Starting phenix.real_space_refine
on Tue May  7 20:06:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/05_2024/8xog_38528_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/05_2024/8xog_38528.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/05_2024/8xog_38528.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/05_2024/8xog_38528.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/05_2024/8xog_38528_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xog_38528/05_2024/8xog_38528_neut.pdb"
  }
  resolution = 2.9
  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=   0.000 sd=   0.032
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      53      5.16       5
     C    5535      2.51       5
     N    1509      2.21       5
     O    1611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU   21": "OE1" <-> "OE2"
    Residue "A GLU  309": "OE1" <-> "OE2"
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "B GLU  138": "OE1" <-> "OE2"
    Residue "B GLU  260": "OE1" <-> "OE2"
    Residue "G GLU   22": "OE1" <-> "OE2"
    Residue "G GLU   42": "OE1" <-> "OE2"
    Residue "G GLU   47": "OE1" <-> "OE2"
    Residue "R GLU   89": "OE1" <-> "OE2"
    Residue "R GLU  121": "OE1" <-> "OE2"
    Residue "R GLU  218": "OE1" <-> "OE2"
    Residue "R GLU  329": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib"
  Total number of atoms: 8708
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1852
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1852
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 24
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "B"
      Number of atoms: 2552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2552
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 51
          Unresolved non-hydrogen angles: 64
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ARG:plan': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 34
    Chain: "E"
      Number of atoms: 1724
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1724
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 9, 'TRANS': 218}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 30
          Unresolved non-hydrogen dihedrals: 20
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "G"
      Number of atoms: 423
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 423
          Classifications: {'peptide': 57}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "R"
      Number of atoms: 2155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 264, 2155
          Classifications: {'peptide': 264}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 256}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "R"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Classifications: {'water': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.23, per 1000 atoms: 0.60
  Number of scatterers: 8708
  At special positions: 0
  Unit cell: (94.76, 120.304, 124.424, 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      53     16.00
     O    1611      8.00
     N    1509      7.00
     C    5535      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  - 3.50
        Amino acid           : False - 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: 3.52
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 13 sheets defined
      40.1% alpha, 23.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 40
      removed outlier: 3.776A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 59
    Processing helix  chain 'A' and resid 233 through 237
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
      removed outlier: 3.604A  pdb=" N   GLU A 299 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 311
    Processing helix  chain 'A' and resid 312 through 318
    Processing helix  chain 'A' and resid 331 through 353
      removed outlier: 3.954A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 391
      removed outlier: 4.488A  pdb=" N   ARG A 373 " --> pdb=" O   THR A 369 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.535A  pdb=" N   ASN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'E' and resid 220 through 224
      removed outlier: 3.644A  pdb=" N   VAL E 224 " --> pdb=" O   ALA E 221 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 7 through 25
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 45 through 48
      removed outlier: 4.025A  pdb=" N   ASP G  48 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'G' and resid 45 through 48'
    Processing helix  chain 'R' and resid 53 through 87
      removed outlier: 4.624A  pdb=" N   PHE R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 88 through 91
    Processing helix  chain 'R' and resid 92 through 116
      removed outlier: 3.510A  pdb=" N   LEU R  96 " --> pdb=" O   THR R  92 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   TYR R  97 " --> pdb=" O   ILE R  93 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   LEU R 113 " --> pdb=" O   VAL R 109 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ILE R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   GLU R 115 " --> pdb=" O   ASP R 111 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 120 through 125
      removed outlier: 4.186A  pdb=" N   ASP R 125 " --> pdb=" O   GLU R 121 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 126 through 161
    Processing helix  chain 'R' and resid 170 through 200
      Proline residue:  R 192  - end of helix
    Processing helix  chain 'R' and resid 211 through 223
    Processing helix  chain 'R' and resid 223 through 246
    Processing helix  chain 'R' and resid 254 through 285
      removed outlier: 3.600A  pdb=" N   VAL R 265 " --> pdb=" O   ILE R 261 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU R 266 " --> pdb=" O   LEU R 262 " (cutoff:3.500A)
      Proline residue:  R 274  - end of helix
    Processing helix  chain 'R' and resid 302 through 325
      removed outlier: 3.623A  pdb=" N   ASN R 316 " --> pdb=" O   ALA R 312 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   SER R 317 " --> pdb=" O   ALA R 313 " (cutoff:3.500A)
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 328 through 342
      removed outlier: 3.624A  pdb=" N   ARG R 332 " --> pdb=" O   GLY R 328 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 6.939A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.916A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.322A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.721A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 6.029A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.532A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.651A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.974A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 4.843A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 5.909A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.724A  pdb=" N   CYS B 148 " --> pdb=" O   SER B 160 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.010A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.892A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.501A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.886A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.925A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.508A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.440A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.695A  pdb=" N   VAL E   5 " --> pdb=" O   SER E  23 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.548A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.556A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 142
    Processing sheet with id=AB3, first strand: chain 'E' and resid 146 through 148
      removed outlier: 6.840A  pdb=" N   LEU E 174 " --> pdb=" O   TYR E 190 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   TYR E 190 " --> pdb=" O   LEU E 174 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   TRP E 176 " --> pdb=" O   LEU E 188 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148
      removed outlier: 3.746A  pdb=" N   GLN E 231 " --> pdb=" O   THR E 238 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   THR E 238 " --> pdb=" O   GLN E 231 " (cutoff:3.500A)

    464 hydrogen bonds defined for protein.
    1293 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: 2.84

  Time building geometry restraints manager: 3.67 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: 2795
        1.34 -     1.45: 1219
        1.45 -     1.57: 4792
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8882
  Sorted by residual:
  bond pdb=" N   SER B  74 "
       pdb=" CA  SER B  74 "
    ideal  model  delta    sigma   weight residual
    1.455  1.421  0.033 1.29e-02 6.01e+03 6.62e+00
  bond pdb=" C   TYR B 289 "
       pdb=" N   ASP B 290 "
    ideal  model  delta    sigma   weight residual
    1.332  1.365 -0.033 1.52e-02 4.33e+03 4.68e+00
  bond pdb=" N   ASP B 290 "
       pdb=" CA  ASP B 290 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.32e-02 5.74e+03 4.64e+00
  bond pdb=" CA  SER B  74 "
       pdb=" CB  SER B  74 "
    ideal  model  delta    sigma   weight residual
    1.535  1.497  0.039 1.90e-02 2.77e+03 4.12e+00
  bond pdb=" CA  SER B  74 "
       pdb=" C   SER B  74 "
    ideal  model  delta    sigma   weight residual
    1.522  1.497  0.025 1.24e-02 6.50e+03 4.06e+00
  ... (remaining 8877 not shown)

  Histogram of bond angle deviations from ideal:
       99.33 -   106.28: 168
      106.28 -   113.24: 4885
      113.24 -   120.19: 3123
      120.19 -   127.14: 3761
      127.14 -   134.10: 96
  Bond angle restraints: 12033
  Sorted by residual:
  angle pdb=" N   ASP B 290 "
        pdb=" CA  ASP B 290 "
        pdb=" C   ASP B 290 "
      ideal   model   delta    sigma   weight residual
     113.20  107.58    5.62 1.21e+00 6.83e-01 2.16e+01
  angle pdb=" CA  PRO R 192 "
        pdb=" N   PRO R 192 "
        pdb=" CD  PRO R 192 "
      ideal   model   delta    sigma   weight residual
     112.00  106.53    5.47 1.40e+00 5.10e-01 1.53e+01
  angle pdb=" C   SER R 325 "
        pdb=" N   PHE R 326 "
        pdb=" CA  PHE R 326 "
      ideal   model   delta    sigma   weight residual
     122.86  117.29    5.57 1.53e+00 4.27e-01 1.32e+01
  angle pdb=" CA  SER B  74 "
        pdb=" CB  SER B  74 "
        pdb=" OG  SER B  74 "
      ideal   model   delta    sigma   weight residual
     111.10  105.40    5.70 2.00e+00 2.50e-01 8.13e+00
  angle pdb=" N   ASP B 290 "
        pdb=" CA  ASP B 290 "
        pdb=" CB  ASP B 290 "
      ideal   model   delta    sigma   weight residual
     110.42  114.92   -4.50 1.62e+00 3.81e-01 7.71e+00
  ... (remaining 12028 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4709
       17.85 -    35.71: 430
       35.71 -    53.56: 96
       53.56 -    71.42: 19
       71.42 -    89.27: 9
  Dihedral angle restraints: 5263
    sinusoidal: 2030
      harmonic: 3233
  Sorted by residual:
  dihedral pdb=" CA  PHE R 326 "
           pdb=" C   PHE R 326 "
           pdb=" N   LEU R 327 "
           pdb=" CA  LEU R 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.64   24.36     0      5.00e+00 4.00e-02 2.37e+01
  dihedral pdb=" CA  PHE R 223 "
           pdb=" C   PHE R 223 "
           pdb=" N   ILE R 224 "
           pdb=" CA  ILE R 224 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.08  -18.92     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  ILE A 207 "
           pdb=" C   ILE A 207 "
           pdb=" N   PHE A 208 "
           pdb=" CA  PHE A 208 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.68   18.32     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 5260 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1050
       0.042 -    0.083: 227
       0.083 -    0.125: 82
       0.125 -    0.166: 14
       0.166 -    0.208: 1
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" CA  ASP B 290 "
            pdb=" N   ASP B 290 "
            pdb=" C   ASP B 290 "
            pdb=" CB  ASP B 290 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  TYR A 391 "
            pdb=" N   TYR A 391 "
            pdb=" C   TYR A 391 "
            pdb=" CB  TYR A 391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.33e-01
  chirality pdb=" CA  VAL E   2 "
            pdb=" N   VAL E   2 "
            pdb=" C   VAL E   2 "
            pdb=" CB  VAL E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.58e-01
  ... (remaining 1371 not shown)

  Planarity restraints: 1529
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL R 191 "   -0.078 5.00e-02 4.00e+02   1.15e-01 2.13e+01
        pdb=" N   PRO R 192 "    0.199 5.00e-02 4.00e+02
        pdb=" CA  PRO R 192 "   -0.058 5.00e-02 4.00e+02
        pdb=" CD  PRO R 192 "   -0.063 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 219 "   -0.156 9.50e-02 1.11e+02   7.03e-02 3.28e+00
        pdb=" NE  ARG B 219 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 219 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 219 "    0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 219 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B  73 "    0.009 2.00e-02 2.50e+03   1.78e-02 3.16e+00
        pdb=" C   ALA B  73 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ALA B  73 "    0.012 2.00e-02 2.50e+03
        pdb=" N   SER B  74 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1526 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2092
        2.79 -     3.32: 8526
        3.32 -     3.84: 14308
        3.84 -     4.37: 17360
        4.37 -     4.90: 29977
  Nonbonded interactions: 72263
  Sorted by model distance:
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.263 2.440
  nonbonded pdb=" OG  SER E  17 "
            pdb=" O   THR E  84 "
     model   vdw
     2.264 2.440
  nonbonded pdb=" O   ASN A 239 "
            pdb=" OD1 ASP A 240 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" OD1 ASP B 170 "
            pdb=" OG1 THR B 173 "
     model   vdw
     2.285 2.440
  nonbonded pdb=" O   ASN A 392 "
            pdb=" ND2 ASN A 392 "
     model   vdw
     2.325 2.520
  ... (remaining 72258 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  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:          4.160
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.560
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  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:11.280
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
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      :  0.003   0.060   8882  Z= 0.218
  Angle     :  0.561   8.446  12033  Z= 0.318
  Chirality :  0.041   0.208   1374
  Planarity :  0.005   0.115   1529
  Dihedral  : 14.841  89.272   3167
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 14.41 %
    Favored  : 85.38 %
  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:  0.78 (0.26), residues: 1091
  helix:  1.40 (0.26), residues: 401
  sheet: -0.07 (0.31), residues: 274
  loop :  0.24 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 234 
 HIS   0.004   0.001   HIS B  91 
 PHE   0.023   0.001   PHE R 326 
 TYR   0.009   0.001   TYR A 391 
 ARG   0.009   0.000   ARG B 219 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7248 (tt0) cc_final: 0.6554 (mt0)
REVERT: A  232 ARG cc_start: 0.7934 (ttm170) cc_final: 0.7684 (ttp-170)
REVERT: A  391 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.6070 (m-80)
REVERT: G   58 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6937 (mt-10)
REVERT: R  141 MET cc_start: 0.6606 (ptp) cc_final: 0.5929 (tmt)
  outliers start: 2
  outliers final: 0
  residues processed: 118
  average time/residue: 1.1724
  time to fit residues: 148.6292
Evaluate side-chains
  108 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 107
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    2.9990
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 84 optimal weight:    8.9990
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 63 optimal weight:    9.9990
   chunk 98 optimal weight:    0.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
B  32 GLN
B 175 GLN
B 259 GLN
E 194 ASN
E 232 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.1124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8882  Z= 0.212
  Angle     :  0.570   8.697  12033  Z= 0.303
  Chirality :  0.043   0.153   1374
  Planarity :  0.004   0.070   1529
  Dihedral  :  4.820  58.357   1205
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 15.37 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.26), residues: 1091
  helix:  1.56 (0.25), residues: 400
  sheet:  0.32 (0.32), residues: 266
  loop :  0.38 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  82 
 HIS   0.005   0.001   HIS B  91 
 PHE   0.017   0.001   PHE R 326 
 TYR   0.011   0.001   TYR E 190 
 ARG   0.004   0.000   ARG B 219 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7344 (tt0) cc_final: 0.6600 (mt0)
REVERT: A  232 ARG cc_start: 0.7788 (ttm170) cc_final: 0.7583 (ttp-170)
REVERT: A  391 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.5789 (m-80)
REVERT: B  165 THR cc_start: 0.7829 (p) cc_final: 0.7569 (t)
REVERT: G   58 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6950 (mt-10)
REVERT: R  141 MET cc_start: 0.6730 (ptp) cc_final: 0.6006 (tmt)
  outliers start: 25
  outliers final: 9
  residues processed: 124
  average time/residue: 1.0343
  time to fit residues: 138.9794
Evaluate side-chains
  107 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  165 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 30 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 66 optimal weight:   50.0000
   chunk 27 optimal weight:    3.9990
   chunk 98 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9990
   chunk 87 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 33 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
R 140 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.1522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   8882  Z= 0.398
  Angle     :  0.652  11.901  12033  Z= 0.340
  Chirality :  0.046   0.184   1374
  Planarity :  0.005   0.060   1529
  Dihedral  :  5.156  57.916   1205
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 14.41 %
    Favored  : 80.90 %
  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:  0.87 (0.26), residues: 1091
  helix:  1.29 (0.26), residues: 395
  sheet:  0.07 (0.31), residues: 282
  loop :  0.46 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 234 
 HIS   0.008   0.002   HIS A 357 
 PHE   0.020   0.002   PHE R 326 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.003   0.001   ARG B 251 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 44
    poor density    : 100
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6648 (mt0)
REVERT: A  232 ARG cc_start: 0.7844 (ttm170) cc_final: 0.7531 (ttp-170)
REVERT: A  266 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7899 (mm)
REVERT: A  391 TYR cc_start: 0.8362 (OUTLIER) cc_final: 0.5969 (m-80)
REVERT: B  153 ASP cc_start: 0.6909 (m-30) cc_final: 0.6520 (m-30)
REVERT: G   58 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6820 (mt-10)
  outliers start: 44
  outliers final: 24
  residues processed: 130
  average time/residue: 1.0736
  time to fit residues: 150.5198
Evaluate side-chains
  119 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  213 GLN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  289 LEU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain E residue   53 SER
Chi-restraints excluded: chain E residue   63 THR
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   91 MET
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  266 LEU
Chi-restraints excluded: chain R residue  311 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 97 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 50 optimal weight:    0.5980
   chunk 10 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 98 optimal weight:    0.7980
   chunk 104 optimal weight:    0.4980
   chunk 51 optimal weight:    0.5980
   chunk 93 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B 175 GLN
R  54 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.1731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8882  Z= 0.155
  Angle     :  0.535  13.151  12033  Z= 0.279
  Chirality :  0.041   0.151   1374
  Planarity :  0.004   0.048   1529
  Dihedral  :  4.690  58.825   1205
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 17.82 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.26), residues: 1091
  helix:  1.64 (0.26), residues: 402
  sheet:  0.31 (0.32), residues: 264
  loop :  0.36 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 362 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.011   0.001   TYR B 289 
 ARG   0.003   0.000   ARG B 219 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7285 (mt-10) cc_final: 0.7004 (mt-10)
REVERT: A  213 GLN cc_start: 0.7396 (tt0) cc_final: 0.6665 (mt0)
REVERT: A  299 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7416 (pm20)
REVERT: A  391 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.5846 (m-80)
REVERT: B  251 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7685 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8030 (tt0) cc_final: 0.7743 (tt0)
REVERT: E  188 LEU cc_start: 0.3956 (mt) cc_final: 0.3574 (pt)
REVERT: E  230 MET cc_start: 0.2473 (ttp) cc_final: 0.1930 (mpt)
REVERT: G   58 GLU cc_start: 0.7111 (mm-30) cc_final: 0.6833 (mt-10)
REVERT: R  141 MET cc_start: 0.6780 (ptp) cc_final: 0.5959 (tmt)
  outliers start: 20
  outliers final: 6
  residues processed: 125
  average time/residue: 1.1806
  time to fit residues: 158.7645
Evaluate side-chains
  104 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain R residue  163 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 86 optimal weight:    0.1980
   chunk 59 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 77 optimal weight:    8.9990
   chunk 43 optimal weight:    0.4980
   chunk 89 optimal weight:    7.9990
   chunk 72 optimal weight:    7.9990
   chunk 0 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0010
   chunk 93 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
B 175 GLN
R 140 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.1940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8882  Z= 0.157
  Angle     :  0.520  10.991  12033  Z= 0.271
  Chirality :  0.041   0.154   1374
  Planarity :  0.003   0.042   1529
  Dihedral  :  4.554  58.927   1205
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 19.00 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.26), residues: 1091
  helix:  1.78 (0.26), residues: 403
  sheet:  0.31 (0.32), residues: 266
  loop :  0.35 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  82 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.017   0.001   TYR A 318 
 ARG   0.002   0.000   ARG E  18 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7036 (mt-10)
REVERT: A  213 GLN cc_start: 0.7438 (tt0) cc_final: 0.6714 (mt0)
REVERT: A  299 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7445 (pm20)
REVERT: A  391 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.5933 (m-80)
REVERT: B   38 ASP cc_start: 0.8172 (t70) cc_final: 0.7852 (t0)
REVERT: B  251 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7625 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8032 (tt0) cc_final: 0.7631 (tt0)
REVERT: E  188 LEU cc_start: 0.3962 (mt) cc_final: 0.3584 (pt)
REVERT: E  230 MET cc_start: 0.2445 (ttp) cc_final: 0.1928 (mpt)
REVERT: G   58 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6815 (mt-10)
REVERT: R  141 MET cc_start: 0.6800 (ptp) cc_final: 0.6003 (tmt)
  outliers start: 20
  outliers final: 10
  residues processed: 117
  average time/residue: 1.1433
  time to fit residues: 143.6886
Evaluate side-chains
  111 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 1.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain E residue  233 LEU
Chi-restraints excluded: chain G residue   11 GLN
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  247 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 94 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:   40.0000
   chunk 25 optimal weight:    2.9990
   chunk 104 optimal weight:    8.9990
   chunk 86 optimal weight:    0.4980
   chunk 48 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8882  Z= 0.211
  Angle     :  0.567  15.856  12033  Z= 0.285
  Chirality :  0.042   0.164   1374
  Planarity :  0.004   0.041   1529
  Dihedral  :  4.606  58.738   1205
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 19.74 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.26), residues: 1091
  helix:  1.79 (0.26), residues: 397
  sheet:  0.28 (0.32), residues: 270
  loop :  0.34 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 326 
 TYR   0.013   0.001   TYR A 318 
 ARG   0.002   0.000   ARG E  18 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 GLN cc_start: 0.7441 (tt0) cc_final: 0.6700 (mt0)
REVERT: A  299 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7449 (pm20)
REVERT: A  370 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6716 (mp0)
REVERT: A  391 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.5899 (m-80)
REVERT: B   38 ASP cc_start: 0.8179 (t70) cc_final: 0.7878 (t0)
REVERT: B  178 THR cc_start: 0.7661 (OUTLIER) cc_final: 0.7454 (p)
REVERT: B  251 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7597 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8022 (tt0) cc_final: 0.7595 (tt0)
REVERT: E   34 MET cc_start: 0.4404 (mmm) cc_final: 0.3788 (mmm)
REVERT: E  230 MET cc_start: 0.2387 (ttp) cc_final: 0.1891 (mpt)
REVERT: G   58 GLU cc_start: 0.7079 (mm-30) cc_final: 0.6763 (mt-10)
REVERT: R  141 MET cc_start: 0.6862 (ptp) cc_final: 0.6018 (tmt)
  outliers start: 27
  outliers final: 13
  residues processed: 114
  average time/residue: 1.1108
  time to fit residues: 136.1408
Evaluate side-chains
  113 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   11 GLN
Chi-restraints excluded: chain R residue   91 MET
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  185 SER
Chi-restraints excluded: chain R residue  247 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 100 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 76 optimal weight:   40.0000
   chunk 87 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 104 optimal weight:    9.9990
   chunk 65 optimal weight:    6.9990
   chunk 63 optimal weight:    3.9990
   chunk 48 optimal weight:    0.2980
   chunk 64 optimal weight:   20.0000
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
A 392 ASN
B 175 GLN
R 140 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7178
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   8882  Z= 0.384
  Angle     :  0.653  15.713  12033  Z= 0.333
  Chirality :  0.046   0.192   1374
  Planarity :  0.004   0.042   1529
  Dihedral  :  4.969  59.370   1205
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.38 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 1091
  helix:  1.46 (0.26), residues: 397
  sheet:  0.24 (0.32), residues: 270
  loop :  0.17 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 234 
 HIS   0.008   0.001   HIS A 357 
 PHE   0.021   0.002   PHE R 326 
 TYR   0.015   0.002   TYR A 339 
 ARG   0.004   0.000   ARG G  27 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 33
    poor density    : 94
  time to evaluate  : 0.971 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6931 (mt-10)
REVERT: A  213 GLN cc_start: 0.7437 (tt0) cc_final: 0.6678 (mt0)
REVERT: A  266 LEU cc_start: 0.8184 (mt) cc_final: 0.7928 (mm)
REVERT: A  299 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7401 (pm20)
REVERT: A  370 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6918 (mp0)
REVERT: A  391 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.6096 (m-80)
REVERT: B  153 ASP cc_start: 0.7036 (m-30) cc_final: 0.6691 (m-30)
REVERT: B  251 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7571 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8063 (tt0) cc_final: 0.7638 (tt0)
REVERT: E   34 MET cc_start: 0.4626 (mmm) cc_final: 0.4291 (mmm)
REVERT: E  230 MET cc_start: 0.2437 (ttp) cc_final: 0.1892 (mpt)
REVERT: G   58 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6704 (mt-10)
  outliers start: 33
  outliers final: 17
  residues processed: 115
  average time/residue: 1.0975
  time to fit residues: 136.0144
Evaluate side-chains
  113 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 VAL
Chi-restraints excluded: chain A residue   50 ASN
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  310 ASP
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  226 GLU
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain B residue  267 ASP
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain R residue   79 LEU
Chi-restraints excluded: chain R residue   91 MET
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    6.9990
   chunk 31 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 70 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 81 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
A 392 ASN
B 175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8882  Z= 0.184
  Angle     :  0.556  16.144  12033  Z= 0.283
  Chirality :  0.041   0.159   1374
  Planarity :  0.004   0.040   1529
  Dihedral  :  4.624  57.613   1205
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 21.45 %
    Favored  : 76.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.26), residues: 1091
  helix:  1.68 (0.26), residues: 397
  sheet:  0.24 (0.32), residues: 268
  loop :  0.17 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 169 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.010   0.001   TYR B 289 
 ARG   0.007   0.000   ARG G  27 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 1.028 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6960 (mt-10)
REVERT: A  213 GLN cc_start: 0.7434 (tt0) cc_final: 0.6683 (mt0)
REVERT: A  299 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7450 (pm20)
REVERT: A  391 TYR cc_start: 0.8289 (OUTLIER) cc_final: 0.6133 (m-80)
REVERT: B   38 ASP cc_start: 0.8220 (t70) cc_final: 0.7893 (t0)
REVERT: B  251 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7642 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8043 (tt0) cc_final: 0.7756 (tt0)
REVERT: E   34 MET cc_start: 0.4562 (mmm) cc_final: 0.4044 (mmm)
REVERT: E  230 MET cc_start: 0.2395 (ttp) cc_final: 0.1911 (mpt)
REVERT: G   58 GLU cc_start: 0.7030 (mm-30) cc_final: 0.6696 (mt-10)
REVERT: R  141 MET cc_start: 0.6840 (ptp) cc_final: 0.5985 (tmt)
REVERT: R  334 LYS cc_start: 0.6757 (tttp) cc_final: 0.6546 (tttp)
  outliers start: 21
  outliers final: 12
  residues processed: 116
  average time/residue: 1.1747
  time to fit residues: 146.4677
Evaluate side-chains
  113 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 0.993 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   11 GLN
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 90 optimal weight:    0.6980
   chunk 97 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 58 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 29 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
A 392 ASN
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7121
moved from start:          0.2353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8882  Z= 0.173
  Angle     :  0.553  15.821  12033  Z= 0.283
  Chirality :  0.041   0.158   1374
  Planarity :  0.004   0.039   1529
  Dihedral  :  4.568  57.188   1205
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.77 %
    Favored  : 76.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.26), residues: 1091
  helix:  1.81 (0.26), residues: 397
  sheet:  0.20 (0.31), residues: 275
  loop :  0.17 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 234 
 HIS   0.004   0.001   HIS A 357 
 PHE   0.014   0.001   PHE R 326 
 TYR   0.011   0.001   TYR B 289 
 ARG   0.006   0.000   ARG G  27 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6983 (mt-10)
REVERT: A  213 GLN cc_start: 0.7451 (tt0) cc_final: 0.6719 (mt0)
REVERT: A  299 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7490 (pm20)
REVERT: A  391 TYR cc_start: 0.8305 (OUTLIER) cc_final: 0.6170 (m-80)
REVERT: B   38 ASP cc_start: 0.8237 (t70) cc_final: 0.7913 (t0)
REVERT: B  251 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7593 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8034 (tt0) cc_final: 0.7639 (tt0)
REVERT: E   34 MET cc_start: 0.4586 (mmm) cc_final: 0.4108 (mmm)
REVERT: E  230 MET cc_start: 0.2394 (ttp) cc_final: 0.1904 (mpt)
REVERT: G   58 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6697 (mt-10)
REVERT: R  141 MET cc_start: 0.6808 (ptp) cc_final: 0.5978 (tmt)
REVERT: R  218 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7190 (tp30)
REVERT: R  334 LYS cc_start: 0.6735 (tttp) cc_final: 0.6533 (tttp)
  outliers start: 19
  outliers final: 13
  residues processed: 113
  average time/residue: 1.1525
  time to fit residues: 139.6654
Evaluate side-chains
  113 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   11 GLN
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 66 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 68 optimal weight:    6.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 292 ASN
A 294 GLN
A 392 ASN
B 175 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8882  Z= 0.252
  Angle     :  0.585  15.855  12033  Z= 0.297
  Chirality :  0.042   0.170   1374
  Planarity :  0.004   0.039   1529
  Dihedral  :  4.684  58.294   1205
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 21.56 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.00 (0.26), residues: 1091
  helix:  1.68 (0.26), residues: 397
  sheet:  0.19 (0.31), residues: 273
  loop :  0.15 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 234 
 HIS   0.006   0.001   HIS A 357 
 PHE   0.016   0.001   PHE R 326 
 TYR   0.012   0.001   TYR R 156 
 ARG   0.007   0.000   ARG G  27 

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

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

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2182 Ramachandran restraints generated.
    1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 1.014 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.7294 (mt-10) cc_final: 0.6972 (mt-10)
REVERT: A  213 GLN cc_start: 0.7459 (tt0) cc_final: 0.6709 (mt0)
REVERT: A  299 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7470 (pm20)
REVERT: A  391 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.6099 (m-80)
REVERT: B   38 ASP cc_start: 0.8260 (t70) cc_final: 0.7943 (t0)
REVERT: B  251 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7590 (mmt-90)
REVERT: B  260 GLU cc_start: 0.8036 (tt0) cc_final: 0.7601 (tt0)
REVERT: E   34 MET cc_start: 0.4515 (mmm) cc_final: 0.3896 (mmm)
REVERT: E  140 MET cc_start: 0.1557 (ptp) cc_final: 0.1016 (ptm)
REVERT: E  230 MET cc_start: 0.2402 (ttp) cc_final: 0.1859 (mpt)
REVERT: R  141 MET cc_start: 0.6856 (ptp) cc_final: 0.5998 (tmt)
REVERT: R  218 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7206 (tp30)
REVERT: R  334 LYS cc_start: 0.6742 (tttp) cc_final: 0.6534 (tttp)
  outliers start: 22
  outliers final: 16
  residues processed: 114
  average time/residue: 1.1848
  time to fit residues: 146.3585
Evaluate side-chains
  116 residues out of total 964 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  247 VAL
Chi-restraints excluded: chain A residue  248 VAL
Chi-restraints excluded: chain A residue  299 GLU
Chi-restraints excluded: chain A residue  307 LYS
Chi-restraints excluded: chain A residue  354 ASP
Chi-restraints excluded: chain A residue  364 THR
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  392 ASN
Chi-restraints excluded: chain B residue   74 SER
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  197 ARG
Chi-restraints excluded: chain B residue  251 ARG
Chi-restraints excluded: chain E residue   71 SER
Chi-restraints excluded: chain E residue  155 VAL
Chi-restraints excluded: chain G residue   11 GLN
Chi-restraints excluded: chain R residue  107 ILE
Chi-restraints excluded: chain R residue  163 MET
Chi-restraints excluded: chain R residue  165 CYS
Chi-restraints excluded: chain R residue  185 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.5980
   chunk 26 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 85 optimal weight:    0.0050
   chunk 35 optimal weight:    0.9980
   chunk 88 optimal weight:   10.0000
   chunk 10 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 75 optimal weight:   50.0000
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
B 175 GLN
** R 140 ASN ** 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 = 0.4373 r_free = 0.4373 target = 0.215344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.135363 restraints weight = 9377.956|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.48
r_work: 0.3422 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3289 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.090   8882  Z= 0.229
  Angle     :  0.897  59.200  12033  Z= 0.507
  Chirality :  0.042   0.163   1374
  Planarity :  0.004   0.040   1529
  Dihedral  :  4.716  56.295   1205
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.66 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 22.09 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.26), residues: 1091
  helix:  1.70 (0.26), residues: 397
  sheet:  0.21 (0.32), residues: 268
  loop :  0.09 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 234 
 HIS   0.005   0.001   HIS A 357 
 PHE   0.015   0.001   PHE R 326 
 TYR   0.012   0.001   TYR R 156 
 ARG   0.006   0.000   ARG G  27 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3465.85 seconds
wall clock time: 62 minutes 55.76 seconds (3775.76 seconds total)