Starting phenix.real_space_refine
on Sat Jul 26 16:24:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8w69_37318/07_2025/8w69_37318.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8w69_37318/07_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_37318/07_2025/8w69_37318.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8w69_37318/07_2025/8w69_37318.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8w69_37318/07_2025/8w69_37318.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8w69_37318/07_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-5711/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: 12.47, per 1000 atoms: 1.44
  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: 2.04
  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: 1.27
  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: 2.68

  Time building geometry restraints manager: 2.44 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:             27.930
  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:          0.700
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     30.330
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   62.260
-------------------------------------------------------------------------------
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  : 0.931 
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: 0.2402
  time to fit residues: 45.3715
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  : 0.937 
-------------------------------------------------------------------------------
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 = 0.120267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.084522 restraints weight = 17992.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.087229 restraints weight = 10094.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.089087 restraints weight = 7002.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
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   8.788  11780  Z= 0.316
  Chirality :  0.047   0.200   1424
  Planarity :  0.004   0.047   1550
  Dihedral  :  4.463  37.819   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        0.04321 (  359)
  hydrogen bonds       : angle       6.90114 (  966)
  covalent geometry    : bond        0.00378 ( 8725)
  covalent geometry    : angle       0.61616 (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  : 1.001 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.7695 (mp0) cc_final: 0.7474 (pm20)
REVERT: A  224 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7145 (mt-10)
REVERT: C  194 LEU cc_start: 0.8612 (mt) cc_final: 0.8386 (tp)
REVERT: B  194 LEU cc_start: 0.8865 (mt) cc_final: 0.8558 (mm)
REVERT: B  327 GLU cc_start: 0.7526 (tt0) cc_final: 0.7218 (tm-30)
  outliers start: 33
  outliers final: 19
  residues processed: 157
  average time/residue: 0.2331
  time to fit residues: 49.0862
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  : 0.926 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 48 optimal weight:    0.0870
   chunk 62 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   overall best weight:    0.9762

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.116644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.081767 restraints weight = 18482.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.084453 restraints weight = 10270.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.086303 restraints weight = 7126.593|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1833

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= 0.144
  Angle     :  0.597   9.627  11780  Z= 0.301
  Chirality :  0.046   0.198   1424
  Planarity :  0.004   0.046   1550
  Dihedral  :  4.068  18.166   1238
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 26.73 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.14 (0.25), residues: 1155
  helix:  0.85 (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 B 202 
 TYR   0.008   0.002   TYR A 103 
 ARG   0.009   0.001   ARG A  57 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03658 (  359)
  hydrogen bonds       : angle       6.19791 (  966)
  covalent geometry    : bond        0.00341 ( 8725)
  covalent geometry    : angle       0.59690 (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: 41
    poor density    : 132
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
REVERT: A  224 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: C   89 GLU cc_start: 0.2865 (pp20) cc_final: 0.2610 (pp20)
REVERT: C  194 LEU cc_start: 0.8640 (mt) cc_final: 0.8363 (tp)
REVERT: C  336 GLU cc_start: 0.8358 (pm20) cc_final: 0.8113 (pm20)
REVERT: C  345 LEU cc_start: 0.8916 (mt) cc_final: 0.8657 (mm)
REVERT: B   93 SER cc_start: 0.8811 (m) cc_final: 0.8507 (t)
REVERT: B  132 ILE cc_start: 0.8567 (mm) cc_final: 0.8101 (tt)
REVERT: B  194 LEU cc_start: 0.8855 (mt) cc_final: 0.8579 (mm)
REVERT: B  312 ASP cc_start: 0.6430 (t0) cc_final: 0.6125 (t0)
REVERT: B  327 GLU cc_start: 0.7544 (tt0) cc_final: 0.7285 (tm-30)
  outliers start: 41
  outliers final: 24
  residues processed: 164
  average time/residue: 0.2013
  time to fit residues: 45.6433
Evaluate side-chains
  146 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  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:    0.2980
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 94 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9990
   chunk 49 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3882 r_free = 0.3882 target = 0.119210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.083811 restraints weight = 18179.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.086565 restraints weight = 10201.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.088396 restraints weight = 7102.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2138

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= 0.122
  Angle     :  0.596  11.285  11780  Z= 0.296
  Chirality :  0.045   0.184   1424
  Planarity :  0.004   0.043   1550
  Dihedral  :  4.006  18.636   1238
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.06 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.21 (0.26), residues: 1155
  helix:  0.88 (0.40), residues: 177
  sheet: -0.01 (0.28), residues: 339
  loop :  0.14 (0.26), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS C 109 
 PHE   0.009   0.001   PHE C 325 
 TYR   0.007   0.001   TYR A 103 
 ARG   0.007   0.001   ARG D 419 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03233 (  359)
  hydrogen bonds       : angle       5.81981 (  966)
  covalent geometry    : bond        0.00288 ( 8725)
  covalent geometry    : angle       0.59594 (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
  175 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 130
  time to evaluate  : 1.020 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8041 (mm) cc_final: 0.7773 (mp)
REVERT: A  200 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7551 (mm-30)
REVERT: A  224 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7119 (mt-10)
REVERT: C   57 ARG cc_start: 0.7255 (mtp-110) cc_final: 0.6892 (ttm110)
REVERT: C  194 LEU cc_start: 0.8623 (mt) cc_final: 0.8413 (tp)
REVERT: C  336 GLU cc_start: 0.8359 (pm20) cc_final: 0.8096 (pm20)
REVERT: C  345 LEU cc_start: 0.8951 (mt) cc_final: 0.8691 (mm)
REVERT: B   93 SER cc_start: 0.8809 (m) cc_final: 0.8512 (t)
REVERT: B  132 ILE cc_start: 0.8568 (mm) cc_final: 0.8130 (tt)
REVERT: B  194 LEU cc_start: 0.8847 (mt) cc_final: 0.8568 (mm)
  outliers start: 45
  outliers final: 31
  residues processed: 164
  average time/residue: 0.1865
  time to fit residues: 43.0990
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  : 0.895 
-------------------------------------------------------------------------------
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  345 LEU
Chi-restraints excluded: chain C residue   54 VAL
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  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 B residue  104 VAL
Chi-restraints excluded: chain B residue  171 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 85 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0970
   chunk 47 optimal weight:    0.0170
   chunk 34 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0070
   chunk 66 optimal weight:    3.9990
   chunk 74 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.3234

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.119882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.084671 restraints weight = 17953.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.087487 restraints weight = 10052.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.089234 restraints weight = 6957.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8725  Z= 0.098
  Angle     :  0.578  12.540  11780  Z= 0.286
  Chirality :  0.045   0.183   1424
  Planarity :  0.004   0.037   1550
  Dihedral  :  3.886  18.538   1238
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 27.72 %
    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:  0.30 (0.26), residues: 1155
  helix:  1.06 (0.41), residues: 177
  sheet:  0.03 (0.28), residues: 339
  loop :  0.18 (0.27), residues: 639

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 109 
 PHE   0.006   0.001   PHE C 293 
 TYR   0.008   0.001   TYR A 103 
 ARG   0.006   0.000   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02970 (  359)
  hydrogen bonds       : angle       5.56297 (  966)
  covalent geometry    : bond        0.00228 ( 8725)
  covalent geometry    : angle       0.57791 (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
  168 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 129
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
REVERT: A   57 ARG cc_start: 0.7161 (ttm110) cc_final: 0.6754 (ttp-110)
REVERT: A  199 LEU cc_start: 0.8070 (mm) cc_final: 0.7799 (mp)
REVERT: A  200 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7554 (mm-30)
REVERT: A  224 GLU cc_start: 0.7531 (mt-10) cc_final: 0.7123 (mt-10)
REVERT: C   49 VAL cc_start: 0.8961 (t) cc_final: 0.8715 (m)
REVERT: C  336 GLU cc_start: 0.8354 (pm20) cc_final: 0.8113 (pm20)
REVERT: C  345 LEU cc_start: 0.8964 (mt) cc_final: 0.8708 (mm)
REVERT: B   93 SER cc_start: 0.8809 (m) cc_final: 0.8523 (t)
REVERT: B  132 ILE cc_start: 0.8555 (mm) cc_final: 0.8133 (tt)
REVERT: B  194 LEU cc_start: 0.8830 (mt) cc_final: 0.8551 (mm)
  outliers start: 39
  outliers final: 24
  residues processed: 160
  average time/residue: 0.2157
  time to fit residues: 46.9665
Evaluate side-chains
  142 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
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  113 GLN
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  221 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain B residue  298 LEU
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  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  380 LEU
Chi-restraints excluded: chain E residue  415 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 110 optimal weight:    8.9990
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 103 optimal weight:    9.9990
   chunk 17 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 22 optimal weight:    0.3980
   chunk 2 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    1.8788

-------------------------------------------------------------------------------
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 195 ASN
C 210 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: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.114011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.079473 restraints weight = 18309.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.082230 restraints weight = 10021.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.084031 restraints weight = 6904.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   8725  Z= 0.232
  Angle     :  0.691  12.316  11780  Z= 0.338
  Chirality :  0.047   0.189   1424
  Planarity :  0.004   0.044   1550
  Dihedral  :  4.369  19.113   1238
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 27.06 %
    Favored  : 67.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.05 (0.25), residues: 1155
  helix:  0.81 (0.40), residues: 177
  sheet: -0.16 (0.28), residues: 342
  loop :  0.04 (0.26), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 109 
 PHE   0.024   0.002   PHE C  88 
 TYR   0.005   0.001   TYR B 103 
 ARG   0.006   0.001   ARG B 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03606 (  359)
  hydrogen bonds       : angle       5.85915 (  966)
  covalent geometry    : bond        0.00549 ( 8725)
  covalent geometry    : angle       0.69075 (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
  175 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 129
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ASP cc_start: 0.7675 (t0) cc_final: 0.7418 (t0)
REVERT: A  200 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7602 (mm-30)
REVERT: A  358 LEU cc_start: 0.9200 (mt) cc_final: 0.8942 (mp)
REVERT: C  336 GLU cc_start: 0.8420 (pm20) cc_final: 0.8105 (pm20)
REVERT: B  132 ILE cc_start: 0.8599 (mm) cc_final: 0.8207 (tt)
REVERT: B  327 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7351 (tm-30)
  outliers start: 46
  outliers final: 38
  residues processed: 166
  average time/residue: 0.1984
  time to fit residues: 46.2176
Evaluate side-chains
  157 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 119
  time to evaluate  : 0.960 
-------------------------------------------------------------------------------
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  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 B residue   54 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  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  280 ILE
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  332 ILE
Chi-restraints excluded: chain B residue  339 THR
Chi-restraints excluded: chain B residue  354 VAL
Chi-restraints excluded: chain D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
Chi-restraints excluded: chain F residue  443 ILE
Chi-restraints excluded: chain E residue  380 LEU
Chi-restraints excluded: chain E residue  385 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:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0030
   chunk 21 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0270
   chunk 94 optimal weight:    8.9990
   chunk 8 optimal weight:    0.0570
   chunk 12 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0670
   chunk 19 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   overall best weight:    0.1504

-------------------------------------------------------------------------------
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
** 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 = 0.3869 r_free = 0.3869 target = 0.118136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.082866 restraints weight = 18350.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.085651 restraints weight = 10365.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.087506 restraints weight = 7215.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8725  Z= 0.099
  Angle     :  0.626  14.559  11780  Z= 0.301
  Chirality :  0.045   0.204   1424
  Planarity :  0.004   0.038   1550
  Dihedral  :  4.032  19.198   1238
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 29.70 %
    Favored  : 67.11 %
  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:  0.92 (0.40), residues: 177
  sheet:  0.15 (0.28), residues: 321
  loop :  0.04 (0.26), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 109 
 PHE   0.020   0.001   PHE C  88 
 TYR   0.009   0.002   TYR A 103 
 ARG   0.007   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02849 (  359)
  hydrogen bonds       : angle       5.45706 (  966)
  covalent geometry    : bond        0.00225 ( 8725)
  covalent geometry    : angle       0.62591 (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
  155 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8137 (mm) cc_final: 0.7610 (mp)
REVERT: A  200 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7509 (mm-30)
REVERT: A  358 LEU cc_start: 0.9180 (mt) cc_final: 0.8929 (mp)
REVERT: C   49 VAL cc_start: 0.8946 (t) cc_final: 0.8706 (m)
REVERT: C  336 GLU cc_start: 0.8380 (pm20) cc_final: 0.8104 (pm20)
REVERT: B   93 SER cc_start: 0.8731 (m) cc_final: 0.8500 (t)
REVERT: B  132 ILE cc_start: 0.8549 (mm) cc_final: 0.8155 (tt)
  outliers start: 29
  outliers final: 20
  residues processed: 148
  average time/residue: 0.2119
  time to fit residues: 43.2689
Evaluate side-chains
  139 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  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  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  242 ILE
Chi-restraints excluded: chain D residue  380 LEU
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  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:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 110 optimal weight:   10.0000
   chunk 112 optimal weight:    6.9990
   chunk 96 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 67 optimal weight:    0.2980
   chunk 114 optimal weight:    1.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.115321 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.080482 restraints weight = 18337.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.083309 restraints weight = 9991.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.085228 restraints weight = 6873.099|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   8725  Z= 0.196
  Angle     :  0.677  13.828  11780  Z= 0.329
  Chirality :  0.047   0.187   1424
  Planarity :  0.004   0.041   1550
  Dihedral  :  4.305  18.825   1238
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 28.49 %
    Favored  : 67.11 %
  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 (0.25), residues: 1155
  helix:  0.77 (0.40), residues: 177
  sheet:  0.06 (0.28), residues: 321
  loop : -0.11 (0.26), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS C 109 
 PHE   0.023   0.002   PHE C  88 
 TYR   0.011   0.002   TYR A 103 
 ARG   0.007   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03332 (  359)
  hydrogen bonds       : angle       5.69184 (  966)
  covalent geometry    : bond        0.00470 ( 8725)
  covalent geometry    : angle       0.67745 (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
  165 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 125
  time to evaluate  : 1.001 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8211 (mm) cc_final: 0.7542 (mp)
REVERT: A  200 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7556 (mm-30)
REVERT: A  358 LEU cc_start: 0.9224 (mt) cc_final: 0.8989 (mp)
REVERT: C  336 GLU cc_start: 0.8427 (pm20) cc_final: 0.8091 (pm20)
REVERT: B   57 ARG cc_start: 0.7383 (mtm110) cc_final: 0.6773 (mtm110)
REVERT: B  132 ILE cc_start: 0.8572 (mm) cc_final: 0.8213 (tt)
REVERT: B  327 GLU cc_start: 0.7797 (tm-30) cc_final: 0.7384 (tm-30)
  outliers start: 40
  outliers final: 31
  residues processed: 153
  average time/residue: 0.2115
  time to fit residues: 45.3725
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  : 1.005 
-------------------------------------------------------------------------------
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  221 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  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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 78 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 114 optimal weight:    0.8980
   chunk 35 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0050
   chunk 63 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6594

-------------------------------------------------------------------------------
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
** 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 = 0.116418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.082002 restraints weight = 18258.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.084676 restraints weight = 10275.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.086487 restraints weight = 7166.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.3310

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= 0.118
  Angle     :  0.647  15.520  11780  Z= 0.311
  Chirality :  0.045   0.180   1424
  Planarity :  0.004   0.068   1550
  Dihedral  :  4.147  19.046   1238
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 29.81 %
    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:  0.11 (0.26), residues: 1155
  helix:  0.82 (0.40), residues: 177
  sheet:  0.11 (0.28), residues: 321
  loop : -0.06 (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   0.015   0.002   TYR A 103 
 ARG   0.007   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02915 (  359)
  hydrogen bonds       : angle       5.50543 (  966)
  covalent geometry    : bond        0.00279 ( 8725)
  covalent geometry    : angle       0.64677 (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
  154 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
REVERT: A  199 LEU cc_start: 0.8217 (mm) cc_final: 0.7557 (mp)
REVERT: A  200 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7512 (mm-30)
REVERT: A  358 LEU cc_start: 0.9203 (mt) cc_final: 0.8966 (mp)
REVERT: C  336 GLU cc_start: 0.8397 (pm20) cc_final: 0.8072 (pm20)
REVERT: B   57 ARG cc_start: 0.7366 (mtm110) cc_final: 0.6881 (mtm110)
REVERT: B   93 SER cc_start: 0.8743 (m) cc_final: 0.8516 (t)
REVERT: B  132 ILE cc_start: 0.8572 (mm) cc_final: 0.8209 (tt)
REVERT: B  345 LEU cc_start: 0.7676 (tp) cc_final: 0.7357 (pp)
  outliers start: 29
  outliers final: 25
  residues processed: 147
  average time/residue: 0.2102
  time to fit residues: 42.9541
Evaluate side-chains
  147 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  104 VAL
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  345 LEU
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 B residue  104 VAL
Chi-restraints excluded: chain B residue  149 SER
Chi-restraints excluded: chain B residue  219 LEU
Chi-restraints excluded: chain B residue  240 VAL
Chi-restraints excluded: chain B residue  280 ILE
Chi-restraints excluded: chain B residue  339 THR
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:    0.7980
   chunk 5 optimal weight:    0.0000
   chunk 102 optimal weight:    0.0870
   chunk 73 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0070
   chunk 113 optimal weight:    7.9990
   chunk 47 optimal weight:    0.0070
   chunk 43 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 83 optimal weight:    0.2980
   overall best weight:    0.0798

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 107 ASN
B 120 GLN
** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 447 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.119784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.084983 restraints weight = 18038.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.087794 restraints weight = 10075.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.089715 restraints weight = 6998.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7605
moved from start:          0.3446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8725  Z= 0.100
  Angle     :  0.637  15.646  11780  Z= 0.303
  Chirality :  0.045   0.171   1424
  Planarity :  0.004   0.040   1550
  Dihedral  :  3.894  17.693   1238
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 30.80 %
    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:  0.28 (0.26), residues: 1155
  helix:  1.11 (0.41), residues: 177
  sheet:  0.20 (0.28), residues: 321
  loop :  0.03 (0.27), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B 109 
 PHE   0.020   0.001   PHE C  88 
 TYR   0.015   0.002   TYR A 103 
 ARG   0.008   0.001   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02640 (  359)
  hydrogen bonds       : angle       5.19159 (  966)
  covalent geometry    : bond        0.00228 ( 8725)
  covalent geometry    : angle       0.63743 (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: 24
    poor density    : 126
  time to evaluate  : 1.024 
Fit side-chains
REVERT: A  199 LEU cc_start: 0.8178 (mm) cc_final: 0.7645 (mp)
REVERT: A  200 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7543 (mm-30)
REVERT: A  358 LEU cc_start: 0.9182 (mt) cc_final: 0.8922 (mp)
REVERT: C  336 GLU cc_start: 0.8378 (pm20) cc_final: 0.8049 (pm20)
REVERT: B   57 ARG cc_start: 0.7390 (mtm110) cc_final: 0.6869 (mtm110)
REVERT: B   93 SER cc_start: 0.8774 (m) cc_final: 0.8540 (t)
REVERT: B  132 ILE cc_start: 0.8544 (mm) cc_final: 0.8199 (tt)
REVERT: B  345 LEU cc_start: 0.7636 (tp) cc_final: 0.7260 (pp)
  outliers start: 24
  outliers final: 22
  residues processed: 145
  average time/residue: 0.2176
  time to fit residues: 43.8551
Evaluate side-chains
  141 residues out of total 909 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   88 PHE
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  345 LEU
Chi-restraints excluded: chain C residue  111 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  120 GLN
Chi-restraints excluded: chain B residue  149 SER
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 D residue  380 LEU
Chi-restraints excluded: chain F residue  370 MET
Chi-restraints excluded: chain F residue  413 VAL
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:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 19 optimal weight:    0.8980
   chunk 100 optimal weight:   10.0000
   chunk 66 optimal weight:    0.7980
   chunk 38 optimal weight:    0.4980
   chunk 27 optimal weight:    0.3980
   chunk 93 optimal weight:   10.0000
   chunk 89 optimal weight:    6.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.9182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.119335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.086465 restraints weight = 18297.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.088947 restraints weight = 9517.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.090050 restraints weight = 6467.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.3497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.202   8725  Z= 0.206
  Angle     :  0.990  59.151  11780  Z= 0.546
  Chirality :  0.047   0.253   1424
  Planarity :  0.004   0.039   1550
  Dihedral  :  3.896  17.624   1238
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 31.13 %
    Favored  : 65.90 %
  Cbeta Deviations :  0.09 %
  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:  0.29 (0.26), residues: 1155
  helix:  1.11 (0.41), residues: 177
  sheet:  0.20 (0.28), residues: 321
  loop :  0.03 (0.27), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS B 109 
 PHE   0.020   0.001   PHE C  88 
 TYR   0.013   0.002   TYR A 103 
 ARG   0.006   0.000   ARG A 290 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02677 (  359)
  hydrogen bonds       : angle       5.18941 (  966)
  covalent geometry    : bond        0.00463 ( 8725)
  covalent geometry    : angle       0.98996 (11780)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5171.39 seconds
wall clock time: 89 minutes 36.62 seconds (5376.62 seconds total)