bond        0.00286 ( 8725)
  covalent geometry    : angle       0.63892 (11780)

*********************** 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
  168 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 128
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7501 (mm-30)
REVERT: A  224 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7248 (mt-10)
REVERT: A  358 LEU cc_start: 0.9197 (mt) cc_final: 0.8943 (mp)
REVERT: C   49 VAL cc_start: 0.8966 (t) cc_final: 0.8728 (m)
REVERT: C  336 GLU cc_start: 0.8429 (pm20) cc_final: 0.8087 (pm20)
REVERT: B   57 ARG cc_start: 0.7522 (mtm110) cc_final: 0.6866 (mtm110)
REVERT: B   93 SER cc_start: 0.8772 (m) cc_final: 0.8508 (t)
REVERT: B  132 ILE cc_start: 0.8586 (mm) cc_final: 0.8197 (tt)
REVERT: B  194 LEU cc_start: 0.8898 (mt) cc_final: 0.8635 (mm)
REVERT: E  454 MET cc_start: 0.6532 (pmm) cc_final: 0.6190 (pmm)
  outliers start: 40
  outliers final: 31
  residues processed: 161
  average time/residue: 0.1921
  time to fit residues: 43.2370
Evaluate side-chains
  157 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.875 
-------------------------------------------------------------------------------
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  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  221 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  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  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  219 LEU
Chi-restraints excluded: chain B residue  221 LEU
Chi-restraints excluded: chain B residue  240 VAL
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  385 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 88 optimal weight:    7.9990
   chunk 49 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 110 optimal weight:    8.9990
   chunk 112 optimal weight:    6.9990
   chunk 96 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 114 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 447 ASN
** F 442 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 = 0.3805 r_free = 0.3805 target = 0.115133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.080658 restraints weight = 18459.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.083550 restraints weight = 9932.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.085450 restraints weight = 6772.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   8725  Z= 0.198
  Angle     :  0.684  14.199  11780  Z= 0.335
  Chirality :  0.047   0.185   1424
  Planarity :  0.004   0.045   1550
  Dihedral  :  4.467  19.411   1238
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 28.27 %
    Favored  : 67.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1155
  helix:  0.68 (0.40), residues: 177
  sheet: -0.02 (0.28), residues: 321
  loop : -0.29 (0.25), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 109 
 PHE   0.020   0.002   PHE C  88 
 TYR   0.015   0.002   TYR E 451 
 ARG   0.007   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 (  359)
  hydrogen bonds       : angle       5.80332 (  966)
  covalent geometry    : bond        0.00472 ( 8725)
  covalent geometry    : angle       0.68358 (11780)

*********************** 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
  175 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 132
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A  135 ASP cc_start: 0.7743 (t0) cc_final: 0.7495 (t0)
REVERT: A  200 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7531 (mm-30)
REVERT: A  224 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7237 (mt-10)
REVERT: A  358 LEU cc_start: 0.9234 (mt) cc_final: 0.9006 (mp)
REVERT: C  336 GLU cc_start: 0.8449 (pm20) cc_final: 0.8049 (pm20)
REVERT: B  132 ILE cc_start: 0.8611 (mm) cc_final: 0.8250 (tt)
REVERT: B  194 LEU cc_start: 0.8937 (mt) cc_final: 0.8670 (mm)
REVERT: B  327 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7474 (tm-30)
REVERT: B  345 LEU cc_start: 0.7696 (tp) cc_final: 0.7437 (pp)
REVERT: E  454 MET cc_start: 0.6727 (pmm) cc_final: 0.6339 (pmm)
  outliers start: 43
  outliers final: 38
  residues processed: 165
  average time/residue: 0.1875
  time to fit residues: 43.9258
Evaluate side-chains
  159 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 121
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  221 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  210 ASN
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  110 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  219 LEU
Chi-restraints excluded: chain B residue  221 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  288 VAL
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 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 78 optimal weight:    0.0870
   chunk 11 optimal weight:    0.8980
   chunk 114 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 97 optimal weight:    0.2980
   chunk 101 optimal weight:    9.9990
   chunk 99 optimal weight:    0.4980
   chunk 63 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
C 107 ASN
B 120 GLN
** 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 = 0.3838 r_free = 0.3838 target = 0.116726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.082321 restraints weight = 18333.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.085029 restraints weight = 10330.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.086917 restraints weight = 7200.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3528

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= 0.110
  Angle     :  0.651  15.204  11780  Z= 0.315
  Chirality :  0.046   0.178   1424
  Planarity :  0.004   0.039   1550
  Dihedral  :  4.165  18.926   1238
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 29.70 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.26), residues: 1155
  helix:  0.87 (0.41), residues: 177
  sheet:  0.08 (0.28), residues: 321
  loop : -0.16 (0.26), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 109 
 PHE   0.022   0.001   PHE C  88 
 TYR   0.019   0.002   TYR A 103 
 ARG   0.006   0.001   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02862 (  359)
  hydrogen bonds       : angle       5.43593 (  966)
  covalent geometry    : bond        0.00253 ( 8725)
  covalent geometry    : angle       0.65120 (11780)

*********************** 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
  168 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 135
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
REVERT: A  200 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7432 (mm-30)
REVERT: A  358 LEU cc_start: 0.9199 (mt) cc_final: 0.8963 (mp)
REVERT: C  140 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7457 (mt)
REVERT: C  336 GLU cc_start: 0.8413 (pm20) cc_final: 0.8044 (pm20)
REVERT: B   57 ARG cc_start: 0.7442 (mtm110) cc_final: 0.6935 (mtm110)
REVERT: B   93 SER cc_start: 0.8801 (m) cc_final: 0.8569 (t)
REVERT: B  132 ILE cc_start: 0.8600 (mm) cc_final: 0.8248 (tt)
REVERT: B  194 LEU cc_start: 0.8863 (mt) cc_final: 0.8605 (mm)
REVERT: B  327 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7466 (tm-30)
REVERT: B  345 LEU cc_start: 0.7667 (tp) cc_final: 0.7376 (pp)
REVERT: E  454 MET cc_start: 0.6875 (pmm) cc_final: 0.6508 (pmm)
  outliers start: 33
  outliers final: 25
  residues processed: 162
  average time/residue: 0.2062
  time to fit residues: 46.6152
Evaluate side-chains
  144 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 118
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  345 LEU
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  140 ILE
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  110 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  171 VAL
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 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  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 44 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 102 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 113 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
C 210 ASN
** 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 = 0.3837 r_free = 0.3837 target = 0.116460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.082029 restraints weight = 18265.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.084693 restraints weight = 10258.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.086565 restraints weight = 7169.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.123   8725  Z= 0.173
  Angle     :  0.942  59.139  11780  Z= 0.531
  Chirality :  0.046   0.239   1424
  Planarity :  0.004   0.039   1550
  Dihedral  :  4.174  18.811   1238
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 30.25 %
    Favored  : 66.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.26), residues: 1155
  helix:  0.86 (0.41), residues: 177
  sheet:  0.07 (0.28), residues: 321
  loop : -0.16 (0.26), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 109 
 PHE   0.022   0.001   PHE C  88 
 TYR   0.018   0.003   TYR A 103 
 ARG   0.006   0.001   ARG D 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02888 (  359)
  hydrogen bonds       : angle       5.43940 (  966)
  covalent geometry    : bond        0.00386 ( 8725)
  covalent geometry    : angle       0.94218 (11780)

********************** 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
  150 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.986 
Fit side-chains
REVERT: A  200 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A  358 LEU cc_start: 0.9198 (mt) cc_final: 0.8963 (mp)
REVERT: C  336 GLU cc_start: 0.8416 (pm20) cc_final: 0.8043 (pm20)
REVERT: B   57 ARG cc_start: 0.7370 (mtm110) cc_final: 0.6767 (mtm110)
REVERT: B   93 SER cc_start: 0.8794 (m) cc_final: 0.8559 (t)
REVERT: B  132 ILE cc_start: 0.8600 (mm) cc_final: 0.8241 (tt)
REVERT: B  194 LEU cc_start: 0.8871 (mt) cc_final: 0.8609 (mm)
REVERT: B  345 LEU cc_start: 0.7661 (tp) cc_final: 0.7377 (pp)
REVERT: E  454 MET cc_start: 0.6864 (pmm) cc_final: 0.6512 (pmm)
  outliers start: 31
  outliers final: 26
  residues processed: 143
  average time/residue: 0.1997
  time to fit residues: 40.1381
Evaluate side-chains
  150 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.870 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  345 LEU
Chi-restraints excluded: chain C residue   58 VAL
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  186 VAL
Chi-restraints excluded: chain C residue  210 ASN
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  221 LEU
Chi-restraints excluded: chain C residue  345 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  110 VAL
Chi-restraints excluded: chain B residue  171 VAL
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 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  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 70 optimal weight:    0.9980
   chunk 29 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   chunk 100 optimal weight:    0.2980
   chunk 66 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 93 optimal weight:   20.0000
   chunk 89 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
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 = 0.3839 r_free = 0.3839 target = 0.116744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.082451 restraints weight = 18345.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.085124 restraints weight = 10258.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.087021 restraints weight = 7143.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.223   8725  Z= 0.240
  Angle     :  1.118  59.173  11780  Z= 0.668
  Chirality :  0.049   0.571   1424
  Planarity :  0.005   0.100   1550
  Dihedral  :  4.177  18.786   1238
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 30.25 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.25), residues: 1155
  helix:  0.86 (0.41), residues: 177
  sheet:  0.07 (0.28), residues: 321
  loop : -0.17 (0.26), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS B 109 
 PHE   0.021   0.001   PHE C  88 
 TYR   0.017   0.002   TYR A 103 
 ARG   0.005   0.000   ARG D 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02899 (  359)
  hydrogen bonds       : angle       5.43863 (  966)
  covalent geometry    : bond        0.00509 ( 8725)
  covalent geometry    : angle       1.11771 (11780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4763.88 seconds
wall clock time: 84 minutes 48.18 seconds (5088.18 seconds total)